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Sample records for binding site-leucine rich

  1. Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis

    Science.gov (United States)

    Tan, Xiaoping; Meyers, Blake C; Kozik, Alexander; West, Marilyn AL; Morgante, Michele; St Clair, Dina A; Bent, Andrew F; Michelmore, Richard W

    2007-01-01

    Background Nucleotide binding site-leucine rich repeat (NBS-LRR)-encoding genes comprise the largest class of plant disease resistance genes. The 149 NBS-LRR-encoding genes and the 58 related genes that do not encode LRRs represent approximately 0.8% of all ORFs so far annotated in Arabidopsis ecotype Col-0. Despite their prevalence in the genome and functional importance, there was little information regarding expression of these genes. Results We analyzed the expression patterns of ~170 NBS-LRR-encoding and related genes in Arabidopsis Col-0 using multiple analytical approaches: expressed sequenced tag (EST) representation, massively parallel signature sequencing (MPSS), microarray analysis, rapid amplification of cDNA ends (RACE) PCR, and gene trap lines. Most of these genes were expressed at low levels with a variety of tissue specificities. Expression was detected by at least one approach for all but 10 of these genes. The expression of some but not the majority of NBS-LRR-encoding and related genes was affected by salicylic acid (SA) treatment; the response to SA varied among different accessions. An analysis of previously published microarray data indicated that ten NBS-LRR-encoding and related genes exhibited increased expression in wild-type Landsberg erecta (Ler) after flagellin treatment. Several of these ten genes also showed altered expression after SA treatment, consistent with the regulation of R gene expression during defense responses and overlap between the basal defense response and salicylic acid signaling pathways. Enhancer trap analysis indicated that neither jasmonic acid nor benzothiadiazole (BTH), a salicylic acid analog, induced detectable expression of the five NBS-LRR-encoding genes and one TIR-NBS-encoding gene tested; however, BTH did induce detectable expression of the other TIR-NBS-encoding gene analyzed. Evidence for alternative mRNA polyadenylation sites was observed for many of the tested genes. Evidence for alternative splicing

  2. Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis

    Directory of Open Access Journals (Sweden)

    St Clair Dina A

    2007-10-01

    Full Text Available Abstract Background Nucleotide binding site-leucine rich repeat (NBS-LRR-encoding genes comprise the largest class of plant disease resistance genes. The 149 NBS-LRR-encoding genes and the 58 related genes that do not encode LRRs represent approximately 0.8% of all ORFs so far annotated in Arabidopsis ecotype Col-0. Despite their prevalence in the genome and functional importance, there was little information regarding expression of these genes. Results We analyzed the expression patterns of ~170 NBS-LRR-encoding and related genes in Arabidopsis Col-0 using multiple analytical approaches: expressed sequenced tag (EST representation, massively parallel signature sequencing (MPSS, microarray analysis, rapid amplification of cDNA ends (RACE PCR, and gene trap lines. Most of these genes were expressed at low levels with a variety of tissue specificities. Expression was detected by at least one approach for all but 10 of these genes. The expression of some but not the majority of NBS-LRR-encoding and related genes was affected by salicylic acid (SA treatment; the response to SA varied among different accessions. An analysis of previously published microarray data indicated that ten NBS-LRR-encoding and related genes exhibited increased expression in wild-type Landsberg erecta (Ler after flagellin treatment. Several of these ten genes also showed altered expression after SA treatment, consistent with the regulation of R gene expression during defense responses and overlap between the basal defense response and salicylic acid signaling pathways. Enhancer trap analysis indicated that neither jasmonic acid nor benzothiadiazole (BTH, a salicylic acid analog, induced detectable expression of the five NBS-LRR-encoding genes and one TIR-NBS-encoding gene tested; however, BTH did induce detectable expression of the other TIR-NBS-encoding gene analyzed. Evidence for alternative mRNA polyadenylation sites was observed for many of the tested genes. Evidence for

  3. Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis.

    Science.gov (United States)

    Tan, Xiaoping; Meyers, Blake C; Kozik, Alexander; West, Marilyn A L; Morgante, Michele; St Clair, Dina A; Bent, Andrew F; Michelmore, Richard W

    2007-10-23

    Nucleotide binding site-leucine rich repeat (NBS-LRR)-encoding genes comprise the largest class of plant disease resistance genes. The 149 NBS-LRR-encoding genes and the 58 related genes that do not encode LRRs represent approximately 0.8% of all ORFs so far annotated in Arabidopsis ecotype Col-0. Despite their prevalence in the genome and functional importance, there was little information regarding expression of these genes. We analyzed the expression patterns of approximately 170 NBS-LRR-encoding and related genes in Arabidopsis Col-0 using multiple analytical approaches: expressed sequenced tag (EST) representation, massively parallel signature sequencing (MPSS), microarray analysis, rapid amplification of cDNA ends (RACE) PCR, and gene trap lines. Most of these genes were expressed at low levels with a variety of tissue specificities. Expression was detected by at least one approach for all but 10 of these genes. The expression of some but not the majority of NBS-LRR-encoding and related genes was affected by salicylic acid (SA) treatment; the response to SA varied among different accessions. An analysis of previously published microarray data indicated that ten NBS-LRR-encoding and related genes exhibited increased expression in wild-type Landsberg erecta (Ler) after flagellin treatment. Several of these ten genes also showed altered expression after SA treatment, consistent with the regulation of R gene expression during defense responses and overlap between the basal defense response and salicylic acid signaling pathways. Enhancer trap analysis indicated that neither jasmonic acid nor benzothiadiazole (BTH), a salicylic acid analog, induced detectable expression of the five NBS-LRR-encoding genes and one TIR-NBS-encoding gene tested; however, BTH did induce detectable expression of the other TIR-NBS-encoding gene analyzed. Evidence for alternative mRNA polyadenylation sites was observed for many of the tested genes. Evidence for alternative splicing was

  4. The stem rust resistance gene Rpg5 encodes a protein with nucleotide-binding-site, leucine-rich, and protein kinase domains.

    Science.gov (United States)

    Brueggeman, R; Druka, A; Nirmala, J; Cavileer, T; Drader, T; Rostoks, N; Mirlohi, A; Bennypaul, H; Gill, U; Kudrna, D; Whitelaw, C; Kilian, A; Han, F; Sun, Y; Gill, K; Steffenson, B; Kleinhofs, A

    2008-09-30

    We isolated the barley stem rust resistance genes Rpg5 and rpg4 by map-based cloning. These genes are colocalized on a 70-kb genomic region that was delimited by recombination. The Rpg5 gene consists of an unusual structure encoding three typical plant disease resistance protein domains: nucleotide-binding site, leucine-rich repeat, and serine threonine protein kinase. The predicted RPG5 protein has two putative transmembrane sites possibly involved in membrane binding. The gene is expressed at low but detectable levels. Posttranscriptional gene silencing using VIGS resulted in a compatible reaction with a normally incompatible stem rust pathogen. Allele sequencing also validated the candidate Rpg5 gene. Allele and recombinant sequencing suggested that the probable rpg4 gene encoded an actin depolymerizing factor-like protein. Involvement of actin depolymerizing factor genes in nonhost resistance has been documented, but discovery of their role in gene-for-gene interaction would be novel and needs to be further substantiated.

  5. Genome-wide identification and tissue-specific expression analysis of nucleotide binding site-leucine rich repeat gene family in Cicer arietinum (kabuli chickpea).

    Science.gov (United States)

    Sharma, Ranu; Rawat, Vimal; Suresh, C G

    2017-12-01

    The nucleotide binding site-leucine rich repeat (NBS-LRR) proteins play an important role in the defense mechanisms against pathogens. Using bioinformatics approach, we identified and annotated 104 NBS-LRR genes in chickpea. Phylogenetic analysis points to their diversification into two families namely TIR-NBS-LRR and non-TIR-NBS-LRR. Gene architecture revealed intron gain/loss events in this resistance gene family during their independent evolution into two families. Comparative genomics analysis elucidated its evolutionary relationship with other fabaceae species. Around 50% NBS-LRRs reside in macro-syntenic blocks underlining positional conservation along with sequence conservation of NBS-LRR genes in chickpea. Transcriptome sequencing data provided evidence for their transcription and tissue-specific expression. Four cis -regulatory elements namely WBOX, DRE, CBF, and GCC boxes, that commonly occur in resistance genes, were present in the promoter regions of these genes. Further, the findings will provide a strong background to use candidate disease resistance NBS-encoding genes and identify their specific roles in chickpea.

  6. Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns1

    Science.gov (United States)

    Shao, Zhu-Qing; Xue, Jia-Yu; Wu, Ping; Zhang, Yan-Mei; Wu, Yue; Hang, Yue-Yu; Wang, Bin; Chen, Jian-Qun

    2016-01-01

    Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes. PMID:26839128

  7. Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns.

    Science.gov (United States)

    Shao, Zhu-Qing; Xue, Jia-Yu; Wu, Ping; Zhang, Yan-Mei; Wu, Yue; Hang, Yue-Yu; Wang, Bin; Chen, Jian-Qun

    2016-04-01

    Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes. © 2016 American Society of Plant Biologists. All Rights Reserved.

  8. The Tomato Nucleotide-binding Leucine-rich Repeat (NLR) Immune Receptor I-2 Couples DNA-Binding to Nucleotide-Binding Domain Nucleotide Exchange

    NARCIS (Netherlands)

    Fenyk, S.; Dixon, C.H.; Gittens, W.H.; Townsend, P.D.; Sharples, G.J.; Pålsson, L.O.; Takken, F.L.W.; Cann, M.J.

    2016-01-01

    Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable plants to recognise and respond to pathogen attack. Previously, we demonstrated that the Rx1 NLR of potato is able to bind and bend DNA in vitro. DNA binding in situ requires its genuine activation following pathogen perception.

  9. Phosphate binding by natural iron-rich colloids in streams

    NARCIS (Netherlands)

    Baken, S.; Moens, C.; Griffioen, J.J.; Smolders, E.

    2016-01-01

    Phosphorus (P) in natural waters may be bound to iron (Fe) bearing colloids. However, the natural variation in composition and P binding strength of these colloids remain unclear. We related the composition of "coarse colloids" (colloids in the 0.1-1.2 μm size range) in 47 Belgian streams to the

  10. Intermolecular binding of blueberry pectin-rich fractions and anthocyanin.

    Science.gov (United States)

    Lin, Z; Fischer, J; Wicker, L

    2016-03-01

    Pectin was extracted from blueberry powder into three fractions of water soluble (WSF), chelator soluble (CSF) and sodium carbonate soluble (NSF). The fractions were incubated with cyanidin-3-glucoside (C3G), a mixture of five anthocyanidins (cyanidin, pelargonidin, malvidin, petunidin and delphinidin) or blueberry juice at pH 2.0-4.5. Free anthocyanins and bound anthocyanin-pectin mixtures were separated by ultrafiltration. WSF bound the least amount of anthocyanin at all pH values. CSF had stronger anthocyanin binding ability at pH 2.0-3.6, while NSF had stronger anthocyanin binding ability at pH 3.6-4.5. The pectin and anthocyanin binding was lowest at pH 4.5 and higher at pH 2.0-3.6. Nearly doubling C3G pigment content increased bound anthocyanin percentage by 16-23% at pH 3.6, which favored anthocyanin aromatic stacking, compared to 3-9% increase at pH 2.0. Ionic interaction between anthocyanin flavylium cations and free pectic carboxyl groups, and anthocyanin stacking may be two major mechanisms for pectin and anthocyanin binding. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. A Heparin Binding Motif Rich in Arginine and Lysine is the Functional Domain of YKL-40

    Directory of Open Access Journals (Sweden)

    Nipaporn Ngernyuang

    2018-02-01

    Full Text Available The heparin-binding glycoprotein YKL-40 (CHI3L1 is intimately associated with microvascularization in multiple human diseases including cancer and inflammation. However, the heparin-binding domain(s pertinent to the angiogenic activity have yet been identified. YKL-40 harbors a consensus heparin-binding motif that consists of positively charged arginine (R and lysine (K (RRDK; residues 144–147; but they don't bind to heparin. Intriguingly, we identified a separate KR-rich domain (residues 334–345 that does display strong heparin binding affinity. A short synthetic peptide spanning this KR-rich domain successfully competed with YKL-40 and blocked its ability to bind heparin. Three individual point mutations, where alanine (A substituted for K or R (K337A, K342A, R344A, led to remarkable decreases in heparin-binding ability and angiogenic activity. In addition, a neutralizing anti-YKL-40 antibody that targets these residues and prevents heparin binding impeded angiogenesis in vitro. MDA-MB-231 breast cancer cells engineered to express ectopic K337A, K342A or R344A mutants displayed reduced tumor development and compromised tumor vessel formation in mice relative to control cells expressing wild-type YKL-40. These data reveal that the KR-rich heparin-binding motif is the functional heparin-binding domain of YKL-40. Our findings shed light on novel molecular mechanisms underlying endothelial cell angiogenesis promoted by YKL-40 in a variety of diseases.

  12. A Heparin Binding Motif Rich in Arginine and Lysine is the Functional Domain of YKL-40.

    Science.gov (United States)

    Ngernyuang, Nipaporn; Yan, Wei; Schwartz, Lawrence M; Oh, Dennis; Liu, Ying-Bin; Chen, Hongzhuan; Shao, Rong

    2018-02-01

    The heparin-binding glycoprotein YKL-40 (CHI3L1) is intimately associated with microvascularization in multiple human diseases including cancer and inflammation. However, the heparin-binding domain(s) pertinent to the angiogenic activity have yet been identified. YKL-40 harbors a consensus heparin-binding motif that consists of positively charged arginine (R) and lysine (K) (RRDK; residues 144-147); but they don't bind to heparin. Intriguingly, we identified a separate KR-rich domain (residues 334-345) that does display strong heparin binding affinity. A short synthetic peptide spanning this KR-rich domain successfully competed with YKL-40 and blocked its ability to bind heparin. Three individual point mutations, where alanine (A) substituted for K or R (K337A, K342A, R344A), led to remarkable decreases in heparin-binding ability and angiogenic activity. In addition, a neutralizing anti-YKL-40 antibody that targets these residues and prevents heparin binding impeded angiogenesis in vitro. MDA-MB-231 breast cancer cells engineered to express ectopic K337A, K342A or R344A mutants displayed reduced tumor development and compromised tumor vessel formation in mice relative to control cells expressing wild-type YKL-40. These data reveal that the KR-rich heparin-binding motif is the functional heparin-binding domain of YKL-40. Our findings shed light on novel molecular mechanisms underlying endothelial cell angiogenesis promoted by YKL-40 in a variety of diseases. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  13. Polyphenol-Rich Pomegranate Juice Reduces IgE Binding to Cashew Nut Allergens

    Science.gov (United States)

    Cashew nut allergy is mediated by IgE binding to seed-storage proteins including Ana o 1, 2, and 3. Cashew nuts commonly cause severe reactions and only small amounts are needed. Polyphenol rich juices and polyphenol compounds have been demonstrated to complex with peanut allergens. The interacti...

  14. The Tomato Nucleotide-binding Leucine-rich Repeat Immune Receptor I-2 Couples DNA-binding to Nucleotide-binding Domain Nucleotide Exchange*

    Science.gov (United States)

    Fenyk, Stepan; Dixon, Christopher H.; Gittens, William H.; Townsend, Philip D.; Sharples, Gary J.; Pålsson, Lars-Olof; Takken, Frank L. W.; Cann, Martin J.

    2016-01-01

    Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable plants to recognize and respond to pathogen attack. Previously, we demonstrated that the Rx1 NLR of potato is able to bind and bend DNA in vitro. DNA binding in situ requires its genuine activation following pathogen perception. However, it is unknown whether other NLR proteins are also able to bind DNA. Nor is it known how DNA binding relates to the ATPase activity intrinsic to NLR switch function required to immune activation. Here we investigate these issues using a recombinant protein corresponding to the N-terminal coiled-coil and nucleotide-binding domain regions of the I-2 NLR of tomato. Wild type I-2 protein bound nucleic acids with a preference of ssDNA ≈ dsDNA > ssRNA, which is distinct from Rx1. I-2 induced bending and melting of DNA. Notably, ATP enhanced DNA binding relative to ADP in the wild type protein, the null P-loop mutant K207R, and the autoactive mutant S233F. DNA binding was found to activate the intrinsic ATPase activity of I-2. Because DNA binding by I-2 was decreased in the presence of ADP when compared with ATP, a cyclic mechanism emerges; activated ATP-associated I-2 binds to DNA, which enhances ATP hydrolysis, releasing ADP-bound I-2 from the DNA. Thus DNA binding is a general property of at least a subset of NLR proteins, and NLR activation is directly linked to its activity at DNA. PMID:26601946

  15. The Tomato Nucleotide-binding Leucine-rich Repeat Immune Receptor I-2 Couples DNA-binding to Nucleotide-binding Domain Nucleotide Exchange.

    Science.gov (United States)

    Fenyk, Stepan; Dixon, Christopher H; Gittens, William H; Townsend, Philip D; Sharples, Gary J; Pålsson, Lars-Olof; Takken, Frank L W; Cann, Martin J

    2016-01-15

    Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable plants to recognize and respond to pathogen attack. Previously, we demonstrated that the Rx1 NLR of potato is able to bind and bend DNA in vitro. DNA binding in situ requires its genuine activation following pathogen perception. However, it is unknown whether other NLR proteins are also able to bind DNA. Nor is it known how DNA binding relates to the ATPase activity intrinsic to NLR switch function required to immune activation. Here we investigate these issues using a recombinant protein corresponding to the N-terminal coiled-coil and nucleotide-binding domain regions of the I-2 NLR of tomato. Wild type I-2 protein bound nucleic acids with a preference of ssDNA ≈ dsDNA > ssRNA, which is distinct from Rx1. I-2 induced bending and melting of DNA. Notably, ATP enhanced DNA binding relative to ADP in the wild type protein, the null P-loop mutant K207R, and the autoactive mutant S233F. DNA binding was found to activate the intrinsic ATPase activity of I-2. Because DNA binding by I-2 was decreased in the presence of ADP when compared with ATP, a cyclic mechanism emerges; activated ATP-associated I-2 binds to DNA, which enhances ATP hydrolysis, releasing ADP-bound I-2 from the DNA. Thus DNA binding is a general property of at least a subset of NLR proteins, and NLR activation is directly linked to its activity at DNA. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Recognition of AT-Rich DNA Binding Sites by the MogR Repressor

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Aimee; Higgins, Darren E.; Panne, Daniel; (Harvard-Med); (EMBL)

    2009-07-22

    The MogR transcriptional repressor of the intracellular pathogen Listeria monocytogenes recognizes AT-rich binding sites in promoters of flagellar genes to downregulate flagellar gene expression during infection. We describe here the 1.8 A resolution crystal structure of MogR bound to the recognition sequence 5' ATTTTTTAAAAAAAT 3' present within the flaA promoter region. Our structure shows that MogR binds as a dimer. Each half-site is recognized in the major groove by a helix-turn-helix motif and in the minor groove by a loop from the symmetry-related molecule, resulting in a 'crossover' binding mode. This oversampling through minor groove interactions is important for specificity. The MogR binding site has structural features of A-tract DNA and is bent by approximately 52 degrees away from the dimer. The structure explains how MogR achieves binding specificity in the AT-rich genome of L. monocytogenes and explains the evolutionary conservation of A-tract sequence elements within promoter regions of MogR-regulated flagellar genes.

  17. Saliva of the graminivorous Theropithecus gelada lacks proline-rich proteins and tannin-binding capacity.

    Science.gov (United States)

    Mau, Marcus; Südekum, Karl-Heinz; Johann, Achim; Sliwa, Alexander; Kaiser, Thomas M

    2009-08-01

    Gelada baboons are the sole survivors of the genus Theropithecus and the only known graminivorous primates. They developed special adaptations to their diet such as high-crowned teeth for processing hard and abrasive feed. The fine-tuning of salivary protein composition might be another key mechanism that is used by species for adapting to the environment and competing with rivals for exploiting new ecological niches. In order to test whether gelada (graminivorous) and hamadryas baboons (omnivorous) differ in their salivary protein composition, we compared whole saliva samples of captive Theropithecus gelada and Papio hamadryas using gel electrophoresis and tannin-binding assay. We hypothesized that the amount of proline-rich salivary proteins with tannin-binding capacity is higher in baboons consuming a feed with high dicot/monocot rations. Dicots produce tannins as a chemical defense system, discouraging animals from eating them. In contrast to dicots, monocots do not synthesize tannins. The presence of tannin-binding proteins in saliva should effectively inactivate the dicot tannin-based defense mechanism and increase the dietary breadth and/or the capability to switch between monocots and dicot leaves. The lack of such tannin-binding proteins in saliva would indicate a narrow dietary spectrum more restricted to monocots. We found T. gelada to completely lack proline-rich proteins (PRPs) and tannin-binding capacity similar to a great variety of other grazing mammals. In contrast, P. hamadryas does possess PRPs with tannin-binding activity. The findings support a growing body of evidence suggesting a high-level specialization of T. gelada to grass diets. However, it remains unclear, whether loss of salivary tannin-binding capacity drove the gelada into its narrow feeding niche, or whether this loss is the result of a long process of increased specialization. Thus, from an ecological point of view, T. gelada appears to be more vulnerable to environmental changes

  18. Location and nature of calcium-binding sites in salivary acidic proline-rich phosphoproteins

    International Nuclear Information System (INIS)

    Bennick, A.; McLaughlin, A.C.; Grey, A.A.; Madapallimattam, G.

    1981-01-01

    The location of the calcium-binding sites in the human acidic proline-rich proteins, salivary proteins A and C, was determined by equilibrium dialysis of the tryptic peptides with buffers containing 45 Ca. All the calcium-binding sites are located in the NH 2 -terminal tryptic peptide (TX peptide). The nature of the calcium binding sites in the TX peptide and native salivary proteins A and C, as well as dephosphorylated proteins was compared. Two types of sites can be distinguished in peptide TX. Type I sites have an apparent dissociation constant (K) of 38 μM and are responsible for the binding of 2.6 mol of Ca/mol of peptide. The corresponding figures for Type II sites are 780 μM and 5.3 mol of Ca/mol of peptide. In the native proteins, the amount of calcium bound at the type II sites decreases to 3.9 mol of Ca/mol of proteins A and C and K increases to 1100 μM. The amount of calcium bound at type I sites decreases to 1.5 mol/mol of protein A and 0.6 mol/mol of protein C, but there is no change in K. Dephosphorylation affects the calcium binding at both types of sites. The experiments indicate that the COOH-terminal parts of the native proteins affect the number and the nature of the protein calcium-binding sites. Proton and phosphorous NMR data demonstrate that β-COOH in aspartic acid, as well as phosphoserine, are part of the calcium-binding sites. The difference in calcium binding to salivary proteins A and C may be due at least partially to differences in the environment of one or more aspartic acids

  19. LFA-1 and Mac-1 integrins bind to the serine/threonine-rich domain of thrombomodulin

    Energy Technology Data Exchange (ETDEWEB)

    Kawamoto, Eiji [Department of Molecular Pathobiology and Cell Adhesion Biology, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie 514-8507 (Japan); Emergency and Critical Care Center, Mie University Hospital, 2-174 Edobashi, Tsu 514-8507 (Japan); Okamoto, Takayuki, E-mail: okamotot@doc.medic.mie-u.ac.jp [Department of Molecular Pathobiology and Cell Adhesion Biology, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie 514-8507 (Japan); Takagi, Yoshimi [Department of Molecular Pathobiology and Cell Adhesion Biology, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie 514-8507 (Japan); Honda, Goichi [Medical Affairs Department, Asahi Kasei Pharma Corporation, 1-105 Kanda Jinbo-cho, Chiyoda-ku, Tokyo 101-8101 (Japan); Suzuki, Koji [Faculty of Pharmaceutical Science, Suzuka University of Medical Science, 3500-3, Minamitamagaki-cho, Suzuka, Mie 513-8679 (Japan); Imai, Hiroshi [Emergency and Critical Care Center, Mie University Hospital, 2-174 Edobashi, Tsu 514-8507 (Japan); Shimaoka, Motomu, E-mail: shimaoka@doc.medic.mie-u.ac.jp [Department of Molecular Pathobiology and Cell Adhesion Biology, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie 514-8507 (Japan)

    2016-05-13

    LFA-1 (αLβ2) and Mac-1 (αMβ2) integrins regulate leukocyte trafficking in health and disease by binding primarily to IgSF ligand ICAM-1 and ICAM-2 on endothelial cells. Here we have shown that the anti-coagulant molecule thrombomodulin (TM), found on the surface of endothelial cells, functions as a potentially new ligand for leukocyte integrins. We generated a recombinant extracellular domain of human TM and Fc fusion protein (TM-domains 123-Fc), and showed that pheripheral blood mononuclear cells (PBMCs) bind to TM-domains 123-Fc dependent upon integrin activation. We then demonstrated that αL integrin-blocking mAb, αM integrin-blocking mAb, and β2 integrin-blocking mAb inhibited the binding of PBMCs to TM-domains 123-Fc. Furthermore, we show that the serine/threonine-rich domain (domain 3) of TM is required for the interaction with the LFA-1 (αLβ2) and Mac-1 (αMβ2) integrins to occur on PBMCs. These results demonstrate that the LFA-1 and Mac-1 integrins on leukocytes bind to TM, thereby establishing the molecular and structural basis underlying LFA-1 and Mac-1 integrin interaction with TM on endothelial cells. In fact, integrin-TM interactions might be involved in the dynamic regulation of leukocyte adhesion with endothelial cells. - Highlights: • LFA-1 and Mac-1 integrins bind to the anti-coagulant molecule thrombomodulin. • The serine/threonine-rich domain of thrombomodulin is essential to interact with the LFA-1 and Mac-1 integrins on PBMCs. • Integrin-TM interactions might be involved in the dynamic regulation of leukocyte adhesion with endothelial cells.

  20. Binding the Mammalian High Mobility Group Protein AT-hook 2 to AT-Rich Deoxyoligonucleotides: Enthalpy-Entropy Compensation

    OpenAIRE

    Joynt, Suzanne; Morillo, Victor; Leng, Fenfei

    2009-01-01

    HMGA2 is a DNA minor-groove binding protein. We previously demonstrated that HMGA2 binds to AT-rich DNA with very high binding affinity where the binding of HMGA2 to poly(dA-dT)2 is enthalpy-driven and to poly(dA)poly(dT) is entropy-driven. This is a typical example of enthalpy-entropy compensation. To further study enthalpy-entropy compensation of HMGA2, we used isothermal-titration-calorimetry to examine the interactions of HMGA2 with two AT-rich DNA hairpins: 5′-CCAAAAAAAAAAAAAAAGCCCCCGCTT...

  1. Cysteine-rich intestinal protein binds zinc during transmucosal zinc transport

    International Nuclear Information System (INIS)

    Hempe, J.M.; Cousins, R.J.

    1991-01-01

    The mechanism of zinc absorption has not been delineated, but kinetic studies show that both passive and carrier-mediated processes are involved. The authors have identified a low molecular mass zinc-binding protein in the soluble fraction of rat intestinal mucosa that could function as an intracellular zinc carrier. The protein was not detected in liver or pancreas, suggesting a role specific to the intestine. The protein binds zinc during transmucosal zinc transport and shows signs of saturation at higher luminal zinc concentrations, characteristics consistent with a role in carrier-mediated zinc absorption. Microsequence analysis of the protein purified by gel-filtration HPCL and SDS/PAGE showed complete identity within the first 41 N-terminal amino acids with the deduced protein sequence of cysteine-rich intestinal protein. These investigators showed that the gene for this protein is developmentally regulated in neonates during the suckling period, conserved in many vertebrate species, and predominantly expressed in the small intestine. Cysteine-rich intestinal protein contains a recently identified conserved sequence of histidine and cysteine residues, the LIM motif, which our results suggest confers metal-binding properties that are important for zinc transport and/or functions of this micronutrient

  2. Native kinesin-1 does not bind preferentially to GTP-tubulin-rich microtubules in vitro.

    Science.gov (United States)

    Li, Qiaochu; King, Stephen J; Xu, Jing

    2017-09-01

    Molecular motors such as kinesin-1 work in small teams to actively shuttle cargos in cells, for example in polarized transport in axons. Here, we examined the potential regulatory role of the nucleotide state of tubulin on the run length of cargos carried by multiple kinesin motors, using an optical trapping-based in vitro assay. Based on a previous report that kinesin binds preferentially to GTP-tubulin-rich microtubules, we anticipated that multiple-kinesin cargos would run substantially greater distances along GMPCPP microtubules than along GDP microtubules. Surprisingly, we did not uncover any significant differences in run length between microtubule types. A combination of single-molecule experiments, comparison with previous theory, and classic microtubule affinity pulldown assays revealed that native kinesin-1 does not bind preferentially to GTP-tubulin-rich microtubules. The apparent discrepancy between our observations and the previous report likely reflects differences in post-translational modifications between the native motors used here and the recombinant motors examined previously. Future investigations will help shed light on the interplay between the motor's post-translational modification and the microtubule's nucleotide-binding state for transport regulation in vivo. © 2017 Wiley Periodicals, Inc.

  3. Selective metal binding by Vanabin2 from the vanadium-rich ascidian, Ascidia sydneiensis samea.

    Science.gov (United States)

    Kawakami, Norifumi; Ueki, Tatsuya; Matsuo, Koichi; Gekko, Kunihiko; Michibata, Hitoshi

    2006-07-01

    Vanadium-binding proteins, or Vanabins, have recently been isolated from the vanadium-rich ascidian, Ascidia sydneiensis samea. Recent reports indicate that Vanabin2 binds twenty V(IV) ions at pH 7.5, and that it has a novel bow-shaped conformation. However, the role of Vanabin2 in vanadium accumulation by the ascidian has not yet been determined. In the present study, the effects of acidic pH on selective metal binding to Vanabin2 and on the secondary structure of Vanabin2 were examined. Vanabin2 selectively bound to V(IV), Fe(III), and Cu(II) ions under acidic conditions. In contrast, Co(II), Ni(II), and Zn(II) ions were bound at pH 6.5 but not at pH 4.5. Changes in pH had no detectable effect on the secondary structure of Vanabin2 under acidic conditions, as determined by circular dichroism spectroscopy, and little variation in the dissociation constant for V(IV) ions was observed in the pH range 4.5-7.5, suggesting that the binding state of the ligands is not affected by acidification. Taken together, these results suggest that the reason for metal ion dissociation upon acidification is attributable not to a change in secondary structure but, rather, that it is caused by protonation of the amino acid ligands that complex with V(IV) ions.

  4. Vanadium-binding proteins (vanabins) from a vanadium-rich ascidian Ascidia sydneiensis samea.

    Science.gov (United States)

    Ueki, Tatsuya; Adachi, Takahiro; Kawano, Sonoko; Aoshima, Masato; Yamaguchi, Nobuo; Kanamori, Kan; Michibata, Hitoshi

    2003-04-15

    Since the beginning of the last century, it has been known that ascidians accumulate high levels of a transition metal, vanadium, in their blood cells, although the mechanism for this curious biological function remains unknown. Recently, we identified three vanadium-binding proteins (vanabins), previously denoted as vanadium-associated proteins (VAPs) [Zool. Sci. 14 (1997) 37], from the cytoplasm fraction of vanadium-containing blood cells (vanadocytes) of the vanadium-rich ascidian Ascidia sydneiensis samea. Here, we describe the cloning, expression, and analysis of the metal-binding ability of vanabins. Recombinant proteins of two independent but related vanabins, vanabin1 and vanabin2, bound to 10 and 20 vanadium(IV) ions with dissociation constants of 2.1x10(-5) and 2.3x10(-5) M, respectively. The binding of vanadium(IV) to these vanabins was inhibited by the addition of copper(II) ions, but not by magnesium(II) or molybdate(VI) ions. Vanabins are the first proteins reported to show specific binding to vanadium ions; this should provide a clue to resolving the problem regarding the selective accumulation of vanadium in ascidians.

  5. Polyphenol-rich pomegranate juice reduces IgE binding to cashew nut allergens.

    Science.gov (United States)

    Li, Yichen; Mattison, Christopher P

    2018-03-01

    Food allergy negatively impacts quality of life and can be life-threatening. Cashew nuts can cause severe reactions in very small amounts, and they are included in a group of foods most commonly responsible for causing food allergy. Polyphenols and polyphenol-rich juices have been demonstrated to complex with peanut allergens. Here, the interaction between cashew nut allergens and polyphenol-rich juices is evaluated biochemically and immunologically. Various juices, including pomegranate (POM), blueberry (BB), and concord grape (CG) juices, were evaluated for polyphenol content and formation of polyphenol-cashew allergen complexes. Among the various juices studied, POM juice showed a greater capacity to form complexes with cashew proteins. Dynamic light scattering (DLS) demonstrated a sharp increase in cashew protein extract particle size to around 3580 nm, and fewer cashew proteins were resolved by electrophoresis after treatment with POM juice. Immunoassays demonstrated reduced IgG and IgE binding to cashew allergens due to allergen precipitation by POM juice. These observations support the formation of complexes between polyphenol and cashew proteins that can prevent antibody recognition of cashew allergens through allergen precipitation. POM juice treatment of cashew extract effectively reduces antibody binding through allergen precipitation, and these findings could be applied to the development of less allergenic cashew nut products and oral immunotherapy. Published 2017. This article is a U.S. Government work and is in the public domain in the USA. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

  6. Binding the mammalian high mobility group protein AT-hook 2 to AT-rich deoxyoligonucleotides: enthalpy-entropy compensation.

    Science.gov (United States)

    Joynt, Suzanne; Morillo, Victor; Leng, Fenfei

    2009-05-20

    HMGA2 is a DNA minor-groove binding protein. We previously demonstrated that HMGA2 binds to AT-rich DNA with very high binding affinity where the binding of HMGA2 to poly(dA-dT)(2) is enthalpy-driven and to poly(dA)poly(dT) is entropy-driven. This is a typical example of enthalpy-entropy compensation. To further study enthalpy-entropy compensation of HMGA2, we used isothermal-titration-calorimetry to examine the interactions of HMGA2 with two AT-rich DNA hairpins: 5'-CCAAAAAAAAAAAAAAAGCCCCCGCTTTTTTTTTTTTTTTGG-3' (FL-AT-1) and 5'-CCATATATATATATATAGCCCCCGCTATATATATATATATGG-3' (FL-AT-2). Surprisingly, we observed an atypical isothermal-titration-calorimetry-binding curve at low-salt aqueous solutions whereby the apparent binding-enthalpy decreased dramatically as the titration approached the end. This unusual behavior can be attributed to the DNA-annealing coupled to the ligand DNA-binding and is eliminated by increasing the salt concentration to approximately 200 mM. At this condition, HMGA2 binding to FL-AT-1 is entropy-driven and to FL-AT-2 is enthalpy-driven. Interestingly, the DNA-binding free energies for HMGA2 binding to both hairpins are almost temperature independent; however, the enthalpy-entropy changes are dependent on temperature, which is another aspect of enthalpy-entropy compensation. The heat capacity change for HMGA2 binding to FL-AT-1 and FL-AT-2 are almost identical, indicating that the solvent displacement and charge-charge interaction in the coupled folding/binding processes for both binding reactions are similar.

  7. Polyamide-scorpion cyclam lexitropsins selectively bind AT-rich DNA independently of the nature of the coordinated metal.

    Directory of Open Access Journals (Sweden)

    Anthony T S Lo

    Full Text Available Cyclam was attached to 1-, 2- and 3-pyrrole lexitropsins for the first time through a synthetically facile copper-catalyzed "click" reaction. The corresponding copper and zinc complexes were synthesized and characterized. The ligand and its complexes bound AT-rich DNA selectively over GC-rich DNA, and the thermodynamic profile of the binding was evaluated by isothermal titration calorimetry. The metal, encapsulated in a scorpion azamacrocyclic complex, did not affect the binding, which was dominated by the organic tail.

  8. Tropical tannin-rich fodder intake modifies saliva-binding capacity in growing sheep.

    Science.gov (United States)

    Vargas-Magaña, J J; Aguilar-Caballero, A J; Torres-Acosta, J F J; Sandoval-Castro, C A; Hoste, H; Capetillo-Leal, C M

    2013-12-01

    We evaluated the effect of feeding dietary tannins from Lysiloma latisiliquum fresh forage on the saliva tannin-binding capacity of hair sheep lambs without previous exposure to tannin-rich (TR) fodder. Twenty-four hair sheep lambs (13.6±3.04 kg LW) were fed a tannin-free diet at the beginning of the experimental period (from day 10 to 13). On day 14, lambs were distributed into three groups (n=8): control group (CG), fed with the tannin-free diet (from D10 to D112); tannin short-term group (TST), fed the basal diet and 650 g of L. latisiliquum forage (from D14 to D55); tannin long-term group (TLT), fed the basal diet and 650 g of L. latisiliquum forage (from D14 to D112). Saliva samples were collected from the mouth of each lamb in the morning before feeding time on D10 and D14 (baseline period), on D49 and D56 (period 1) and on D97 and D112 (period 2). The tannin binding response of salivary protein (∆% turbidity) was determined with the haze development test (HDT) using either tannic acid or L. latisiliquum forage acetone extract. A turbidity protein index (TPI) was calculated as (∆% turbidity/[salivary protein (mg)]). Differences in HDT and TPI in the different groups were compared by repeated measures ANOVA using Proc Mixed. All groups had similar ∆% turbidity throughout the experiment (P>0.05). At baseline and period 1, the TPI of the different groups was similar (P>0.05). On period 2 the TLT group showed higher TPI compared with CG (Ptannins.

  9. Entropically-driven binding of mithramycin in the minor groove of C/G-rich DNA sequences

    Science.gov (United States)

    Barceló, Francisca; Scotta, Claudia; Ortiz-Lombardía, Miguel; Méndez, Carmen; Salas, José A.; Portugal, José

    2007-01-01

    The antitumour antibiotic mithramycin A (MTA) is a DNA minor-groove binding ligand. It binds to C/G-rich tracts as a dimer that forms in the presence of divalent cations such as Mg2+. Differential scanning calorimetry, UV thermal denaturation, isothermal titration calorimetry and competition dialysis were used, together with computations of the hydrophobic free energy of binding, to determine the thermodynamic profile of MTA binding to DNA. The results were compared to those obtained in parallel using the structurally related mithramycin SK (MSK). The binding of MTA to salmon testes DNA determined by UV melting studies (Kobs = 1.2 (±0.3) × 105 M−1) is tighter than that of MSK (2.9 (±1.0) × 104 M−1) at 25°C. Competition dialysis studies showed a tighter MTA binding to both salmon testes DNA (42% C + G) and Micrococcus lysodeikticus DNA (72% C + G). The thermodynamic analysis of binding data at 25°C shows that the binding of MTA and MSK to DNA is entropically driven, dominated by the hydrophobic transfer of the antibiotics from solution to the DNA-binding site. Direct molecular recognition between MTA or MSK and DNA through hydrogen bonding and van der Waals contacts may also contribute significantly to complex formation. PMID:17369273

  10. Glutamine rich and basic region/leucine zipper (bZIP) domains stabilize cAMP-response element-binding protein (CREB) binding to chromatin.

    Science.gov (United States)

    Mayr, Bernhard M; Guzman, Ernesto; Montminy, Marc

    2005-04-15

    We have examined the dynamics of cAMP-response element-binding protein (CREB) binding to chromatin in live cells using fluorescence recovery after photobleaching (FRAP). CREB was found to bind to target sites with a residence time of 100 s, and exposure to a cAMP agonist had no effect on these kinetics. In addition to the basic region/leucine zipper (bZIP) domain, a glutamine-rich trans-activation domain in CREB called Q2 also appeared to be critical for promoter occupancy. Indeed, mutations in Q2 that reduced residence time by FRAP assay disrupted target gene activation via CREB in cells exposed to a cAMP agonist. Notably, insertion of the glutamine-rich B trans-activation domain of SP1 into a mutant CREB polypeptide lacking Q2 stabilized CREB occupancy and rescued target gene activation. These results suggest a novel mechanism by which the family of glutamine-rich activators promotes cellular gene expression.

  11. Improving the binding capacity of Ni2+ decorated porous magnetic silica spheres for histidine-rich protein separation.

    Science.gov (United States)

    Benelmekki, M; Caparros, C; Xuriguera, E; Lanceros-Mendez, S; Rodriguez-Carmona, E; Mendoza, R; Corchero, J L; Martinez, Ll M

    2013-01-01

    Biomagnetic immobilization of histidine-rich proteins based on the single-step affinity adsorption of transition metal ions continues to be a suitable practice as a cost effective and a up scaled alternative to the to multiple-step chromatographic separations. In our previous work, we synthesised Porous Magnetic silica (PMS) spheres by one-step hydrothermal-assisted modified-stöber method. The obtained spheres were decorated with Ni(2+) and Co(2+), and evaluated for the capture of a H6-Tagged green fluorescence protein (GFP-H6) protein. The binding capacity of the obtained spheres was found to be slightly higher in the case Ni(2+) decorated PMS spheres (PMSNi). However, comparing with commercial products, the binding capacity was found to be lower than the expected. In this way, the present work is an attempt to improve the binding capacity of PMSNi to histidine-rich proteins. We find that increasing the amount of Ni(2+) onto the surface of the PMS spheres leads to an increment of the binding capacity to GFP-H6 by a factor of two. On the other hand, we explore how the size of histidine-rich protein can affect the binding capacity comparing the results of the GFP-6H to those of the His-tagged α-galactosidase (α-GLA). Finally, we demonstrate that the optimization of the magnetophoresis parameters during washing and eluting steps can lead to an additional improvement of the binding capacity. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Vanadium-binding protein in a vanadium-rich ascidian Ascidia sydneiensissamea: CW and pulsed EPR studies.

    Science.gov (United States)

    Fukui, Kôichi; Ueki, Tatsuya; Ohya, Hiroaki; Michibata, Hitoshi

    2003-05-28

    Some of the ascidians belonging to the suborder Phlebobranchia accumulate vanadium ion efficiently from seawater. Clarification of the mechanism of this surprisingly efficient metal-accumulation system is desirable. Two mutually similar vanadium-binding proteins (vanabin1 and vanabin2) have recently been isolated from a vanadium-rich ascidian Ascidia sydneiensis samea. In this study, the vanadium-binding properties of vanabin2 have been investigated by X-band CW EPR and pulsed EPR spectroscopy. CW EPR spectra of samples containing various ratios of VO2+ and vanabin2 invariably exhibited a usual mononuclear-type VO2+ EPR signal with the intensity dependent on the ratio [vanabin]/[V]. EPR titration has shown that vanabin2 can bind up to approximately 23.9 vanadium ions per one molecule, almost all of which ( approximately 84%) are in a mononuclear VO2+ state as estimated by EPR quantitation. Electron spin-echo envelope modulation (ESEEM) spectra of VO-vanabin2 exhibited reasonably intense peaks attributable to amine nitrogen. This is consistent with the fact that vanabin2 is a lysine-rich protein (14 lysines out of 91 amino acids). The present study reveals the uniqueness of vanabin2, which can bind a large number of metal ions in a mononuclear fashion in contrast to the situation for ferritin and metallothionein.

  13. HuR binding to AU-rich elements present in the 3' untranslated region of Classical swine fever virus

    Directory of Open Access Journals (Sweden)

    Huang Chin-Cheng

    2011-07-01

    Full Text Available Abstract Background Classical swine fever virus (CSFV is the member of the genus Pestivirus under the family Flaviviridae. The 5' untranslated region (UTR of CSFV contains the IRES, which is a highly structured element that recruits the translation machinery. The 3' UTR is usually the recognition site of the viral replicase to initiate minus-strand RNA synthesis. Adenosine-uridine rich elements (ARE are instability determinants present in the 3' UTR of short-lived mRNAs. However, the presence of AREs in the 3' UTR of CSFV conserved in all known strains has never been reported. This study inspects a possible role of the ARE in the 3' UTR of CSFV. Results Using RNA pull-down and LC/MS/MS assays, this study identified at least 32 possible host factors derived from the cytoplasmic extracts of PK-15 cells that bind to the CSFV 3' UTR, one of which is HuR. HuR is known to bind the AREs and protect the mRNA from degradation. Using recombinant GST-HuR, this study demonstrates that HuR binds to the ARE present in the 3' UTR of CSFV in vitro and that the binding ability is conserved in strains irrespective of virulence. Conclusions This study identified one of the CSFV 3' UTR binding proteins HuR is specifically binding to in the ARE region.

  14. A Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors

    Energy Technology Data Exchange (ETDEWEB)

    Pyburn, Tasia M.; Bensing, Barbara A.; Xiong, Yan Q.; Melancon, Bruce J.; Tomasiak, Thomas M.; Ward, Nicholas J.; Yankovskaya, Victoria; Oliver, Kevin M.; Cecchini, Gary; Sulikowski, Gary A.; Tyska, Matthew J.; Sullam, Paul M.; Iverson, T.M. (VA); (UCLA); (Vanderbilt); (UCSF)

    2014-10-02

    GspB is a serine-rich repeat (SRR) adhesin of Streptococcus gordonii that mediates binding of this organism to human platelets via its interaction with sialyl-T antigen on the receptor GPIb{alpha}. This interaction appears to be a major virulence determinant in the pathogenesis of infective endocarditis. To address the mechanism by which GspB recognizes its carbohydrate ligand, we determined the high-resolution x-ray crystal structure of the GspB binding region (GspB{sub BR}), both alone and in complex with a disaccharide precursor to sialyl-T antigen. Analysis of the GspB{sub BR} structure revealed that it is comprised of three independently folded subdomains or modules: (1) an Ig-fold resembling a CnaA domain from prokaryotic pathogens; (2) a second Ig-fold resembling the binding region of mammalian Siglecs; (3) a subdomain of unique fold. The disaccharide was found to bind in a pocket within the Siglec subdomain, but at a site distinct from that observed in mammalian Siglecs. Confirming the biological relevance of this binding pocket, we produced three isogenic variants of S. gordonii, each containing a single point mutation of a residue lining this binding pocket. These variants have reduced binding to carbohydrates of GPIb{alpha}. Further examination of purified GspB{sub BR}-R484E showed reduced binding to sialyl-T antigen while S. gordonii harboring this mutation did not efficiently bind platelets and showed a significant reduction in virulence, as measured by an animal model of endocarditis. Analysis of other SRR proteins revealed that the predicted binding regions of these adhesins also had a modular organization, with those known to bind carbohydrate receptors having modules homologous to the Siglec and Unique subdomains of GspBBR. This suggests that the binding specificity of the SRR family of adhesins is determined by the type and organization of discrete modules within the binding domains, which may affect the tropism of organisms for different tissues.

  15. A leucine-rich repeat motif of Leishmania parasite surface antigen 2 binds to macrophages through the complement receptor 3.

    Science.gov (United States)

    Kedzierski, Lukasz; Montgomery, Jacqui; Bullen, Denise; Curtis, Joan; Gardiner, Elizabeth; Jimenez-Ruiz, Antonio; Handman, Emanuela

    2004-04-15

    Membrane glycoconjugates on the Leishmania parasites, notably leishmanolysin and lipophosphoglycan, have been implicated in attachment and invasion of host macrophages. However, the function of parasite surface Ag 2 (PSA-2) and membrane proteophosphoglycan (PPG) has not been elucidated. In this study we demonstrate that native and recombinant Leishmania infantum PSA-2, which consists predominantly of 15 leucine-rich repeats (LRR) and a recombinant LRR domain derived from L. major PPG, bind to macrophages. The interaction is restricted to macrophages and appears to be calcium independent. We have investigated the PSA-2-macrophage interaction to identify the host receptor involved in binding and we show that binding of PSA-2 to macrophages can be blocked by Abs to the complement receptor 3 (CR3, Mac-1). Data derived from mouse macrophage studies were further confirmed using cell lines expressing human CR3, and showed that PSA-2 also binds to the human receptor. This is the first demonstration of a functional role for PSA-2. Our data indicate that in addition to leishmanolysin and lipophosphoglycan, parasite attachment and invasion of macrophages involve a third ligand comprising the LRRs shared by PSA-2 and PPG and that these interactions occur via the CR3.

  16. New Cysteine-Rich Ice-Binding Protein Secreted from Antarctic Microalga, Chloromonas sp.

    Science.gov (United States)

    Jung, Woongsic; Campbell, Robert L; Gwak, Yunho; Kim, Jong Im; Davies, Peter L; Jin, EonSeon

    2016-01-01

    Many microorganisms in Antarctica survive in the cold environment there by producing ice-binding proteins (IBPs) to control the growth of ice around them. An IBP from the Antarctic freshwater microalga, Chloromonas sp., was identified and characterized. The length of the Chloromonas sp. IBP (ChloroIBP) gene was 3.2 kb with 12 exons, and the molecular weight of the protein deduced from the ChloroIBP cDNA was 34.0 kDa. Expression of the ChloroIBP gene was up- and down-regulated by freezing and warming conditions, respectively. Western blot analysis revealed that native ChloroIBP was secreted into the culture medium. This protein has fifteen cysteines and is extensively disulfide bonded as shown by in-gel mobility shifts between oxidizing and reducing conditions. The open-reading frame of ChloroIBP was cloned and over-expressed in Escherichia coli to investigate the IBP's biochemical characteristics. Recombinant ChloroIBP produced as a fusion protein with thioredoxin was purified by affinity chromatography and formed single ice crystals of a dendritic shape with a thermal hysteresis activity of 0.4±0.02°C at a concentration of 5 mg/ml. In silico structural modeling indicated that the three-dimensional structure of ChloroIBP was that of a right-handed β-helix. Site-directed mutagenesis of ChloroIBP showed that a conserved region of six parallel T-X-T motifs on the β-2 face was the ice-binding region, as predicted from the model. In addition to disulfide bonding, hydrophobic interactions between inward-pointing residues on the β-1 and β-2 faces, in the region of ice-binding motifs, were crucial to maintaining the structural conformation of ice-binding site and the ice-binding activity of ChloroIBP.

  17. Cell surface binding and uptake of arginine- and lysine-rich penetratin peptides in absence and presence of proteoglycans.

    Science.gov (United States)

    Amand, Helene L; Rydberg, Hanna A; Fornander, Louise H; Lincoln, Per; Nordén, Bengt; Esbjörner, Elin K

    2012-11-01

    Cell surface proteoglycans (PGs) appear to promote uptake of arginine-rich cell-penetrating peptides (CPPs), but their exact functions are unclear. To address if there is specificity in the interactions of arginines and PGs leading to improved internalization, we used flow cytometry to examine uptake in relation to cell surface binding for penetratin and two arginine/lysine substituted variants (PenArg and PenLys) in wildtype CHO-K1 and PG-deficient A745 cells. All peptides were more efficiently internalized into CHO-K1 than into A745, but their cell surface binding was independent of cell type. Thus, PGs promote internalization of cationic peptides, irrespective of the chemical nature of their positive charges. Uptake of each peptide was linearly dependent on its cell surface binding, and affinity is thus important for efficiency. However, the gradients of these linear dependencies varied significantly. Thus each peptide's ability to stimulate uptake once bound to the cell surface is reliant on formation of specific uptake-promoting interactions. Heparin affinity chromatography and clustering experiments showed that penetratin and PenArg binding to sulfated sugars is stabilized by hydrophobic interactions and result in clustering, whereas PenLys only interacts through electrostatic attraction. This may have implications for the molecular mechanisms behind arginine-specific uptake stimulation as penetratin and PenArg are more efficiently internalized than PenLys upon interaction with PGs. However, PenArg is also least affected by removal of PGs. This indicates that an increased arginine content not only improve PG-dependent uptake but also that PenArg is more adaptable as it can use several portals of entry into the cell. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. Cell surface binding and uptake of arginine- and lysine-rich penetratin peptides in absence and presence of proteoglycans

    KAUST Repository

    Åmand, Helene L.

    2012-11-01

    Cell surface proteoglycans (PGs) appear to promote uptake of arginine-rich cell-penetrating peptides (CPPs), but their exact functions are unclear. To address if there is specificity in the interactions of arginines and PGs leading to improved internalization, we used flow cytometry to examine uptake in relation to cell surface binding for penetratin and two arginine/lysine substituted variants (PenArg and PenLys) in wildtype CHO-K1 and PG-deficient A745 cells. All peptides were more efficiently internalized into CHO-K1 than into A745, but their cell surface binding was independent of cell type. Thus, PGs promote internalization of cationic peptides, irrespective of the chemical nature of their positive charges. Uptake of each peptide was linearly dependent on its cell surface binding, and affinity is thus important for efficiency. However, the gradients of these linear dependencies varied significantly. Thus each peptide\\'s ability to stimulate uptake once bound to the cell surface is reliant on formation of specific uptake-promoting interactions. Heparin affinity chromatography and clustering experiments showed that penetratin and PenArg binding to sulfated sugars is stabilized by hydrophobic interactions and result in clustering, whereas PenLys only interacts through electrostatic attraction. This may have implications for the molecular mechanisms behind arginine-specific uptake stimulation as penetratin and PenArg are more efficiently internalized than PenLys upon interaction with PGs. However, PenArg is also least affected by removal of PGs. This indicates that an increased arginine content not only improve PG-dependent uptake but also that PenArg is more adaptable as it can use several portals of entry into the cell. © 2012 Elsevier B.V.

  19. Localization of vanabins, vanadium-binding proteins, in the blood cells of the vanadium-rich ascidian, Ascidia sydneiensis samea.

    Science.gov (United States)

    Yamaguchi, Nobuo; Amakawa, Yuko; Yamada, Hiroshi; Ueki, Tatsuya; Michibata, Hitoshi

    2006-10-01

    Some species of the family Ascidiidae accumulate vanadium in concentrations in excess of 350 mM, which is about 10 (7)-fold higher than the concentration of vanadium in seawater. In these species, signet ring cells with a single large vacuole in which vanadium ions are contained function as vanadium-accumulating cells. These have been termed vanadocytes. We recently isolated five vanadium-binding proteins, which we named Vanabin1, Vanabin2, Vanabin3, Vanabin4, and VanabinP, from vanadocytes of the vanadium-rich ascidian Ascidia sydneiensis samea. In this study, we analyzed localization of the Vanabins in the blood cells of A. sydneiensis samea using monoclonal antibodies and confocal microscopy. The Vanabin1 and Vanabin2 proteins were found in the cytoplasm and/or in some organelles of vanadocytes. Vanabin3 was also detected in the cytoplasm, while Vanabin4 was found exclusively in the cytoplasmic membrane.

  20. Phenylalanine-Rich Peptide Mediated Binding with Graphene Oxide and Bioinspired Synthesis of Silver Nanoparticles for Electrochemical Sensing

    Directory of Open Access Journals (Sweden)

    Li Wang

    2017-02-01

    Full Text Available We demonstrated that a phenylalanine-rich peptide molecule, (FEFEFKFK2, could be used for the biofunctionalization of graphene oxide (GO and the bioinspired synthesis of silver nanoparticles (AgNPs for the creation of functional GO–AgNPs nanohybrids. The successful synthesis of GO–AgNPs nanohybrids was proven by the characterizations of atomic force microscopy, transmission electron microscope, and X-ray photoelectron spectroscopy. The fabricated electrochemical H2O2 sensor based on the synthesized GO–AgNPs nanohybrids showed high performances with a linear detection range 0.02–18 mM and a detection limit of 0.13 μM. The design of graphene-binding peptides is of benefit to the biofunctionalization of graphene-based materials, the synthesis of novel graphene–peptide nanohybrids, and the potential applications of graphene in biomedical fields.

  1. Identification of a novel vanadium-binding protein by EST analysis on the most vanadium-rich ascidian, Ascidia gemmata.

    Science.gov (United States)

    Samino, Setijono; Michibata, Hitoshi; Ueki, Tatsuya

    2012-04-01

    Ascidians are known to accumulate extremely high levels of vanadium in their blood cells (up to 350 mM). The branchial sac and the intestine are thought to be the first tissues to contact the outer environment and absorb vanadium ions. The concentration of vanadium in the branchial sac and the intestine of the most vanadium-rich ascidian Ascidia gemmata were determined to be 32.4 and 11.9 mM, respectively. Using an expressed sequence tag (EST) analysis of a cDNA library from the intestine of A. gemmata, we determined 960 ESTs and found 55 clones of metal-related gene orthologs, 6 redox-related orthologs, and 18 membrane transporter orthologs. Among them, two genes, which exhibited significant similarity to the vanadium-binding proteins of other vanadium-rich ascidian species, were designated AgVanabin1 and AgVanabin2. Immobilized metal ion affinity chromatography revealed that recombinant AgVanabin1 bound to metal ions with an increasing affinity for Cu(II) > Zn(II) > Co(II) and AgVanabin2 bound to metal ions with an increasing affinity for Cu(II) > Fe(III) > V(IV). To examine the use of AgVanabins for a metal absorption system, we constructed Escherichia coli strains that expressed AgVanabin1 or AgVanabin2 fused to maltose-binding protein and secreted into the periplasmic space. We found that the strain expressing AgVanabin2 accumulated about 13.5 times more Cu(II) ions than the control TB1 strain. Significant accumulation of vanadium was also observed in the AgVanabin2-expressing strain as seen by a 1.5-fold increase.

  2. Differential binding with ERα and ERβ of the phytoestrogen-rich plant Pueraria mirifica

    Directory of Open Access Journals (Sweden)

    C. Boonchird

    2010-02-01

    Full Text Available Variations in the estrogenic activity of the phytoestrogen-rich plant, Pueraria mirifica, were determined with yeast estrogen screen (YES consisting of human estrogen receptors (hER hERα and hERβ and human transcriptional intermediary factor 2 (hTIF2 or human steroid receptor coactivator 1 (hSRC1, respectively, together with the β-galactosidase expression cassette. Relative estrogenic potency was expressed by determining the β-galactosidase activity (EC50 of the tuber extracts in relation to 17β-estradiol. Twenty-four and 22 of the plant tuber ethanolic extracts interacted with hERα and hERβ, respectively, with a higher relative estrogenic potency with hERβ than with hERα. Antiestrogenic activity of the plant extracts was also determined by incubation of plant extracts with 17β-estradiol prior to YES assay. The plant extracts tested exhibited antiestrogenic activity. Both the estrogenic and the antiestrogenic activity of the tuber extracts were metabolically activated with the rat liver S9-fraction prior to the assay indicating the positive influence of liver enzymes. Correlation analysis between estrogenic potency and the five major isoflavonoid contents within the previously HPLC-analyzed tuberous samples namely puerarin, daidzin, genistin, daidzein, and genistein revealed a negative result.

  3. Bacteria binding by DMBT1/SAG/gp-340 is confined to the VEVLXXXXW motif in its scavenger receptor cysteine-rich domains

    DEFF Research Database (Denmark)

    Bikker, Floris J; Ligtenberg, Antoon J M; End, Caroline

    2004-01-01

    The scavenger receptor cysteine-rich (SRCR) proteins form an archaic group of metazoan proteins characterized by the presence of SRCR domains. These proteins are classified in group A and B based on the number of conserved cysteine residues in their SRCR domains, i.e. six for group A and eight...... acid motif (DMBT1 pathogen-binding site 1 or DMBT1pbs1; GRVEVLYRGSW). An alanine substitution scan revealed that VEVL and Trp are critical residues in this motif. Bacteria binding by DMBT1pbs1 was different from the bacteria binding by the macrophage receptor MARCO in which an RXR motif was critical...

  4. Silencing of a unique integrated domain nucleotide-binding leucine-rich repeat gene in wheat abolishes Diuraphis noxia resistance.

    Science.gov (United States)

    Nicolis, Vittorio Filippo; Venter, Eduard

    2018-03-13

    Plants respond in a similar manner to aphid feeding as to pathogen attack. Diuraphis noxia is a specialist aphid, feeding only on selected grasses that include wheat, barley, and oats. The wheat-Diuraphis noxia interaction is characterized by very similar responses as seen in wheat-pathogen interactions with none of the underlying resistance pathways and genes characterized yet. From wheat harboring the Dn1 resistance gene, we have identified a nucleotide-binding leucine-rich repeat (NLR) gene containing two integrated domains (IDs). These are three C-terminus ankyrin repeat-domains and an N-terminus WRKY domain. The NLR core of the gene can be traced through speciation events within the grass family, with a recent WRKY domain integration that is Triticum specific. Virus induced gene silencing of the gene in a resistant wheat line resulted in the abolishment of the resistance response and induced a highly susceptible phenotype. Silenced plants supported a higher number of aphids similar to the susceptible NIL and the intrinsic rate of increase of the aphids matched that of aphids feeding on the susceptible NIL. The presence of the gene is necessary for Dn1 resistance and we have named the gene Associated with Dn resistance 1 (Adr1) to reflect this function.

  5. Deletion in the first cysteine-rich repeat of low density lipoprotein receptor impairs its transport but not lipoprotein binding in fibroblasts from a subject with familial hypercholesterolemia

    Energy Technology Data Exchange (ETDEWEB)

    Leitersdorf, E.; Hobbs, H.H.; Fourie, A.M.; Jacobs, M.; Van Der Westhuyzen, D.R.; Coetzee, G.A. (Univ. of Texas Southwestern Medical Center, Dallas (USA))

    1988-11-01

    The ligand-binding domain of the low density lipoprotein (LDL) receptor is composed of seven cysteine-rich repeats, each {approx} 40 amino acids long. Previous studies showed that if the first repeat of the ligand-binding domain (encoded by exon 2) is deleted, the receptor fails to bind an anti-LDL receptor monoclonal antibody (IgG-C7) but continues to bind LDL with high affinity. Cultured fibroblasts from a Black South African Xhosa patient (TT) with the clinical syndrome of homozygous familial hypercholesterolemia demonstrated high-affinity cell-surface binding of {sup 125}I-labeled LDL but not {sup 125}I-labeled IgG-C7. previous haplotype analysis, using 10 restriction fragment length polymorphic sites, suggested that the patient inherited two identical LDL receptor alleles. The polymerase chain reaction technique was used to selectively amplify exon 2 of the LDL receptor gene from this patient. Sequence analysis of the amplified fragment disclosed a deletion of six base pairs that removes two amino acids, aspartic acid and glycine, from the first cysteine-rich ligand binding repeat. The mutation creates a new Pst I restriction site that can be used to detect the deletion. The existence of this mutant allele confirms that the epitope of IgG-C7 is located in the first cysteine-rich repeat and that this repeat is not necessary for LDL binding. The mutant gene produced a normally sized 120-kilodalton LDL receptor precursor protein that matured to the 160-kilodalton form at less than one-fourth the normal rate.

  6. The Potato Nucleotide-binding Leucine-rich Repeat (NLR) Immune Receptor Rx1 Is a Pathogen-dependent DNA-deforming Protein.

    Science.gov (United States)

    Fenyk, Stepan; Townsend, Philip D; Dixon, Christopher H; Spies, Gerhard B; de San Eustaquio Campillo, Alba; Slootweg, Erik J; Westerhof, Lotte B; Gawehns, Fleur K K; Knight, Marc R; Sharples, Gary J; Goverse, Aska; Pålsson, Lars-Olof; Takken, Frank L W; Cann, Martin J

    2015-10-09

    Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable cells to respond to pathogen attack. Several NLRs act in the nucleus; however, conserved nuclear targets that support their role in immunity are unknown. Previously, we noted a structural homology between the nucleotide-binding domain of NLRs and DNA replication origin-binding Cdc6/Orc1 proteins. Here we show that the NB-ARC (nucleotide-binding, Apaf-1, R-proteins, and CED-4) domain of the Rx1 NLR of potato binds nucleic acids. Rx1 induces ATP-dependent bending and melting of DNA in vitro, dependent upon a functional P-loop. In situ full-length Rx1 binds nuclear DNA following activation by its cognate pathogen-derived effector protein, the coat protein of potato virus X. In line with its obligatory nucleocytoplasmic distribution, DNA binding was only observed when Rx1 was allowed to freely translocate between both compartments and was activated in the cytoplasm. Immune activation induced by an unrelated NLR-effector pair did not trigger an Rx1-DNA interaction. DNA binding is therefore not merely a consequence of immune activation. These data establish a role for DNA distortion in Rx1 immune signaling and define DNA as a molecular target of an activated NLR. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. The Potato Nucleotide-binding Leucine-rich Repeat (NLR) Immune Receptor Rx1 Is a Pathogen-dependent DNA-deforming Protein*

    Science.gov (United States)

    Fenyk, Stepan; Townsend, Philip D.; Dixon, Christopher H.; Spies, Gerhard B.; de San Eustaquio Campillo, Alba; Slootweg, Erik J.; Westerhof, Lotte B.; Gawehns, Fleur K. K.; Knight, Marc R.; Sharples, Gary J.; Goverse, Aska; Pålsson, Lars-Olof; Takken, Frank L. W.; Cann, Martin J.

    2015-01-01

    Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable cells to respond to pathogen attack. Several NLRs act in the nucleus; however, conserved nuclear targets that support their role in immunity are unknown. Previously, we noted a structural homology between the nucleotide-binding domain of NLRs and DNA replication origin-binding Cdc6/Orc1 proteins. Here we show that the NB-ARC (nucleotide-binding, Apaf-1, R-proteins, and CED-4) domain of the Rx1 NLR of potato binds nucleic acids. Rx1 induces ATP-dependent bending and melting of DNA in vitro, dependent upon a functional P-loop. In situ full-length Rx1 binds nuclear DNA following activation by its cognate pathogen-derived effector protein, the coat protein of potato virus X. In line with its obligatory nucleocytoplasmic distribution, DNA binding was only observed when Rx1 was allowed to freely translocate between both compartments and was activated in the cytoplasm. Immune activation induced by an unrelated NLR-effector pair did not trigger an Rx1-DNA interaction. DNA binding is therefore not merely a consequence of immune activation. These data establish a role for DNA distortion in Rx1 immune signaling and define DNA as a molecular target of an activated NLR. PMID:26306038

  8. Genome-Wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

    OpenAIRE

    Seo, Eunyoung; Kim, Seungill; Yeom, Seon-In; Choi, Doil

    2016-01-01

    Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR) immune receptors are known play critical roles in effector-triggered immunity (ETI) plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267...

  9. Metal-binding thermodynamics of the histidine-rich sequence from the metal-transport protein IRT1 of Arabidopsis thaliana.

    Science.gov (United States)

    Grossoehme, Nicholas E; Akilesh, Shreeram; Guerinot, Mary Lou; Wilcox, Dean E

    2006-10-16

    The widespread ZIP family of transmembrane metal-transporting proteins is characterized by a large intracellular loop that contains a histidine-rich sequence whose biological role is unknown. To provide a chemical basis for this role, we prepared and studied a peptide corresponding to this sequence from the first iron-regulated transporter (IRT1) of Arabidopsis thaliana, which transports Fe2+ as well as Mn2+, Co2+, Zn2+, and Cd2+. Isothermal titration calorimetry (ITC) measurements, which required novel experiments and data analysis, and supporting spectroscopic methods were used to quantify IRT1's metal-binding affinity and associated thermodynamics. The peptide, PHGHGHGHGP, binds metal ions with 1:1 stoichiometry and stabilities that are consistent with the Irving-Williams series. Comparison of the metal-binding thermodynamics of the peptide with those of trien provides new insight about enthalpic and entropic contributions to the stability of the metal-peptide complex. Although Fe2+ and other IRT1-transported metal ions do not bind very tightly, this His-rich sequence has a very high entropy-driven affinity for Fe3+, which may have biological significance.

  10. Molecular characterization of the haptoglobin.hemoglobin receptor CD163. Ligand binding properties of the scavenger receptor cysteine-rich domain region

    DEFF Research Database (Denmark)

    Madsen, Mette; Møller, Holger J; Nielsen, Marianne Jensby

    2004-01-01

    CD163 is the macrophage receptor for endocytosis of haptoglobin.hemoglobin complexes. The extracellular region consisting of nine scavenger receptor cysteine rich (SRCR) domains also circulates in plasma as a soluble protein. By ligand binding analysis of a broad spectrum of soluble CD163...... truncation variants, the amino-terminal third of the SRCR region was shown to be crucial for the binding of haptoglobin.hemoglobin complexes. By Western blotting of the CD163 variants, a panel of ten monoclonal antibodies was mapped to SRCR domains 1, 3, 4, 6, 7, and 9, respectively. Only the two antibodies...... to CD163 demonstrated that optimal ligand binding requires physiological plasma calcium concentrations, and an immediate ligand release occurs at the low calcium concentrations measured in acidifying endosomes. In conclusion, SRCR domain 3 of CD163 is an exposed domain and a critical determinant...

  11. Metal binding ability of glutathione transferases conserved between two animal species, the vanadium-rich ascidian Ascidia sydneiensis samea and the schistosome Schistosoma japonicum.

    Science.gov (United States)

    Yoshinaga, Masafumi; Ueki, Tatsuya; Michibata, Hitoshi

    2007-09-01

    Glutathione transferases (GSTs) are multifunctional enzymes found in many organisms. We recently identified vanadium-binding GSTs, designated AsGSTs, from the vanadium-rich ascidian, Ascidia sydneiensis samea. In this study, the metal-selectivity of AsGST-I was investigated. Immobilized metal ion affinity chromatography (IMAC) analysis revealed that AsGST-I binds to V(IV), Fe(III), and Cu(II) with high affinity in the following order Cu(II)>V(IV)>Fe(III), and to Co(II), Ni(II), and Zn(II) with low affinity. The GST activity of AsGST-I was inhibited dose-dependently by not V(IV) but Cu(II). A competition experiment demonstrated that the binding of V(IV) to AsGST-I was not inhibited by Cu(II). These results suggest that AsGST-I has high V(IV)-selectivity, which can confer the specific vanadium accumulation of ascidians. Because there are few reports on the metal-binding ability of GSTs, we performed the same analysis on SjGST (GST from the schistosome, Schistosoma japonicum). SjGST also demonstrated metal-binding ability although the binding pattern differed from that of AsGST-I. The GST activity of SjGST was inhibited by Cu(II) only, as that of AsGST-I. Our results indicate a possibility that metal-binding abilities of GSTs are conserved among organisms, at least animals, which is suggestive of a new role for these enzymes in metal homeostasis or detoxification.

  12. The differences in heparin binding for the C-terminal basic-sequence-rich peptides of HPV-16 and HPV-18 capsid protein L1

    International Nuclear Information System (INIS)

    Sun Jian; Yu Jisheng; Yu Zhiwu; Zha Xiao; Wu Yuqing

    2012-01-01

    Graphial abstract: The differences in heparin binding for the C-terminal basic-sequence-rich peptides of HPV-16 and HPV-18 capsid protein L1. Highlights: ► Several driving forces contribute to the interaction between heparin and peptides. ► C-terminal of HPV L1 is a potential candidate for the attachment to host cells. ► The C-terminal peptides of HPV-16 and -18 L1 have different heparin-binding. ► The different heparin-binding provides an explanation for the distinct prevalences. - Abstract: The high-risk types of human papillomaviruses (HPV) HPV-16 and -18 are the predominant types associated with cervical cancer. HPV-16 and -18 account for about 50% and 20%, respectively, of cervical cancers worldwide. While the reason and molecular mechanism of the distinct prevalence and distributions between them remain poorly understood, the binding affinity of cell surface receptor with capsid proteins, especially L1, may be involved. We examined heparin binding with two synthetic peptides corresponding to the 14 amino acid C-terminal peptides of HPV-16 and -18 L1 with the goal of comparing the equivalent residues in different HPV types. Using isothermal titration calorimetry (ITC) and static right-angle light scattering (SLS), we determined the binding constant K, reaction enthalpy ΔH, and other thermodynamic parameters in the interaction. Especially, we assessed the role of specific residues in binding with heparin by comparing the NMR spectra of free and heparin-bound peptides.

  13. Binding Mechanism of the N-Terminal SH3 Domain of CrkII and Proline-Rich Motifs in cAbl

    OpenAIRE

    Bhatt, Veer��S.; Zeng, Danyun; Krieger, Inna; Sacchettini, James��C.; Cho, Jae-Hyun

    2016-01-01

    The N-terminal Src homology 3 (nSH3) domain of a signaling adaptor protein, CT-10 regulator of kinase II (CrkII), recognizes proline-rich motifs (PRMs) of binding partners, such as cAbl kinase. The interaction between CrkII and cAbl kinase is��involved in the regulation of cell spreading, microbial pathogenesis, and cancer metastasis. Here, we report the detailed biophysical characterizations of the interactions between the nSH3 domain of CrkII and PRMs in cAbl. We identified that the nSH3 do...

  14. Different roles of glycine-rich RNA-binding protein7 in plant defense against Pectobacterium carotovorum, Botrytis cinerea, and tobacco mosaic viruses.

    Science.gov (United States)

    Lee, Hwa Jung; Kim, Jin Seo; Yoo, Seung Jin; Kang, Eun Young; Han, Song Hee; Yang, Kwang-Yeol; Kim, Young Cheol; McSpadden Gardener, Brian; Kang, Hunseung

    2012-11-01

    Glycine-rich RNA-binding protein7 (AtGRP7) has previously been demonstrated to confer plant defense against Pseudomonas syringae DC3000. Here, we show that AtGRP7 can play different roles in plant defense against diverse pathogens. AtGRP7 enhances resistance against a necrotrophic bacterium Pectobacterium carotovorum SCC1 or a biotrophic virus tobacco mosaic virus. By contrast, AtGRP7 plays a negative role in defense against a necrotrophic fungus Botrytis cinerea. These results provide evidence that AtGRP7 is a potent regulator in plant defense response to diverse pathogens, and suggest that the regulation of RNA metabolism by RNA-binding proteins is important for plant innate immunity. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  15. A novel mechanism of “metal gel-shift” by histidine-rich Ni2+-binding Hpn protein from Helicobacter pylori strain SS1

    Science.gov (United States)

    Ito, Yuki; Masumoto, Junya; Morita, Eugene Hayato; Hayashi, Hidenori

    2017-01-01

    Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) is a universally used method for determining approximate molecular weight (MW) in protein research. Migration of protein that does not correlate with formula MW, termed “gel shifting” appears to be common for histidine-rich proteins but not yet studied in detail. We investigated “gel shifting” in Ni2+-binding histidine-rich Hpn protein cloned from Helicobacter pylori strain SS1. Our data demonstrate two important factors determining “gel shifting” of Hpn, polyacrylamide-gel concentration and metal binding. Higher polyacrylamide-gel concentrations resulted in faster Hpn migration. Irrespective of polyacrylamide-gel concentration, preserved Hpn-Ni2+ complex migrated faster (3–4 kDa) than apo-Hpn, phenomenon termed “metal gel-shift” demonstrating an intimate link between Ni2+ binding and “gel shifting”. To examine this discrepancy, eluted samples from corresponding spots on SDS-gel were analyzed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS). The MW of all samples was the same (6945.66±0.34 Da) and identical to formula MW with or without added mass of Ni2+. MALDI-TOF-MS of Ni2+-treated Hpn revealed that monomer bound up to six Ni2+ ions non-cooperatively, and equilibrium between protein-metal species was reliant on Ni2+ availability. This corroborates with gradually increased heterogeneity of apo-Hpn band followed by compact "metal-gel shift" band on SDS-PAGE. In view of presented data metal-binding and “metal-gel shift” models are discussed. PMID:28207866

  16. DNA-methyltransferase1 (DNMT1) binding to CpG rich GABAergic and BDNF promoters is increased in the brain of schizophrenia and bipolar disorder patients.

    Science.gov (United States)

    Dong, E; Ruzicka, W B; Grayson, D R; Guidotti, A

    2015-09-01

    The down regulation of glutamic acid decarboxylase67 (GAD1), reelin (RELN), and BDNF expression in brain of schizophrenia (SZ) and bipolar (BP) disorder patients is associated with overexpression of DNA methyltransferase1 (DNMT1) and ten-eleven translocase methylcytosine dioxygenase1 (TET1). DNMT1 and TET1 belong to families of enzymes that methylate and hydroxymethylate cytosines located proximal to and within cytosine phosphodiester guanine (CpG) islands of many gene promoters, respectively. Altered promoter methylation may be one mechanism underlying the down-regulation of GABAergic and glutamatergic gene expression. However, recent reports suggest that both DNMT1 and TET1 directly bind to unmethylated CpG rich promoters through their respective Zinc Finger (ZF-CXXC) domains. We report here, that the binding of DNMT1 to GABAergic (GAD1, RELN) and glutamatergic (BDNF-IX) promoters is increased in SZ and BP disorder patients and this increase does not necessarily correlate with enrichment in promoter methylation. The increased DNMT1 binding to these promoter regions is detected in the cortex but not in the cerebellum of SZ and BP disorder patients, suggesting a brain region and neuron specific dependent mechanism. Increased binding of DNMT1 positively correlates with increased expression of DNMT1 and with increased binding of MBD2. In contrast, the binding of TET1 to RELN, GAD1 and BDNF-IX promoters failed to change. These data are consistent with the hypothesis that the down-regulation of specific GABAergic and glutamatergic genes in SZ and BP disorder patients may be mediated, at least in part, by a brain region specific and neuronal-activity dependent DNMT1 action that is likely independent of its DNA methylation activity. Copyright © 2014. Published by Elsevier B.V.

  17. Heterologous expression of a novel Zoysia japonica salt-induced glycine-rich RNA-binding protein gene, ZjGRP, caused salt sensitivity in Arabidopsis.

    Science.gov (United States)

    Teng, Ke; Tan, Penghui; Xiao, Guozeng; Han, Liebao; Chang, Zhihui; Chao, Yuehui

    2017-01-01

    A novel Zoysia japonica salt-induced glycine-rich RNA-binding protein gene was cloned in this study and its overexpression caused salt sensitivity in transgenic Arabidopsis. Glycine-rich RNA-binding proteins (GRPs) play crucial roles in diverse plant developmental processes. However, the mechanisms and functions of GRPs in salinity stress responses remain largely unknown. In this study, rapid amplification of cDNA end (RACE) PCR methods was adopted to isolate ZjGRP from Zosyia japonica, a salt-tolerant grass species. ZjGRP cDNA was 456 bp in length, corresponding to 151 amino acids. ZjGRP was localized in the nucleus and cytoplasm, and was found particularly abundantly in stomatal guard cells. Quantitative real-time PCR showed that ZjGRP was expressed in the roots, stems, and leaves of Zoysia japonica, with the greatest expression seen in the fast-growing leaves. Furthermore, expression of ZjGRP was strongly induced by treatment with NaCl, ABA, MeJA, and SA. Overexpression of ZjGRP in Arabidopsis reduced the rate of germination and retarded seedling growth. ZjGRP-overexpressing Arabidopsis thaliana exhibited weakened salinity tolerance, likely as a result of effects on ion transportation, osmosis, and antioxidation. This study indicates that ZjGRP plays an essential role in inducing salt sensitivity in transgenic plants.

  18. Improving the binding capacity of Ni2+ decorated porous magnetic silica spheres for histidine-rich protein separation

    OpenAIRE

    Benelmekki, Maria; Caparrós Vázquez, Cristina Maria; Xuriguera, Elena; Lanceros Méndez, Senentxu; Rodriguez-Carmona, Escar; Mendoza, R; Corchero, Jose Luis; Martinez, lluis Maria

    2012-01-01

    Biomagnetic immobilization of histidine-rich proteins based on the single-step affinity adsorption of transition metal ions continues to be a suitable practice as a cost effective and a up scaled alternative to the to multiple-step chromatographic separations. In our previous work [12], we synthesised Porous Magnetic silica (PMS) spheres by one-step hydrothermal-assisted modified-stöber method. The obtained spheres were decorated with Ni2+ and Co2+, and evaluated for the capture of a H6-Tagge...

  19. Binding water clusters to an aromatic-rich hydrophobic pocket: [2.2.2]paracyclophane-(H2O)n, n = 1-5.

    Science.gov (United States)

    Buchanan, Evan G; Zwier, Timothy S

    2014-09-18

    [2.2.2]Paracylcophane (tricyclophane, TCP) is a macrocycle with three phenyl substituents linked by ethyl bridges (-CH2CH2-) in the para-position, forming an aromatic-rich pocket capable of binding various substituents, including nature's solvent, water. Building on previous work [Buchanan, E. G.; et al. J. Chem. Phys. 2013, 138, 064308] that reported on the ground state conformational preferences of TCP, the focus of the present study is on the infrared and ultraviolet spectroscopy of TCP-(H2O)n clusters with n = 1-5. Resonant two-photon ionization (R2PI) was used to interrogate the mass selected electronic spectrum of the clusters, reporting on the perturbations imposed on the electronic states of TCP as the size of the water clusters bound to it vary in size from n = 1-5. The TCP-(H2O)n S0-S1 origins are shifted to lower frequency from the monomer, indicating an increased binding energy of the water or water network in the excited state. Ground state resonant ion-dip infrared (RIDIR) spectra of TCP-(H2O)n (n = 1-5) clusters were recorded in the OH stretch region, which probes the H-bonded water networks present and the perturbations imposed on them by TCP. The experimental frequencies are compared with harmonic vibrational frequencies calculated using density functional theory (DFT) with the dispersion-corrected functional ωB97X-D and a 6-311+g(d,p) basis set, providing firm assignments for their H-bonding structures. The H2O molecule in TCP-(H2O)1 sits on top of the binding pocket, donating both of its hydrogen atoms to the aromatic-rich interior of the monomer. The antisymmetric stretch fundamental of H2O in the complex is composed of a closely spaced set of transitions that likely reflect contributions from both para- and ortho-forms of H2O due to internal rotation of the H2O in the binding pocket. TCP-(H2O)2 also exists in a single conformational isomer that retains the same double-donor binding motif for the first water molecule, with the second H2O acting

  20. Structural studies and SH3 domain binding properties of a human antiviral salivary proline-rich peptide.

    Science.gov (United States)

    Righino, Benedetta; Pirolli, Davide; Radicioni, Giorgia; Marzano, Valeria; Longhi, Renato; Arcovito, Alessandro; Sanna, Maria Teresa; De Rosa, Maria Cristina; Paoluzi, Serena; Cesareni, Gianni; Messana, Irene; Castagnola, Massimo; Vitali, Alberto

    2016-09-01

    Human saliva contains hundreds of small proline-rich peptides originated by the proteolytic cleavage of the salivary basic Proline-Rich Proteins. Nevertheless only for few of them a specific biological activity has been assigned to date. Among them, the 1932 Da peptide (p1932) has been patented as an anti-HIV agent. In order to shed light on the possible mechanism of action of this peptide, we assessed in this study, by means of molecular dynamics calculations, circular dichroism and FTIR spectroscopic techniques, that p1932 has an intrinsic propensity to adopt a polyproline-II helix arrangement. This structural feature combined with the presence of PxxP motifs in its primary structure, represents an essential property for the exploitation of several biological activities. Next to these findings, we recently demonstrated the ability of this peptide to be internalized within cells of the oral mucosa, thus we focused onto a possible intracellular target, represented by the SH3 domains family. Its ability to interact with selected SH3 domains was finally assayed by Surface Plasmon Resonance spectroscopy. As a result, only Fyn, Hck, and c-Src SH3 domains gave positive results in terms of interaction, showing dissociation constants ranging from nanomolar to micromolar values having the best performer a KD of 148 nM. It is noteworthy that all the interacting domains belong to the Src kinases family, suggesting a role for p1932 as a modulator of the signal transduction pathways mediated by these kinases. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 714-725, 2016. © 2016 Wiley Periodicals, Inc.

  1. Binding Mechanism of the N-Terminal SH3 Domain of CrkII and Proline-Rich Motifs in cAbl.

    Science.gov (United States)

    Bhatt, Veer S; Zeng, Danyun; Krieger, Inna; Sacchettini, James C; Cho, Jae-Hyun

    2016-06-21

    The N-terminal Src homology 3 (nSH3) domain of a signaling adaptor protein, CT-10 regulator of kinase II (CrkII), recognizes proline-rich motifs (PRMs) of binding partners, such as cAbl kinase. The interaction between CrkII and cAbl kinase is involved in the regulation of cell spreading, microbial pathogenesis, and cancer metastasis. Here, we report the detailed biophysical characterizations of the interactions between the nSH3 domain of CrkII and PRMs in cAbl. We identified that the nSH3 domain of CrkII binds to three PRMs in cAbl with virtually identical affinities. Structural studies, by using x-ray crystallography and NMR spectroscopy, revealed that the binding modes of all three nSH3:PRM complexes are highly similar to each other. Van 't Hoff analysis revealed that nSH3:PRM interaction is associated with favorable enthalpy and unfavorable entropy change. The combination of experimentally determined thermodynamic parameters, structure-based calculations, and (15)N NMR relaxation analysis highlights the energetic contribution of conformational entropy change upon the complex formation, and water molecules structured in the binding interface of the nSH3:PRM complex. Understanding the molecular basis of nSH3:PRM interaction will provide, to our knowledge, new insights for the rational design of small molecules targeting the interaction between CrkII and cAbl. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  2. A new cytolytic protein from the sea anemone Urticina crassicornis that binds to cholesterol- and sphingomyelin-rich membranes.

    Science.gov (United States)

    Razpotnik, Andrej; Krizaj, Igor; Kem, William R; Macek, Peter; Turk, Tom

    2009-06-01

    A new pore-forming cytolytic protein was isolated from the Northern red sea anemone, Urticina crassicornis. Its biochemical properties were characterized and partial N-terminal amino acid sequence was determined. The cytolysin, named UcI, has a molecular mass of around 30kDa and lacks phospholipase A(2) activity. UcI lyses bovine erythrocytes at nanomolar concentrations. Hemolysis is a result of a colloid-osmotic shock caused by the opening of toxin-induced ionic pores and can be prevented by osmotic protectants of size >600Da. The functional radius of an average pore was estimated to be about 0.66nm. A more detailed study of the cytolytic activity of UcI was performed with lipid vesicles and monolayers. The toxin binds to monolayers and efficiently permeabilizes small lipid vesicles composed of sphingomyelin and cholesterol. However, the cytolytic activity is not prevented by preincubation with either pure cholesterol or sphingomyelin dispersions. We conclude that the presence of both sphingomyelin and cholesterol, key components of lipid rafts, greatly enhances toxin binding to membranes and probably facilitates pore formation. Alignment of the toxin partial amino acid sequence with sequences of cytolysins belonging to the actinoporin family reveals no sequence homology. We conclude that partial sequence of UcI resembles only the N-terminal part of UpI, a cytolytic protein isolated from a related sea anemone species, Urticina piscivora. The two proteins most probably belong to a separate family of sea anemone cytolysins that are worthy of further characterization.

  3. The Arginine/Lysine-Rich Element within the DNA-Binding Domain Is Essential for Nuclear Localization and Function of the Intracellular Pathogen Resistance 1.

    Science.gov (United States)

    Yao, Kezhen; Wu, Yongyan; Chen, Qi; Zhang, Zihan; Chen, Xin; Zhang, Yong

    2016-01-01

    The mouse intracellular pathogen resistance 1 (Ipr1) gene plays important roles in mediating host immunity and previous work showed that it enhances macrophage apoptosis upon mycobacterium infection. However, to date, little is known about the regulation pattern of Ipr1 action. Recent studies have investigated the protein-coding genes and microRNAs regulated by Ipr1 in mouse macrophages, but the structure and the functional motif of the Ipr1 protein have yet to be explored. In this study, we analyzed the domains and functional motif of the Ipr1 protein. The resulting data reveal that Ipr1 protein forms a homodimer and that the Sp100-like domain mediates the targeting of Ipr1 protein to nuclear dots (NDs). Moreover, we found that an Ipr1 mutant lacking the classic nuclear localization signal (cNLS) also translocated into the nuclei, suggesting that the cNLS is not the only factor that directs Ipr1 nuclear localization. Additionally, mechanistic studies revealed that an arginine/lysine-rich element within the DNA-binding domain (SAND domain) is critical for Ipr1 binding to the importin protein receptor NPI-1, demonstrating that this element plays an essential role in mediating the nuclear localization of Ipr1 protein. Furthermore, our results show that this arginine/lysine-rich element contributes to the transcriptional regulation and apoptotic activity of Ipr1. These findings highlight the structural foundations of Ipr1 action and provide new insights into the mechanism of Ipr1-mediated resistance to mycobacterium.

  4. Solution structure of Vanabin2, a vanadium(IV)-binding protein from the vanadium-rich ascidian Ascidia sydneiensis samea.

    Science.gov (United States)

    Hamada, Toshiyuki; Asanuma, Miwako; Ueki, Tatsuya; Hayashi, Fumiaki; Kobayashi, Naohiro; Yokoyama, Shigeyuki; Michibata, Hitoshi; Hirota, Hiroshi

    2005-03-30

    Ascidians belonging to the suborder Phlebobranchia are known to accumulate high levels of a transition metal, vanadium, in their blood cells, called vanadocytes, although the mechanism for this biological phenomenon remains unclear. Recently, we identified vanadium(IV)-binding proteins, designated as Vanabins, from vanadium-accumulating ascidians. Here, we report the first 3D structure of Vanabin2 from an ascidian, Ascidia sydneiensis samea, in an aqueous solution. The structure revealed a novel bow-shaped conformation, with four alpha-helices connected by nine disulfide bonds. There are no structural homologues reported so far. The 15N heteronuclear single-quantum coherence (HSQC) perturbation experiments of Vanabin2 indicated that vanadyl cations, which are exclusively localized on the same face of the molecule, are coordinated by amine nitrogens derived from amino acid residues such as lysines, arginines, and histidines, as suggested by the electron paramagnetic resonance (EPR) results. The present NMR studies provide information that will contribute toward elucidating the mechanism of vanadium accumulation in ascidians.

  5. Glutathione transferases with vanadium-binding activity isolated from the vanadium-rich ascidian Ascidia sydneiensis samea.

    Science.gov (United States)

    Yoshinaga, Masafumi; Ueki, Tatsuya; Yamaguchi, Nobuo; Kamino, Kei; Michibata, Hitoshi

    2006-03-01

    Some ascidians accumulate vanadium in vanadocytes, which are vanadium-containing blood cells, at high levels and with high selectivity. However, the mechanism and physiological significance of vanadium accumulation remain unknown. In this study, we isolated novel proteins with a striking homology to glutathione transferases (GSTs), designated AsGST-I and AsGST-II, from the digestive system of the vanadium-accumulating ascidian Ascidia sydneiensis samea, in which the digestive system is thought to be involved in vanadium uptake. Analysis of recombinant AsGST-I confirmed that AsGST-I has GST activity and forms a dimer, as do other GSTs. In addition, AsGST-I was revealed to have vanadium-binding activity, which has never been reported for GSTs isolated from other organisms. AsGST-I bound about 16 vanadium atoms as either V(IV) or V(V) per dimer, and the apparent dissociation constants for V(IV) and V(V) were 1.8 x 10(-4) M and 1.2 x 10(-4) M, respectively. Western blot analysis revealed that AsGSTs were expressed in the digestive system at exceptionally high levels, although they were localized in almost all organs and tissues examined. Considering these results, we postulate that AsGSTs play important roles in vanadium accumulation in the ascidian digestive system.

  6. Histidine-rich glycoprotein binds DNA and RNA and attenuates their capacity to activate the intrinsic coagulation pathway.

    Science.gov (United States)

    Vu, Trang T; Leslie, Beverly A; Stafford, Alan R; Zhou, Ji; Fredenburgh, James C; Weitz, Jeffrey I

    2016-01-01

    When triggered by factor (F) XII and nucleic acids, we showed that thrombosis in HRG-deficient mice is accelerated compared with that in wild-type mice. In this study, we set out to identify the mechanisms by which nucleic acids promote contact activation, and to determine whether HRG attenuates their effects. DNA or RNA addition to human plasma enhances thrombin generation via the intrinsic pathway and shortens the clotting time. Their effect on the clotting time is seven- to 14-fold greater in HRG-deficient plasma than in control plasma. Investigations into the mechanisms of activation reveal that nucleic acids a) promote FXII activation in the presence of prekallikrein- and high molecular weight kininogen (HK), and b) enhance thrombin-mediated FXI activation by 10- to 12-fold. Surface plasmon resonance studies show that DNA and RNA bind FXII, FXIIa, HK, FXI, FXIa and thrombin with high affinity. HRG attenuates DNA- and RNA-mediated FXII activation, and FXI activation by FXIIa or by thrombin, suggesting that HRG down regulates the capacity of DNA and RNA to activate the intrinsic pathway. Therefore, HRG attenuates the procoagulant activity of nucleic acids at multiple levels.

  7. Identification of special AT-rich sequence binding protein 1 as a novel tumor antigen recognized by CD8+ T cells: implication for cancer immunotherapy.

    Directory of Open Access Journals (Sweden)

    Mingjun Wang

    Full Text Available BACKGROUND: A large number of human tumor-associated antigens that are recognized by CD8(+ T cells in a human leukocyte antigen class I (HLA-I-restricted fashion have been identified. Special AT-rich sequence binding protein 1 (SATB1 is highly expressed in many types of human cancers as part of their neoplastic phenotype, and up-regulation of SATB1 expression is essential for tumor survival and metastasis, thus this protein may serve as a rational target for cancer vaccines. METHODOLOGY/PRINCIPAL FINDINGS: Twelve SATB1-derived peptides were predicted by an immuno-informatics approach based on the HLA-A*02 binding motif. These peptides were examined for their ability to induce peptide-specific T cell responses in peripheral blood mononuclear cells (PBMCs obtained from HLA-A*02(+ healthy donors and/or HLA-A*02(+ cancer patients. The recognition of HLA-A*02(+ SATB1-expressing cancer cells was also tested. Among the twelve SATB1-derived peptides, SATB1(565-574 frequently induced peptide-specific T cell responses in PBMCs from both healthy donors and cancer patients. Importantly, SATB1(565-574-specific T cells recognized and killed HLA-A*02(+ SATB1(+ cancer cells in an HLA-I-restricted manner. CONCLUSIONS/SIGNIFICANCE: We have identified a novel HLA-A*02-restricted SATB1-derived peptide epitope recognized by CD8(+ T cells, which, in turn, recognizes and kills HLA-A*02(+ SATB1(+ tumor cells. The SATB1-derived epitope identified may be used as a diagnostic marker as well as an immune target for development of cancer vaccines.

  8. Isolation and characterization of nucleotide-binding site and C-terminal leucine-rich repeat-resistance gene candidates in bananas.

    Science.gov (United States)

    Lu, Y; Xu, W H; Xie, Y X; Zhang, X; Pu, J J; Qi, Y X; Li, H P

    2011-12-15

    Commercial banana varieties are highly susceptible to fungal pathogens, as well as bacterial pathogens, nematodes, viruses, and insect pests. The largest known family of plant resistance genes encodes proteins with nucleotide-binding site (NBS) and C-terminal leucine-rich repeat (LRR) domains. Conserved motifs in such genes in diverse plant species offer a means for the isolation of candidate genes in banana that may be involved in plant defense. Six degenerate PCR primers were designed to target NBS and additional domains were tested on commercial banana species Musa acuminata subsp malaccensis and the Musa AAB Group propagated in vitro and plants maintained in a greenhouse. Total DNA was isolated by a modified CTAB extraction technique. Four resistance gene analogs were amplified and deposited in GenBank and assigned numbers HQ199833-HQ199836. The predicted amino acid sequences compared to the amino acid sequences of known resistance genes (MRGL1, MRGL2, MRGL3, and MRGL4) revealed significant sequence similarity. The presence of consensus domains, namely kinase-1a, kinase-2 and hydrophobic domain, provided evidence that the cloned sequences belong to the typical non-Toll/interleukin-1 receptor-like domain NBS-LRR gene family.

  9. Genome-Wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

    Science.gov (United States)

    Seo, Eunyoung; Kim, Seungill; Yeom, Seon-In; Choi, Doil

    2016-01-01

    Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR) immune receptors are known play critical roles in effector-triggered immunity (ETI) plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analysis and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL) subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analysis of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding. PMID:27559340

  10. The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis

    KAUST Repository

    Chen, Tao

    2015-07-30

    MicroRNAs are a class of small regulatory RNAs that are generated from primary miRNA (pri-miRNA) transcripts with a stem-loop structure. Accuracy of the processing of pri-miRNA into mature miRNA in plants can be enhanced by SERRATE (SE) and HYPONASTIC LEAVES 1 (HYL1). HYL1 activity is regulated by the FIERY2 (FRY2)/RNA polymerase II C-terminal domain phosphatase-like 1 (CPL1). Here, we discover that HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5) and two serine/arginine-rich splicing factors RS40 and RS41, previously shown to be involved in pre-mRNA splicing, affect the biogenesis of a subset of miRNA. These proteins are required for correct miRNA strand selection and the maintenance of miRNA levels. FRY2 dephosphorylates HOS5 whose phosphorylation status affects its subnuclear localization. HOS5 and the RS proteins bind both intronless and intron-containing pri-miRNAs. Importantly, all of these splicing-related factors directly interact with both HYL1 and SE in nuclear splicing speckles. Our results indicate that these splicing factors are directly involved in the biogenesis of a group of miRNA.

  11. Genome-wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

    Directory of Open Access Journals (Sweden)

    Eunyoung Seo

    2016-08-01

    Full Text Available Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR immune receptors are known play critical roles in effector-triggered immunity (ETI plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analyses and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analyses of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding.

  12. A Cluster of Nucleotide-Binding Site–Leucine-Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL

    Directory of Open Access Journals (Sweden)

    Carlos P. Cantalapiedra

    2016-07-01

    Full Text Available Powdery mildew causes severe yield losses in barley production worldwide. Although many resistance genes have been described, only a few have already been cloned. A strong QTL (quantitative trait locus conferring resistance to a wide array of powdery mildew isolates was identified in a Spanish barley landrace on the long arm of chromosome 7H. Previous studies narrowed down the QTL position, but were unable to identify candidate genes or physically locate the resistance. In this study, the exome of three recombinant lines from a high-resolution mapping population was sequenced and analyzed, narrowing the position of the resistance down to a single physical contig. Closer inspection of the region revealed a cluster of closely related NBS-LRR (nucleotide-binding site–leucine-rich repeat containing protein genes. Large differences were found between the resistant lines and the reference genome of cultivar Morex, in the form of PAV (presence-absence variation in the composition of the NBS-LRR cluster. Finally, a template-guided assembly was performed and subsequent expression analysis revealed that one of the new assembled candidate genes is transcribed. In summary, the results suggest that NBS-LRR genes, absent from the reference and the susceptible genotypes, could be functional and responsible for the powdery mildew resistance. The procedure followed is an example of the use of NGS (next-generation sequencing tools to tackle the challenges of gene cloning when the target gene is absent from the reference genome.

  13. Genome-Wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants.

    Science.gov (United States)

    Seo, Eunyoung; Kim, Seungill; Yeom, Seon-In; Choi, Doil

    2016-01-01

    Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR) immune receptors are known play critical roles in effector-triggered immunity (ETI) plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analysis and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL) subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analysis of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding.

  14. Molecular characterization of the haptoglobin.hemoglobin receptor CD163. Ligand binding properties of the scavenger receptor cysteine-rich domain region

    DEFF Research Database (Denmark)

    Madsen, Mette; Møller, Holger J; Nielsen, Marianne Jensby

    2004-01-01

    binding to SRCR domain 3 exhibited effective inhibition of ligand binding. Furthermore, analysis of purified native CD163 revealed that proteolytic cleavage in SRCR domain 3 inactivates ligand binding. Calcium protects against cleavage in this domain. Analysis of the calcium sensitivity of ligand binding...

  15. Characterization of a novel vanadium-binding protein (VBP-129) from blood plasma of the vanadium-rich ascidian Ascidia sydneiensis samea.

    Science.gov (United States)

    Yoshihara, Masao; Ueki, Tatsuya; Yamaguchi, Nobuo; Kamino, Kei; Michibata, Hitoshi

    2008-02-01

    The ascidians, the so-called sea squirts, accumulate high levels of vanadium, a transition metal. Since Henze first observed this physiologically unusual phenomenon about one hundred years ago, it has attracted interdisciplinary attention from chemists, physiologists, and biochemists. The maximum concentration of vanadium in ascidians can reach 350 mM, and most of the vanadium ions are stored in the +3 oxidation state in the vacuoles of vanadium-accumulating blood cells known as vanadocytes. Many proteins involved in the accumulation and reduction of vanadium in the vanadocytes, blood plasma, and digestive tract have been identified. However, the process by which vanadium is taken in prior to its accumulation in vanadocytes has not been elucidated. In the present study, a novel vanadium-binding protein, designated VBP-129, was identified from blood plasma of the vanadium-rich ascidian Ascidia sydneiensis samea. Although VBP-129 mRNA was transcribed in all A. sydneiensis samea tissues examined, the VBP-129 protein was exclusively localized in blood plasma and muscle cells of this ascidian. It bound not only to VO(2+) but also to Fe(3+), Co(2+), Cu(2+), and Zn(2+); on the other hand, a truncated form of VBP-129, designated VBP-88, bound only to Co(2+), Cu(2+) and Zn(2+). In a pull-down assay, an interaction between VanabinP and VBP-129 occurred both in the presence and the absence of VO(2+). These results suggest that VBP-129 and VanabinP function cooperatively as metallochaperones in blood plasma.

  16. Leucine-rich repeat-containing G protein-coupled receptor 4 facilitates vesicular stomatitis virus infection by binding vesicular stomatitis virus glycoprotein.

    Science.gov (United States)

    Zhang, Na; Huang, Hongjun; Tan, Binghe; Wei, Yinglei; Xiong, Qingqing; Yan, Yan; Hou, Lili; Wu, Nannan; Siwko, Stefan; Cimarelli, Andrea; Xu, Jianrong; Han, Honghui; Qian, Min; Liu, Mingyao; Du, Bing

    2017-10-06

    Vesicular stomatitis virus (VSV) and rabies and Chandipura viruses belong to the Rhabdovirus family. VSV is a common laboratory virus to study viral evolution and host immune responses to viral infection, and recombinant VSV-based vectors have been widely used for viral oncolysis, vaccination, and gene therapy. Although the tropism of VSV is broad, and its envelope glycoprotein G is often used for pseudotyping other viruses, the host cellular components involved in VSV infection remain unclear. Here, we demonstrate that the host protein leucine-rich repeat-containing G protein-coupled receptor 4 (Lgr4) is essential for VSV and VSV-G pseudotyped lentivirus (VSVG-LV) to infect susceptible cells. Accordingly, Lgr4-deficient mice had dramatically decreased VSV levels in the olfactory bulb. Furthermore, Lgr4 knockdown in RAW 264.7 cells also significantly suppressed VSV infection, and Lgr4 overexpression in RAW 264.7 cells enhanced VSV infection. Interestingly, only VSV infection relied on Lgr4, whereas infections with Newcastle disease virus, influenza A virus (A/WSN/33), and herpes simplex virus were unaffected by Lgr4 status. Of note, assays of virus entry, cell ELISA, immunoprecipitation, and surface plasmon resonance indicated that VSV bound susceptible cells via the Lgr4 extracellular domain. Pretreating cells with an Lgr4 antibody, soluble LGR4 extracellular domain, or R-spondin 1 blocked VSV infection by competitively inhibiting VSV binding to Lgr4. Taken together, the identification of Lgr4 as a VSV-specific host factor provides important insights into understanding VSV entry and its pathogenesis and lays the foundation for VSV-based gene therapy and viral oncolytic therapeutics. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Suppression among alleles encoding nucleotide-binding-leucine-rich repeat resistance proteins interferes with resistance in F1 hybrid and allele-pyramided wheat plants.

    Science.gov (United States)

    Stirnweis, Daniel; Milani, Samira D; Brunner, Susanne; Herren, Gerhard; Buchmann, Gabriele; Peditto, David; Jordan, Tina; Keller, Beat

    2014-09-01

    The development of high-yielding varieties with broad-spectrum durable disease resistance is the ultimate goal of crop breeding. In plants, immune receptors of the nucleotide-binding-leucine-rich repeat (NB-LRR) class mediate race-specific resistance against pathogen attack. When employed in agriculture this type of resistance is often rapidly overcome by newly adapted pathogen races. The stacking of different resistance genes or alleles in F1 hybrids or in pyramided lines is a promising strategy for achieving more durable resistance. Here, we identify a molecular mechanism which can negatively interfere with the allele-pyramiding approach. We show that pairwise combinations of different alleles of the powdery mildew resistance gene Pm3 in F1 hybrids and stacked transgenic wheat lines can result in suppression of Pm3-based resistance. This effect is independent of the genetic background and solely dependent on the Pm3 alleles. Suppression occurs at the post-translational level, as levels of RNA and protein in the suppressed alleles are unaffected. Using a transient expression system in Nicotiana benthamiana, the LRR domain was identified as the domain conferring suppression. The results of this study suggest that the expression of closely related NB-LRR resistance genes or alleles in the same genotype can lead to dominant-negative interactions. These findings provide a molecular explanation for the frequently observed ineffectiveness of resistance genes introduced from the secondary gene pool into polyploid crop species and mark an important step in overcoming this limitation. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

  18. The second and fourth cluster of class A cysteine-rich repeats of the low density lipoprotein receptor-related protein share ligand-binding properties

    NARCIS (Netherlands)

    Neels, J. G.; van den Berg, B. M.; Lookene, A.; Olivecrona, G.; Pannekoek, H.; van Zonneveld, A. J.

    1999-01-01

    The low density lipoprotein receptor-related protein (LRP) is a multifunctional endocytic cell-surface receptor that binds and internalizes a diverse array of ligands. The receptor contains four putative ligand-binding domains, generally referred to as clusters I, II, III, and IV. In this study,

  19. A Bifunctional Intronic Element Regulates the Expression of the Arginine/Lysine Transporter Cat-1 via Mechanisms Involving the Purine-rich Element Binding Protein A (Purα)*

    Science.gov (United States)

    Huang, Charlie C.; Chiribau, Calin-Bogdan; Majumder, Mithu; Chiang, Cheng-Ming; Wek, Ronald C.; Kelm, Robert J.; Khalili, Kamel; Snider, Martin D.; Hatzoglou, Maria

    2009-01-01

    Expression of the arginine/lysine transporter Cat-1 is highly induced in proliferating and stressed cells via mechanisms that include transcriptional activation. A bifunctional INE (intronic element) within the first intron of the Cat-1 gene was identified and characterized in this study. The INE had high sequence homology to an amino acid response element and was shown to act as a transcriptional enhancer in unstressed cells by binding the transcription factor, purine-rich element binding protein A (Purα). During endoplasmic reticulum stress, binding of Purα to the INE decreased; the element acted as a positive regulator in early stress by binding of the transcription factor ATF4 and as a negative regulator in prolonged stress by binding the stress-induced C/EBP family member, CHOP. We conclude that transcriptional control of the Cat-1 gene is tightly controlled by multiple cis-DNA elements, contributing to regulation of cationic amino acid transport for cell growth and proliferation. In addition, we propose that genes may use stress-response elements such as the INE to support basal expression in the absence of stress. PMID:19720825

  20. Increased type I collagen content and DNA binding activity of a single-stranded, cytosine-rich sequence in the high-salt buffer protein extract of the copper-deficient rat heart.

    Science.gov (United States)

    Zeng, Huawei; Saari, Jack T

    2004-11-01

    Dietary copper (Cu) deficiency not only causes a hypertrophic cardiomyopathy but also increases cancer risk in rodent models. However, a possible alteration in gene expression has not been fully examined. The present study was undertaken to determine the effect of Cu deficiency on protein profiles in rat heart tissue. Male Sprague-Dawley rats were fed diets that were either a Cu-adequate diet (6.0 microg Cu/g diet, n = 6) or a Cu-deficient diet (0.3 microg Cu/g diet, n = 6) for 5 weeks. The high-salt buffer (HSB) protein extract from heart tissue of Cu-deficient, but not Cu-adequate rats showed a 132 kDa protein band by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. This protein band stained pink with Coomassie Blue, suggesting the presence of collagens or other proline-rich proteins. Dot immunoblotting demonstrated that total type I collagen was increased by 110% in HSB protein extract from Cu-deficient, relative to Cu-adequate, rats. Liquid chromatography with mass spectrometry analysis indicated that the 132 kDa protein band contained a collagen alpha (I) chain precursor as well as a leucine-rich protein 130 (LRP130) in HSB protein extract from Cu-deficient but not Cu-adequate rats. A gel shift assay showed that HSB protein extract from Cu-deficient rats bound to a single-stranded cytosine-rich DNA with higher affinity than the extract of Cu-adequate rats, similar to reports of an increase in LRP130 single-stranded DNA binding activity in several types of tumor cells. Collectively, these results not only suggest an additional feature of altered collagen metabolism with Cu deficiency but also demonstrate for the first time an increase in single-stranded cytosine-rich DNA binding in Cu-deficient rat heart.

  1. A mutation in the glutamate-rich region of RNA-binding motif protein 20 causes dilated cardiomyopathy through missplicing of titin and impaired Frank-Starling mechanism

    DEFF Research Database (Denmark)

    Beqqali, Abdelaziz; Bollen, I. A. E.; Rasmussen, T. B.

    2016-01-01

    -rich region of RBM20. Western blot analysis of endogenous RBM20 protein revealed strongly reduced protein levels in the heart of an RBM20(E913K/+) carrier. RNA deep-sequencing demonstrated massive inclusion of exons coding for the spring region of titin in the RBM20(E913K/+) carrier. Titin isoform analysis...

  2. The Potato Nucleotide-Binding Leucine-Rich Repeat (NLR) Immune Receptor Rx1 is a Pathogen Dependent DNA-Deforming Protein

    NARCIS (Netherlands)

    Fenyk, S.; Townsend, P.D.; Dixon, C.H.; Spies, G.B.; Campillo, A.S.E.; Slootweg, E.J.; Westerhof, L.B.; Gawehns, F.K.K.; Knight, M.R.; Sharples, G.J.; Goverse, A.; Palsson, L.O.; Takken, F.L.W.; Cann, M.J.

    2015-01-01

    Plant NLR proteins enable cells to respond to pathogen attack. Several NLRs act in the nucleus, however, conserved nuclear targets that support their role in immunity are unknown. Previously we noted a structural homology between the NB domain of NLRs and DNA replication origin-binding Cdc6/Orc1

  3. Identification of the bacteria-binding peptide domain on salivary agglutinin (gp-340/DMBT1), a member of the scavenger receptor cysteine-rich superfamily

    DEFF Research Database (Denmark)

    Bikker, Floris J; Ligtenberg, Antoon J M; Nazmi, Kamran

    2002-01-01

    SRCR domains that are separated by SRCR-interspersed domains (SIDs), 2 CUB (C1r/C1s Uegf Bmp1) domains, and a zona pellucida domain. We have searched for the peptide domains of agglutinin/DMBT1 responsible for bacteria binding. Digestion with endoproteinase Lys-C resulted in a protein fragment...

  4. Expression and localization of special AT-rich sequence binding protein 2 in murine molar development and the pulp-dentin complex of human healthy teeth and teeth with pulpitis

    Science.gov (United States)

    He, Lina; Liu, Huimei; Shi, Lei; Pan, Shuang; Yang, Xu; Zhang, Lin; Niu, Yumei

    2017-01-01

    Special AT-rich sequence binding protein 2 (SATB2) is a member of the special family of AT-rich binding transcription factors and has a critical role in osteoblast differentiation and craniofacial patterning. However, the expression and distribution of SATB2 in tooth development is largely unknown. The aim of the present study was to detect the expression and distribution of SATB2 during murine molar development and, in human healthy teeth and teeth with pulpitis using immunohistochemistry. Molars were obtained from Kunming mice at embryonic day (E) 13.5, E14.5, E16.5 and E18.5, and postnatal day (P) 1, P5 and P7. In addition, 20 human teeth (10 healthy and 10 teeth with pulpitis) were obtained from young adult patients (age, 24.90±1.65 years) who were scheduled for routine extraction. Immunohistochemical analyses were performed to detect the expression and distribution of SATB2. The present results revealed that SATB2 exhibits a spatiotemporal expression pattern in murine molar development and was expressed in odontoblasts, predentin, dental pulp cells and the blood vessels in human teeth. These findings suggested that SATB2 may have an important role in odontoblast differentiation and dentin matrix mineralization during tooth development. PMID:29042940

  5. A protein binding AT-rich sequence in the soybean leghemoglobin c3 promoter is a general cis element that requires proximal DNA elements to stimulate transcription

    DEFF Research Database (Denmark)

    Laursen, N B; Larsen, K; Knudsen, J Y

    1994-01-01

    that the interaction between NAT2 and NAT2 BS1 is responsible for the observed reactivation. Further activation experiments with the lbc3 and the leaf-specific Nicotiana plumbaginifolia ribulose bisphosphate carboxylase/oxygenase small subunit (rbcS-8B) promoter suggested that another specific cis element...... in combination with other trans-acting factor(s) to increase expression. The finding of NAT2-like binding activities in different plant organs and the specific expression of the hybrid NAT2 BS1/-312 rbcS-8B promoter in leaves suggest that NAT2 is a general activator of transcription. Udgivelsesdato: 1994-May...

  6. Crystal Structure of the Ubiquitin-like Domain-CUT Repeat-like Tandem of Special AT-rich Sequence Binding Protein 1 (SATB1) Reveals a Coordinating DNA-binding Mechanism*

    Science.gov (United States)

    Wang, Zheng; Yang, Xue; Guo, Shuang; Yang, Yin; Su, Xun-Cheng; Shen, Yuequan; Long, Jiafu

    2014-01-01

    SATB1 is essential for T-cell development and growth and metastasis of multitype tumors and acts as a global chromatin organizer and gene expression regulator. The DNA binding ability of SATB1 plays vital roles in its various biological functions. We report the crystal structure of the N-terminal module of SATB1. Interestingly, this module contains a ubiquitin-like domain (ULD) and a CUT repeat-like (CUTL) domain (ULD-CUTL tandem). Detailed biochemical experiments indicate that the N terminus of SATB1 (residues 1–248, SATB1(1–248)), including the extreme 70 N-terminal amino acids, and the ULD-CUTL tandem bind specifically to DNA targets. Our results show that the DNA binding ability of full-length SATB1 requires the contribution of the CUTL domain, as well as the CUT1-CUT2 tandem domain and the homeodomain. These findings may reveal a multiple-domain-coordinated mechanism whereby SATB1 recognizes DNA targets. PMID:25124042

  7. Crystal structure of the ubiquitin-like domain-CUT repeat-like tandem of special AT-rich sequence binding protein 1 (SATB1) reveals a coordinating DNA-binding mechanism.

    Science.gov (United States)

    Wang, Zheng; Yang, Xue; Guo, Shuang; Yang, Yin; Su, Xun-Cheng; Shen, Yuequan; Long, Jiafu

    2014-10-03

    SATB1 is essential for T-cell development and growth and metastasis of multitype tumors and acts as a global chromatin organizer and gene expression regulator. The DNA binding ability of SATB1 plays vital roles in its various biological functions. We report the crystal structure of the N-terminal module of SATB1. Interestingly, this module contains a ubiquitin-like domain (ULD) and a CUT repeat-like (CUTL) domain (ULD-CUTL tandem). Detailed biochemical experiments indicate that the N terminus of SATB1 (residues 1-248, SATB1((1-248))), including the extreme 70 N-terminal amino acids, and the ULD-CUTL tandem bind specifically to DNA targets. Our results show that the DNA binding ability of full-length SATB1 requires the contribution of the CUTL domain, as well as the CUT1-CUT2 tandem domain and the homeodomain. These findings may reveal a multiple-domain-coordinated mechanism whereby SATB1 recognizes DNA targets. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. The central proline rich region of POB1/REPS2 plays a regulatory role in epidermal growth factor receptor endocytosis by binding to 14-3-3 and SH3 domain-containing proteins

    Directory of Open Access Journals (Sweden)

    Cesareni Gianni

    2008-07-01

    Full Text Available Abstract Background The human POB1/REPS2 (Partner of RalBP1 protein is highly conserved in mammals where it has been suggested to function as a molecular scaffold recruiting proteins involved in vesicular traffic and linking them to the actin cytoskeleton remodeling machinery. More recently POB1/REPS2 was found highly expressed in androgen-dependent prostate cancer cell lines, while one of its isoforms (isoform 2 is down regulated during prostate cancer progression. Results In this report we characterize the central proline rich domain of POB1/REPS2 and we describe for the first time its functional role in receptor endocytosis. We show that the ectopic expression of this domain has a dominant negative effect on the endocytosis of activated epidermal growth factor receptor (EGFR while leaving transferrin receptor endocytosis unaffected. By a combination of different approaches (phage display, bioinformatics predictions, peptide arrays, mutagenic analysis, in vivo co-immunoprecipitation, we have identified two closely spaced binding motifs for 14-3-3 and for the SH3 of the proteins Amphiphysin II and Grb2. Differently from wild type, proline rich domains that are altered in these motifs do not inhibit EGFR endocytosis, suggesting that these binding motifs play a functional role in this process. Conclusion Our findings are relevant to the characterization of the molecular mechanism underlying the involvement of POB1/REPS2, SH3 and 14-3-3 proteins in receptor endocytosis, suggesting that 14-3-3 could work by bridging the EGF receptor and the scaffold protein POB1/REPS2.

  9. 3'UTR AU-Rich Elements (AREs) and the RNA-Binding Protein Tristetraprolin (TTP) Are Not Required for the LPS-Mediated Destabilization of Phospholipase-Cβ-2 mRNA in Murine Macrophages.

    Science.gov (United States)

    Shukla, Smita; Elson, Genie; Blackshear, Perry J; Lutz, Carol S; Leibovich, S Joseph

    2017-04-01

    We have shown previously that bacterial lipopolysaccharide (LPS)-mediated suppression of phospholipase-Cβ-2 (PLCβ-2) expression is involved in M1 (inflammatory) to M2-like (wound healing) phenotypic switching of macrophages triggered by adenosine. This suppression is mediated post-transcriptionally by destabilization of PLCβ-2 mRNA (messenger ribonucleic acid). To investigate the mechanism of this LPS-mediated destabilization, we examined the roles of RNA-binding agents including microRNAs and RNA-binding proteins that are involved in regulating stability of mRNAs encoding growth factors, inflammatory mediators, and proto-oncogenes. Adenylate and uridylate (AU)-rich elements (AREs) in 3'UTRs are specific recognition sites for RNA-binding proteins including tristetraprolin (TTP), HuR, and AUF1 and for microRNAs that are involved in regulating mRNA stability. In this study, we investigated the role of TTP and AREs in regulating PLCβ-2 mRNA stability. The 3'UTR of the PLCβ-2 gene was inserted into the pLightswitch luciferase reporter plasmid and transfected into RAW264.7 cells. LPS suppressed luciferase expression from this reporter. Luciferase expression from mutant 3'UTR constructs lacking AREs was similarly downregulated, suggesting that these regions are not required for LPS-mediated suppression of PLCβ-2. TTP was rapidly upregulated in both primary murine macrophages and RAW264.7 cells in response to LPS. Suppression of PLCβ-2 by LPS was examined using macrophages from mice lacking TTP (TTP -/- ). LPS suppressed PLCβ-2 expression to the same extent in wild type (WT) and TTP -/- macrophages. Also, the rate of decay of PLCβ-2 mRNA in LPS-treated macrophages following transcriptional blockade was similar in WT and TTP -/- macrophages, clearly indicating that TTP is not involved in LPS-mediated destabilization of PLCβ-2 mRNA in macrophages.

  10. Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana).

    Science.gov (United States)

    Baurens, Franc-Christophe; Bocs, Stéphanie; Rouard, Mathieu; Matsumoto, Takashi; Miller, Robert N G; Rodier-Goud, Marguerite; MBéguié-A-MBéguié, Didier; Yahiaoui, Nabila

    2010-07-16

    Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. In banana (Musa sp.), two diploid wild species Musa acuminata (A genome) and Musa balbisiana (B genome) contribute to the polyploid genome of many cultivars. The M. balbisiana species is associated with vigour and tolerance to pests and disease and little is known on the genome structure and haplotype diversity within this species. Here, we compare two genomic sequences of 253 and 223 kb corresponding to two haplotypes of the RGA08 resistance gene analog locus in M. balbisiana "Pisang Klutuk Wulung" (PKW). Sequence comparison revealed two regions of contrasting features. The first is a highly colinear gene-rich region where the two haplotypes diverge only by single nucleotide polymorphisms and two repetitive element insertions. The second corresponds to a large cluster of RGA08 genes, with 13 and 18 predicted RGA genes and pseudogenes spread over 131 and 152 kb respectively on each haplotype. The RGA08 cluster is enriched in repetitive element insertions, in duplicated non-coding intergenic sequences including low complexity regions and shows structural variations between haplotypes. Although some allelic relationships are retained, a large diversity of RGA08 genes occurs in this single M. balbisiana genotype, with several RGA08 paralogs specific to each haplotype. The RGA08 gene family has evolved by mechanisms of unequal recombination, intragenic sequence exchange and diversifying selection. An unequal recombination event taking place between duplicated non-coding intergenic sequences resulted in a different RGA08 gene content between haplotypes pointing out the role of such duplicated regions in the evolution of RGA clusters. Based on the synonymous substitution rate in coding sequences, we estimated a 1 million year divergence time for these M. balbisiana haplotypes. A

  11. Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana

    Directory of Open Access Journals (Sweden)

    Miller Robert NG

    2010-07-01

    Full Text Available Abstract Background Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. In banana (Musa sp., two diploid wild species Musa acuminata (A genome and Musa balbisiana (B genome contribute to the polyploid genome of many cultivars. The M. balbisiana species is associated with vigour and tolerance to pests and disease and little is known on the genome structure and haplotype diversity within this species. Here, we compare two genomic sequences of 253 and 223 kb corresponding to two haplotypes of the RGA08 resistance gene analog locus in M. balbisiana "Pisang Klutuk Wulung" (PKW. Results Sequence comparison revealed two regions of contrasting features. The first is a highly colinear gene-rich region where the two haplotypes diverge only by single nucleotide polymorphisms and two repetitive element insertions. The second corresponds to a large cluster of RGA08 genes, with 13 and 18 predicted RGA genes and pseudogenes spread over 131 and 152 kb respectively on each haplotype. The RGA08 cluster is enriched in repetitive element insertions, in duplicated non-coding intergenic sequences including low complexity regions and shows structural variations between haplotypes. Although some allelic relationships are retained, a large diversity of RGA08 genes occurs in this single M. balbisiana genotype, with several RGA08 paralogs specific to each haplotype. The RGA08 gene family has evolved by mechanisms of unequal recombination, intragenic sequence exchange and diversifying selection. An unequal recombination event taking place between duplicated non-coding intergenic sequences resulted in a different RGA08 gene content between haplotypes pointing out the role of such duplicated regions in the evolution of RGA clusters. Based on the synonymous substitution rate in coding sequences, we estimated a 1 million year

  12. ¹H, ¹³C and ¹⁵N chemical shift assignments of Na-FAR-1, a helix-rich fatty acid and retinol binding protein of the parasitic nematode Necator americanus.

    Science.gov (United States)

    Rey-Burusco, M Florencia; Ibañez-Shimabukuro, Marina; Cooper, Alan; Kennedy, Malcolm W; Córsico, Betina; Smith, Brian O

    2014-04-01

    The fatty acid and retinol-binding (FAR) proteins are a family of unusual helix-rich lipid binding proteins found exclusively in nematodes, and are secreted by a range of parasites of humans, animals and plants. Na-FAR-1 is from the parasitic nematode Necator americanus, an intestinal blood-feeding parasite of humans. Sequence-specific (1)H, (13)C and (15)N resonance assignments have been obtained for the recombinant 170 amino acid protein, using three-dimensional triple-resonance heteronuclear magnetic resonance experiments. Backbone assignments have been obtained for 99.3% of the non-proline HN/N pairs (146 out of 147). The amide resonance of T45 was not observed, probably due to rapid exchange with solvent water. A total of 96.9% of backbone resonances were identified, while 97.7% assignment of amino acid sidechain protons is complete. All Hα(166), Hβ(250) and Hγ(160) and 98.4% of the Hδ (126 out of 128) atoms were assigned. In addition, 99.4% Cα (154 out of 155) and 99.3% Cβ (143 out of 144) resonances have been assigned. No resonances were observed for the NH(n) groups of R93 NεHε, arginine, N(η1)H2, N(η2)H2, histidine N(δ1)H(δ1), N(ε1)H(ε1) and lysine N(ζ3)H3. Na-FAR-1 has a similar overall arrangement of α-helices to Ce-FAR-7 of the free-living Caeorhabditis elegans, but with an extra C-terminal helix.

  13. A harpin elicitor induces the expression of a coiled-coil nucleotide binding leucine rich repeat (CC-NB-LRR) defense signaling gene and others functioning during defense to parasitic nematodes.

    Science.gov (United States)

    Aljaafri, Weasam A R; McNeece, Brant T; Lawaju, Bisho R; Sharma, Keshav; Niruala, Prakash M; Pant, Shankar R; Long, David H; Lawrence, Kathy S; Lawrence, Gary W; Klink, Vincent P

    2017-12-01

    The bacterial effector harpin induces the transcription of the Arabidopsis thaliana NON-RACE SPECIFIC DISEASE RESISTANCE 1/HARPIN INDUCED1 (NDR1/HIN1) coiled-coil nucleotide binding leucine rich repeat (CC-NB-LRR) defense signaling gene. In Glycine max, Gm-NDR1-1 transcripts have been detected within root cells undergoing a natural resistant reaction to parasitism by the syncytium-forming nematode Heterodera glycines, functioning in the defense response. Expressing Gm-NDR1-1 in Gossypium hirsutum leads to resistance to Meloidogyne incognita parasitism. In experiments presented here, the heterologous expression of Gm-NDR1-1 in G. hirsutum impairs Rotylenchulus reniformis parasitism. These results are consistent with the hypothesis that Gm-NDR1-1 expression functions broadly in generating a defense response. To examine a possible relationship with harpin, G. max plants topically treated with harpin result in induction of the transcription of Gm-NDR1-1. The result indicates the topical treatment of plants with harpin, itself, may lead to impaired nematode parasitism. Topical harpin treatments are shown to impair G. max parasitism by H. glycines, M. incognita and R. reniformis and G. hirsutum parasitism by M. incognita and R. reniformis. How harpin could function in defense has been examined in experiments showing it also induces transcription of G. max homologs of the proven defense genes ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1), TGA2, galactinol synthase, reticuline oxidase, xyloglucan endotransglycosylase/hydrolase, alpha soluble N-ethylmaleimide-sensitive fusion protein (α-SNAP) and serine hydroxymethyltransferase (SHMT). In contrast, other defense genes are not directly transcriptionally activated by harpin. The results indicate harpin induces pathogen associated molecular pattern (PAMP) triggered immunity (PTI) and effector-triggered immunity (ETI) defense processes in the root, activating defense to parasitic nematodes. Copyright © 2017. Published by Elsevier

  14. The novel flightless-I gene brings together two gene families, actin-binding proteins related to gelsolin and leucine-rich-repeat proteins involved in Ras signal transduction.

    Science.gov (United States)

    Claudianos, C; Campbell, H D

    1995-05-01

    The Drosophila melanogaster gene flightless-I, involved in gastrulation and muscle degeneration, has Caenorhabditis elegans and human homologues. In these highly conserved genes, two previously known gene families have been brought together, families encoding the actin-binding proteins related to gelsolin and the leucine-rich-repeat (LRR) group of proteins involved in protein-protein interactions. Both these gene families exhibit characteristics of molecular changes involving replication slippage and exon shuffling. Phylogenetic analyses of 19 amino acid sequences of 6 related protein types indicate that actin-associated proteins related to gelsolin are monophyletic to a common ancestor and include flightless proteins. Conversely, comparison of 24 amino acid sequences of LRR proteins including the flightless proteins indicates that flightless proteins are members of a structurally related subgroup. Included in the flightless cluster are human and mouse rsp-1 proteins involved in suppressing v-Ras transformation of cells and the membrane-associated yeast (Saccharomyces cerevisae) adenylate cyclase whose analogous LRRs are required for interaction with Ras proteins. There is a strong possibility that ligands for this group could be related and that flightless may have a similar role in Ras signal transduction. It is hypothesized that an ancestral monomeric gelsolin precursor protein has undergone at least four independent gene reorganization events to account for the structural diversity of the extant family of gelsolin-related proteins and that gene duplication and exon shuffling events occurred prior to or at the beginning of multicellular life, resulting in the evolution of some members of the family soon after the appearance of actin-type proteins.

  15. The Brassicaceae family displays divergent, shoot-skewed NLR resistance gene expression

    DEFF Research Database (Denmark)

    Munch, David; Gupta, Vikas; Bachmann, Asger

    2018-01-01

    Nucleotide-binding site leucine-rich repeat resistance genes (NLRs) allow plants to detect microbial effectors. We hypothesized that NLR expression patterns could reflect organ-specific differences in effector challenge and tested this by carrying out a meta-analysis of expression data for 1,235 ...

  16. A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers

    NARCIS (Netherlands)

    Syed, N.; Sorensen, A.P.; Antonise, R.; Wiel, van de C.C.M.; Linden, van der C.G.; Westende, van 't W.P.C.; Hooftman, D.A.P.; Nijs, den H.C.M.; Flavell, A.

    2006-01-01

    Molecular markers based upon a novel lettuce LTR retrotransposon and the nucleotide binding site-leucine-rich repeat (NBS-LRR) family of disease resistance-associated genes have been combined with AFLP markers to generate a 458 locus genetic linkage map for lettuce. A total of 187

  17. Quantitative and temporal definition of the Mla transcriptional regulon during barley-powdery mildew interactions

    Science.gov (United States)

    Barley Mildew resistance locus a (Mla) is a major determinant of immunity to the powdery mildew pathogen, Blumeria graminis f. sp. hordei. Alleles of Mla encode cytoplasmic- and membrane-localized coiled-coil, nucleotide binding site, leucine-rich repeat proteins that mediate resistance when complem...

  18. Gene Isolation Using Degenerate Primers Targeting Protein Motif: A Laboratory Exercise

    Science.gov (United States)

    Yeo, Brandon Pei Hui; Foong, Lian Chee; Tam, Sheh May; Lee, Vivian; Hwang, Siaw San

    2018-01-01

    Structures and functions of protein motifs are widely included in many biology-based course syllabi. However, little emphasis is placed to link this knowledge to applications in biotechnology to enhance the learning experience. Here, the conserved motifs of nucleotide binding site-leucine rich repeats (NBS-LRR) proteins, successfully used for the…

  19. IgG antibodies to endothelial protein C receptor-binding Cysteine-rich interdomain region domains of Plasmodium falciparum erythrocyte membrane protein 1 are acquired early in life in individuals exposed to malaria

    DEFF Research Database (Denmark)

    Turner, Louise; Lavstsen, Thomas; Mmbando, Bruno P

    2015-01-01

    Severe malaria syndromes are precipitated by Plasmodium falciparum parasites binding to endothelial receptors on the vascular lining. This binding is mediated by members of the highly variant P. falciparum erythrocyte membrane protein 1 (PfEMP1) family. We have previously identified a subset of Pf...

  20. Coordinate regulation/localization of the carbohydrate responsive binding protein (ChREBP) by two nuclear export signal sites: Discovery of a new leucine-rich nuclear export signal site

    International Nuclear Information System (INIS)

    Fukasawa, Masashi; Ge, Qing; Wynn, R. Max; Ishii, Seiji; Uyeda, Kosaku

    2010-01-01

    Carbohydrate response element binding protein (ChREBP) is responsible for conversion of dietary carbohydrate to storage fat in liver by coordinating expression of the enzymes that channel glycolytic pyruvate into lipogenesis. The activation of ChREBP in response to high glucose is nuclear localization and transcription, and the inactivation of ChREBP under low glucose involves export from the nucleus to the cytosol. Here we report a new nuclear export signal site ('NES1') of ChREBP. Together these signals provide ChREBP with two NES sequences, both the previously reported NES2 and now the new NES1 coordinate to interact together with CRM1 (exportin) for nuclear export of the carbohydrate response element binding protein.

  1. The CAPRICE RICH detector

    International Nuclear Information System (INIS)

    Basini, G.; De Pascale, M.P.; Golden, R.L.; Barbiellini, G.; Boezio, M.

    1995-01-01

    A compact RICH detector has been developed and used for particle identification in a balloon borne spectrometer to measure the flux of antimatter in the cosmic radiation. This is the first RICH detector ever used in space experiments that is capable of detecting unit charged particles, such as antiprotons. The RICH and all other detectors performed well during the 27 hours long flight

  2. The CAPRICE RICH detector

    Energy Technology Data Exchange (ETDEWEB)

    Basini, G. [INFN, Laboratori Nazionali di Frascati, Rome (Italy); Codino, A.; Grimani, C. [Perugia Univ. (Italy)]|[INFN, Perugia (Italy); De Pascale, M.P. [Rome Univ. `Tor Vergata` (Italy). Dip. di Fisica]|[INFN, Sezione Univ. `Tor Vergata` Rome (Italy); Cafagna, F. [Bari Univ. (Italy)]|[INFN, Bari (Italy); Golden, R.L. [New Mexico State Univ., Las Cruces, NM (United States). Particle Astrophysics Lab.; Brancaccio, F.; Bocciolini, M. [Florence Univ. (Italy)]|[INFN, Florence (Italy); Barbiellini, G.; Boezio, M. [Trieste Univ. (Italy)]|[INFN, Trieste (Italy)

    1995-09-01

    A compact RICH detector has been developed and used for particle identification in a balloon borne spectrometer to measure the flux of antimatter in the cosmic radiation. This is the first RICH detector ever used in space experiments that is capable of detecting unit charged particles, such as antiprotons. The RICH and all other detectors performed well during the 27 hours long flight.

  3. Developments on RICH detectors

    International Nuclear Information System (INIS)

    Besson, P.; Bourgeois, P.

    1996-01-01

    The RICH (ring imaging Cherenkov) detector which is dedicated to Cherenkov radiation detection is described. An improvement made by replacing photo sensible vapor with solid photocathode is studied. A RICH detector prototype with a CsI photocathode has been built in Saclay and used with Saturne. The first results are presented. (A.C.)

  4. Kings Today, Rich Tomorrow

    DEFF Research Database (Denmark)

    Fattoum, Asma

    2013-01-01

    This study investigates the King vs. Rich dilemma that founder-CEOs face at IPO. When undertaking IPO, founders face two options. They can either get rich, but then run the risk of losing the control over their firms; or they can remain kings by introducing defensive mechanisms, but this is likel...

  5. Molecular Cloning and Characterization of a Wild Eggplant Solanum aculeatissimum NBS-LRR Gene, Involved in Plant Resistance to Meloidogyne incognita

    OpenAIRE

    Xiaohui Zhou; Jun Liu; Shengyou Bao; Yan Yang; Yong Zhuang

    2018-01-01

    Root-knot nematodes, Meloidogyne spp., cause considerable damage in eggplant production. Transferring of resistance genes from wild relatives would be valuable for the continued improvement of eggplant. Solanum aculeatissimum, a wild relative of eggplant possessing resistance to Meloidogyne incognita, is potentially useful for genetically enhancing eggplant. In the present study, we have isolated and characterized a nucleotide-binding site leucine-rich repeat (NBS-LRR) resistance gene, design...

  6. The decorin sequence SYIRIADTNIT binds collagen type I

    DEFF Research Database (Denmark)

    Kalamajski, Sebastian; Aspberg, Anders; Oldberg, Ake

    2007-01-01

    Decorin belongs to the small leucine-rich repeat proteoglycan family, interacts with fibrillar collagens, and regulates the assembly, structure, and biomechanical properties of connective tissues. The decorin-collagen type I-binding region is located in leucine-rich repeats 5-6. Site......-directed mutagenesis of this 54-residue-long collagen-binding sequence identifies Arg-207 and Asp-210 in leucine-rich repeat 6 as crucial for the binding to collagen. The synthetic peptide SYIRIADTNIT, which includes Arg-207 and Asp-210, inhibits the binding of full-length recombinant decorin to collagen in vitro....... These collagen-binding amino acids are exposed on the exterior of the beta-sheet-loop structure of the leucine-rich repeat. This resembles the location of interacting residues in other leucine-rich repeat proteins....

  7. Rich Design Research Space

    Directory of Open Access Journals (Sweden)

    Birger Sevaldson

    2008-10-01

    Full Text Available This paper introduces and discusses a Rich Research Space as an inclusive methodological framework and scaffold for research-by-design. The Rich Research Space especially addresses the issue of richness in design processes and design-led research. There is a general trend towards increased complexity in design processes, caused on one hand by the increasing depth and width in the use of design media and methods, and on the other hand by the increasing complexity and interdependency of society due to globalisation. These issues confront the designer-researcher with new challenges. This paper formulates a research strategy for research-by-design in fields that have a high degree of richness in the use of media, the amount of information, and the methods involved. The Rich Research Space concept proposed takes into account the physical, social, and cultural spaces, and the virtual and visual media spaces in which the research-by-design takes place. The concept takes the form of a specific integral approach to design, and a holistic theoretical mindset. It embraces many types of investigation, from analytical to intuitive. The Rich Research Space provides a flexible framework within which the complexity of research-by-design can be interrelated, discussed, and reflected upon. Potentially, it can create a more involved role for the designer-researcher, a role that allows contributions towards the resolution of ever more pressing issues in our society. This approach is currently one of a limited number of possible frameworks that the design professions can utilize in order to make a difference in a world of at times overwhelming complexity. The concept of the Rich Research Space is discussed with reference to an art installation called Barely.Keywords: Research by design, collaborative design, complexity, creativity, research methods.

  8. Mannose-Binding Lectin Binds to Amyloid Protein and Modulates Inflammation

    Directory of Open Access Journals (Sweden)

    Mykol Larvie

    2012-01-01

    Full Text Available Mannose-binding lectin (MBL, a soluble factor of the innate immune system, is a pattern recognition molecule with a number of known ligands, including viruses, bacteria, and molecules from abnormal self tissues. In addition to its role in immunity, MBL also functions in the maintenance of tissue homeostasis. We present evidence here that MBL binds to amyloid β peptides. MBL binding to other known carbohydrate ligands is calcium-dependent and has been attributed to the carbohydrate-recognition domain, a common feature of other C-type lectins. In contrast, we find that the features of MBL binding to Aβ are more similar to the reported binding characteristics of the cysteine-rich domain of the unrelated mannose receptor and therefore may involve the MBL cysteine-rich domain. Differences in MBL ligand binding may contribute to modulation of inflammatory response and may correlate with the function of MBL in processes such as coagulation and tissue homeostasis.

  9. Neutron rich nuclei

    International Nuclear Information System (INIS)

    Foucher, R.

    1979-01-01

    If some β - emitters are particularly interesting to study in light, medium, and heavy nuclei, another (and also) difficult problem is to know systematically the properties of these neutron rich nuclei far from the stability line. A review of some of their characteristics is presented. How far is it possible to be objective in the interpretation of data is questioned and implications are discussed

  10. Kings Today, Rich Tomorrow

    DEFF Research Database (Denmark)

    Fattoum, Asma

    2013-01-01

    This study investigates the King vs. Rich dilemma that founder-CEOs face at IPO. When undertaking IPO, founders face two options. They can either get rich, but then run the risk of losing the control over their firms; or they can remain kings by introducing defensive mechanisms, but this is likely...... to lead to lower IPO valuation. Using psychological ownership theory, we argue founder-CEOs to be more likely to choose the King option. This option forces them to leave money on the table at the IPO. However, their stewardship behavior allows them to recover that money on the long-run post IPO. We...... provide support for all hypotheses using a unique hand-collected dataset covering the full population of 467 IPOs undertaken in France between 1992 and 2011....

  11. Get rich blogging

    CERN Document Server

    Griffin, Zoe

    2013-01-01

    The Sunday Mirror's former showbiz gossip columnist, Zoe Griffin, explains how she quit her job and started a blog in order to work less and earn more. In this book she explains how to Get Rich Blogging and how she has done just that with her Live Like A VIP blog ? which generates a six figure income. There is no need to be a technical wizard. All you need is this book, a laptop and internet access and you too could be blogging your way to wealth and happiness. Contributors include The Clothes Whisperer, The Fashion Editor at Large, Mumsnet, Tech Week, Music News and Mr Porter ? all finan

  12. Structural and dynamic studies of the dimerization and DNA-binding domains of the transcription factors v-Myc and Max

    International Nuclear Information System (INIS)

    Fieber, W.

    2001-05-01

    In the present work, solution structural and dynamic properties of the dimerization and DNA binding domains of the transcription factors v-Myc and Max were characterized by NMR and CD spectroscopy. It could be demonstrated that v-Myc in the absence of its authentic binding partner Max does not homodimerize, but exists in a monomeric and prestructured form. Two separated α-helical regions in the leucine zipper region and in the basic-H1 region, respectively, could be identified, while the latter appeared to be less stable. Both helices lack stabilizing tertiary side chain interactions and represent exceptional examples for loosely coupled, structured segments in a native protein. The structure of v-Myc is dynamic and can be described as a distribution of conformational substates. Motion within the substates comprise fast (picosecond to nanosecond) local backbone fluctuations like helical fraying, whereas motion between the substates comprise the relative orientation of the two helices and occur at larger time scales (microsecond to millisecond). The preformation of the specific protein and DNA binding sites, leucine zipper and the basic region, presumably allows rapid and accurate recognition of the respective binding partners. v-Myc-Max and Max-Max protein preparations were shown to form stable dimers. Thermodynamic analysis of the dissociation reactions of v-Myc-Max revealed a significant higher stability of the heterodimer than of the Max-Max homodimer over the whole temperature range. It could be demonstrated that the restricted conformational space of the v-Myc bHLHZip domain reduces the entropy penalty associated with dimerization and contributes to the preference of Max to form heterodimers with v-Myc rather than homodimers. (author)

  13. Binding Characteristics Of Ivermectin To Blood Cells | Nweke ...

    African Journals Online (AJOL)

    The binding characteristics of Ivermectin were determined using scatchard plots. The percentage binding to platelet rich plasma, white blood cells and red blood cells were 90.00 + 1.00, 96-90 + 1.05 and 46.20 + 1.10 S.D respectively. It was found to bind the highest to white blood cells and the least to red blood cells.

  14. LHCB RICH gas system proposal

    CERN Document Server

    Bosteels, Michel; Haider, S

    2001-01-01

    Both LHCb RICH will be operated with fluorocarbon as gas radiator. RICH 1 will be filled with 4m^3 of C4F10 and RICH 2 with 100m^3 of CF4. The gas systems will run as a closed loop circulation and a gas recovery system within the closed loop is planned for RICH 1, where the recovery of the CF4 will only be realised during filling and emptying of the detector. Inline gas purification is foreseen for the gas systems in order to limit water and oxygen impurities.

  15. Information rich display design

    International Nuclear Information System (INIS)

    Welch, Robin; Braseth, Alf Ove; Veland, Oeystein

    2004-01-01

    This paper presents the concept Information Rich Displays. The purpose of Information Rich Displays (IRDs) is to condensate prevailing information in process displays in such a way that each display format (picture) contains more relevant information for the user. Compared to traditional process control displays, this new concept allows the operator to attain key information at a glance and at the same time allows for improved monitoring of larger portions of the process. This again allows for reduced navigation between both process and trend displays and ease the cognitive demand on the operator. This concept has been created while working on designing display prototypes for the offshore petroleum production facilities of tomorrow. Offshore installations basically consist of wells, separation trains (where oil, gas and water are separated from each other), an oil tax measurement system (where oil quality is measured and the pressure increased to allow for export), gas compression (compression of gas for export) and utility systems (water treatment, chemical systems etc.). This means that an offshore control room operator has to deal with a complex process that comprises several functionally different systems. The need for a new approach to offshore display format design is in particular based on shortcomings in today's designs related to the keyhole effect, where the display format only reveals a fraction of the whole process. Furthermore, the upcoming introduction of larger off- and on-shore operation centres will increase the size and complexity of the operators' work domain. In the light of the increased demands on the operator, the proposed IRDs aim to counter the negative effects this may have on the workload. In this work we have attempted to classify the wide range of different roles an operator can have in different situations. The information content and amount being presented to the operator in a display should be viewed in context of the roles the

  16. Asporin competes with decorin for collagen binding, binds calcium and promotes osteoblast collagen mineralization

    DEFF Research Database (Denmark)

    Kalamajski, Sebastian; Aspberg, Anders; Lindblom, Karin

    2009-01-01

    The interactions of the ECM (extracellular matrix) protein asporin with ECM components have previously not been investigated. Here, we show that asporin binds collagen type I. This binding is inhibited by recombinant asporin fragment LRR (leucine-rich repeat) 10-12 and by full-length decorin......, but not by biglycan. We demonstrate that the polyaspartate domain binds calcium and regulates hydroxyapatite formation in vitro. In the presence of asporin, the number of collagen nodules, and mRNA of osteoblastic markers Osterix and Runx2, were increased. Moreover, decorin or the collagen-binding asporin fragment...... LRR 10-12 inhibited the pro-osteoblastic activity of full-length asporin. Our results suggest that asporin and decorin compete for binding to collagen and that the polyaspartate in asporin directly regulates collagen mineralization. Therefore asporin has a role in osteoblast-driven collagen...

  17. An Improved Cluster Richness Estimator

    Energy Technology Data Exchange (ETDEWEB)

    Rozo, Eduardo; /Ohio State U.; Rykoff, Eli S.; /UC, Santa Barbara; Koester, Benjamin P.; /Chicago U. /KICP, Chicago; McKay, Timothy; /Michigan U.; Hao, Jiangang; /Michigan U.; Evrard, August; /Michigan U.; Wechsler, Risa H.; /SLAC; Hansen, Sarah; /Chicago U. /KICP, Chicago; Sheldon, Erin; /New York U.; Johnston, David; /Houston U.; Becker, Matthew R.; /Chicago U. /KICP, Chicago; Annis, James T.; /Fermilab; Bleem, Lindsey; /Chicago U.; Scranton, Ryan; /Pittsburgh U.

    2009-08-03

    Minimizing the scatter between cluster mass and accessible observables is an important goal for cluster cosmology. In this work, we introduce a new matched filter richness estimator, and test its performance using the maxBCG cluster catalog. Our new estimator significantly reduces the variance in the L{sub X}-richness relation, from {sigma}{sub lnL{sub X}}{sup 2} = (0.86 {+-} 0.02){sup 2} to {sigma}{sub lnL{sub X}}{sup 2} = (0.69 {+-} 0.02){sup 2}. Relative to the maxBCG richness estimate, it also removes the strong redshift dependence of the richness scaling relations, and is significantly more robust to photometric and redshift errors. These improvements are largely due to our more sophisticated treatment of galaxy color data. We also demonstrate the scatter in the L{sub X}-richness relation depends on the aperture used to estimate cluster richness, and introduce a novel approach for optimizing said aperture which can be easily generalized to other mass tracers.

  18. Adaptive Reactive Rich Internet Applications

    Science.gov (United States)

    Schmidt, Kay-Uwe; Stühmer, Roland; Dörflinger, Jörg; Rahmani, Tirdad; Thomas, Susan; Stojanovic, Ljiljana

    Rich Internet Applications significantly raise the user experience compared with legacy page-based Web applications because of their highly responsive user interfaces. Although this is a tremendous advance, it does not solve the problem of the one-size-fits-all approach1 of current Web applications. So although Rich Internet Applications put the user in a position to interact seamlessly with the Web application, they do not adapt to the context in which the user is currently working. In this paper we address the on-the-fly personalization of Rich Internet Applications. We introduce the concept of ARRIAs: Adaptive Reactive Rich Internet Applications and elaborate on how they are able to adapt to the current working context the user is engaged in. An architecture for the ad hoc adaptation of Rich Internet Applications is presented as well as a holistic framework and tools for the realization of our on-the-fly personalization approach. We divided both the architecture and the framework into two levels: offline/design-time and online/run-time. For design-time we explain how to use ontologies in order to annotate Rich Internet Applications and how to use these annotations for conceptual Web usage mining. Furthermore, we describe how to create client-side executable rules from the semantic data mining results. We present our declarative lightweight rule language tailored to the needs of being executed directly on the client. Because of the event-driven nature of the user interfaces of Rich Internet Applications, we designed a lightweight rule language based on the event-condition-action paradigm.2 At run-time the interactions of a user are tracked directly on the client and in real-time a user model is built up. The user model then acts as input to and is evaluated by our client-side complex event processing and rule engine.

  19. Total iron binding capacity

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003489.htm Total iron binding capacity To use the sharing features on this page, please enable JavaScript. Total iron binding capacity (TIBC) is a blood test to ...

  20. Telomere-binding proteins of Arabidopsis thaliana.

    Science.gov (United States)

    Zentgraf, U

    1995-02-01

    The nucleoprotein structure of Arabidopsis thaliana telomeres was investigated. A protein specifically binding to telomeric sequences was characterized by gel mobility shift assays with synthetic oligonucleotides consisting of four 7 bp telomeric repeats of Arabidopsis (TTTAGGG) and crude nuclear protein extracts of Arabidopsis leaves. These DNA-protein binding studies revealed that the binding affinity of this telomere-binding protein to the G-rich single-strand as well as to the double-stranded telomeric DNA is much higher than to the C-rich single-strand. The molecular mass of the protein was identified by SDS-PAGE to be 67 kDa. The isoelectric points were determined to be 5.0, 4.85 and 4.7, respectively, indicating that either one protein with different modifications or three slightly different proteins have been isolated. An RNA component, possibly serving as a template for reverse transcription of a plant telomerase, does not mediate the DNA-protein contact because the DNA-protein interactions were not RNAse-sensitive.

  1. Detection of cholesterol-rich microdomains in the inner leaflet of the plasma membrane

    International Nuclear Information System (INIS)

    Hayashi, Masami; Shimada, Yukiko; Inomata, Mitsushi; Ohno-Iwashita, Yoshiko

    2006-01-01

    The C-terminal domain (D4) of perfringolysin O binds selectively to cholesterol in cholesterol-rich microdomains. To address the issue of whether cholesterol-rich microdomains exist in the inner leaflet of the plasma membrane, we expressed D4 as a fusion protein with EGFP in MEF cells. More than half of the EGFP-D4 expressed in stable cell clones was bound to membranes in raft fractions. Depletion of membrane cholesterol with β-cyclodextrin reduced the amount of EGFP-D4 localized in raft fractions, confirming EGFP-D4 binding to cholesterol-rich microdomains. Subfractionation of the raft fractions showed most of the EGFP-D4 bound to the plasma membrane rather than to intracellular membranes. Taken together, these results strongly suggest the existence of cholesterol-rich microdomains in the inner leaflet of the plasma membrane

  2. The STAR-RICH Detector

    CERN Document Server

    Lasiuk, B; Braem, André; Cozza, D; Davenport, M; De Cataldo, G; Dell'Olio, L; Di Bari, D; Di Mauro, A; Dunlop, J C; Finch, E; Fraissard, Daniel; Franco, A; Gans, J; Ghidini, B; Harris, J W; Horsley, M; Kunde, G J; Lasiuk, B; Lesenechal, Y; Majka, R D; Martinengo, P; Morsch, Andreas; Nappi, E; Paic, G; Piuz, François; Posa, F; Raynaud, J; Salur, S; Sandweiss, J; Santiard, Jean-Claude; Satinover, J; Schyns, E M; Smirnov, N; Van Beelen, J; Williams, T D; Xu, Z

    2002-01-01

    The STAR-RICH detector extends the particle idenfication capabilities of the STAR spectrometer for charged hadrons at mid-rapidity. It allows identification of pions and kaons up to ~3 GeV/c and protons up to ~5 GeV/c. The characteristics and performance of the device in the inaugural RHIC run are described.

  3. (Hochst ex A. Rich.) Harms

    African Journals Online (AJOL)

    Michael Horsfall

    ABSTRACT: Phytochemical investigations carried out on the seeds of Sphenostylis stenocarpa (Hochst ex A. Rich.) Harms (Family Fabaceae) revealed the presence of the flavonoids (tricin, apigenin, chrysoeriol and genisten), tannin and alkaloids. The three putative varieties previously separated on the basis of seed ...

  4. The HERA-B RICH

    CERN Document Server

    Korpar, S; Atiya, M; Broemmelsiek, D R; Carvalho, J; Dujmic, D; Eckmann, R; Garrido, L; Gorisek, A; Ivaniouchenkov, Yu; Ispirian, M; Karabekian, S I; Krizan, P; Lau, K; Maas, P; McGill, J; Miquel, R; Pestotnik, R; Pyrlik, J; Ramachadran, D; Reeves, K; Rosen, J; Schwitters, Roy F; Staric, M; Stanovnik, A; Skrk, D

    1999-01-01

    The essential components of the ring imaging Cherenkov detector for the HERA-B experiment are briefly described. Results of the first test measurements with the HERA proton beam are presented and the capability of the RICH to identify kaons is estimated.

  5. An Arg-rich putative prebiotic protein is as stable as its Lys-rich variant.

    Science.gov (United States)

    Diez-García, Fernando; Chakrabartty, Avijit; González, Carlos; Laurents, Douglas V

    2012-12-15

    An Arg-rich peptide called RIA7; sequence ac-ARAAAAAIRAIAAIIRAGGY-am, tetramerizes to form a well folded, four helix X-bundle protein. The Arg side chains are solvent exposed and the hydrophobic core is composed of the side chains from some Alas, all the Iles and the C-terminal Tyr. Since Gly, Ala and Ile, and in lesser amounts Arg and Tyr have been reported to form under putative prebiotic Earth conditions, it is plausible that RIA7-like peptides might have formed on the primitive Earth and interacted with RNAs. The interaction of RIA7 with two RNAs was tested and the formation of insoluble aggregates was observed. These results contrast with previous studies of a Lys-rich variant, called KIA7, which promotes the cleavage of RNAs. Their close structural similarity makes RIA7 and KIA7 an excellent system to compare the relative contributions of Arg and Lys to protein conformational stability. NMR-monitored hydrogen/deuterium exchange measurements and CD-monitored thermal denaturation experiments performed at different peptide and salt concentrations reveal that the conformational stabilities of RIA7 and KIA7 are practically the same. This finding has relevance for protein engineering as Lys is frequently replaced by Arg to improve ligand binding and membrane association and penetration. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Feature Binding in Zebrafish

    Directory of Open Access Journals (Sweden)

    P Neri

    2012-07-01

    Full Text Available Binding operations are primarily ascribed to cortex or similarly complex avian structures. My experiments show that the zebrafish, a lower vertebrate lacking cortex, supports visual feature binding of form and motion for the purpose of social behavior. These results challenge the notion that feature binding may require highly evolved neural structures and demonstrate that the nervous system of lower vertebrates can afford unexpectedly complex computations.

  7. DNS & Bind Cookbook

    CERN Document Server

    Liu, Cricket

    2011-01-01

    The DNS & BIND Cookbook presents solutions to the many problems faced by network administrators responsible for a name server. Following O'Reilly's popular problem-and-solution cookbook format, this title is an indispensable companion to DNS & BIND, 4th Edition, the definitive guide to the critical task of name server administration. The cookbook contains dozens of code recipes showing solutions to everyday problems, ranging from simple questions, like, "How do I get BIND?" to more advanced topics like providing name service for IPv6 addresses. It's full of BIND configuration files that yo

  8. DNA minor groove binding of small molecules: Experimental and ...

    Indian Academy of Sciences (India)

    Administrator

    to DNA have been studied and summarized by several workers. 3–6. Rich, Dervan, Wemmer, Lown and other workers have described Netropsin, Dista- mycin A, and Hoechst-33258, etc. as DNA minor groove binding drugs. 7–10. It is observed that tryptophan and indole do not intercalate with either single-stranded DNA or.

  9. Differential mode of antimicrobial actions of arginine-rich and lysine-rich histones against Gram-positive Staphylococcus aureus.

    Science.gov (United States)

    Morita, Shuu; Tagai, Chihiro; Shiraishi, Takayuki; Miyaji, Kazuyuki; Iwamuro, Shawichi

    2013-10-01

    We previously reported the activities and modes of action of arginine (Arg)-rich histones H3 and H4 against Gram-negative bacteria. In the present study, we investigated the properties of the Arg-rich histones against Gram-positive bacteria in comparison with those of lysine (Lys)-rich histone H2B. In a standard microdilution assay, calf thymus histones H2B, H3, and H4 showed growth inhibitory activity against Staphylococcus aureus with minimum effective concentration values of 4.0, 4.0, and 5.6 μM, respectively. Laser confocal microscopic analyses revealed that both the Arg-rich and Lys-rich histones associated with the surface of S. aureus. However, while the morphology of S. aureus treated with histone H2B appeared intact, those treated with the histones H3 and H4 closely resembled each other, and the cells were blurred. Electrophoretic mobility shift assay results revealed these histones have binding affinity to lipoteichoic acid (LTA), one of major cell surface components of Gram-positive bacteria. Scanning electron microscopic analyses demonstrated that while histone H2B elicited no obvious changes in cell morphology, histones H3 and H4 disrupted the cell membrane structure with bleb formation in a manner similar to general antimicrobial peptides. Consequently, our results suggest that bacterial cell surface LTA initially attracts both the Arg- and Lys-rich histones, but the modes of antimicrobial action of these histones are different; the former involves cell membrane disruption and the latter involves the cell integrity disruption. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. DNS BIND Server Configuration

    Directory of Open Access Journals (Sweden)

    Radu MARSANU

    2011-01-01

    Full Text Available After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

  11. DNS BIND Server Configuratio

    OpenAIRE

    Radu MARSANU

    2011-01-01

    After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

  12. DNS BIND Server Configuration

    OpenAIRE

    Radu MARSANU

    2011-01-01

    After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

  13. Melanin-binding radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Packer, S; Fairchild, R G; Watts, K P; Greenberg, D; Hannon, S J

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed. (PSB)

  14. Melanin-binding radiopharmaceuticals

    International Nuclear Information System (INIS)

    Packer, S.; Fairchild, R.G.; Watts, K.P.; Greenberg, D.; Hannon, S.J.

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed

  15. Tryptophan-Rich and Proline-Rich Antimicrobial Peptides

    Directory of Open Access Journals (Sweden)

    Awdhesh Kumar Mishra

    2018-04-01

    Full Text Available Due to the increasing emergence of drug-resistant pathogenic microorganisms, there is a world-wide quest to develop new-generation antibiotics. Antimicrobial peptides (AMPs are small peptides with a broad spectrum of antibiotic activities against bacteria, fungi, protozoa, viruses and sometimes exhibit cytotoxic activity toward cancer cells. As a part of the native host defense system, most AMPs target the membrane integrity of the microorganism, leading to cell death by lysis. These membrane lytic effects are often toxic to mammalian cells and restrict their systemic application. However, AMPs containing predominantly either tryptophan or proline can kill microorganisms by targeting intracellular pathways and are therefore a promising source of next-generation antibiotics. A minimum length of six amino acids is required for high antimicrobial activity in tryptophan-rich AMPs and the position of these residues also affects their antimicrobial activity. The aromatic side chain of tryptophan is able to rapidly form hydrogen bonds with membrane bilayer components. Proline-rich AMPs interact with the 70S ribosome and disrupt protein synthesis. In addition, they can also target the heat shock protein in target pathogens, and consequently lead to protein misfolding. In this review, we will focus on describing the structures, sources, and mechanisms of action of the aforementioned AMPs.

  16. Conservation and Biodiversity of Rich Fens

    DEFF Research Database (Denmark)

    Andersen, Dagmar Kappel

    2014-01-01

    Rich fen is a habitat type dependent on a constant supply of nutrient poor, calcium rich groundwater. A high, stable groundwater table, relatively high pH combined with nutrient poor conditions support a special and very species rich vegetation including many rare and threatened plant species. In...

  17. The leucine-rich repeat structure.

    Science.gov (United States)

    Bella, J; Hindle, K L; McEwan, P A; Lovell, S C

    2008-08-01

    The leucine-rich repeat is a widespread structural motif of 20-30 amino acids with a characteristic repetitive sequence pattern rich in leucines. Leucine-rich repeat domains are built from tandems of two or more repeats and form curved solenoid structures that are particularly suitable for protein-protein interactions. Thousands of protein sequences containing leucine-rich repeats have been identified by automatic annotation methods. Three-dimensional structures of leucine-rich repeat domains determined to date reveal a degree of structural variability that translates into the considerable functional versatility of this protein superfamily. As the essential structural principles become well established, the leucine-rich repeat architecture is emerging as an attractive framework for structural prediction and protein engineering. This review presents an update of the current understanding of leucine-rich repeat structure at the primary, secondary, tertiary and quaternary levels and discusses specific examples from recently determined three-dimensional structures.

  18. SOFTWARE SUPPORT FOR RICH PICTURES

    DEFF Research Database (Denmark)

    Valente, Andrea; Marchetti, Emanuela

    2010-01-01

    Rich pictures (RP) are common in object-oriented analysis and design courses, but students seem to have problems in integrating them in their projects' workflow. A new software tool is being developed, specific for RP authoring. To better understand students' issues and working practice with RP......, and gather requirements for the tool, we followed a user-centered design approach and performed a usability test with an early prototype. The findings suggest the presence of a gap between some of the modern object-oriented development practices and engineering students' values: some techniques, like RP......, presuppose design skills that are alien to our students. To bridge this gap our tool aims at making design-specific skills optional, enhancing the conceptual analytical skills that software analysis shares with design. Further studies will be conducted to assess the impact of the tool on learning....

  19. CARBOHYDRATE-CONTAINING COMPOUNDS WHICH BIND TO CARBOHYDRATE BINDING RECEPTORS

    DEFF Research Database (Denmark)

    1995-01-01

    Carbohydrate-containing compounds which contain saccharides or derivatives thereof and which bind to carbohydrate binding receptors are useful in pharmaceutical products for treatment of inflammatory diseases and other diseases.......Carbohydrate-containing compounds which contain saccharides or derivatives thereof and which bind to carbohydrate binding receptors are useful in pharmaceutical products for treatment of inflammatory diseases and other diseases....

  20. RNA-binding region of Macrobrachium rosenbergii nodavirus capsid protein.

    Science.gov (United States)

    Goh, Zee Hong; Mohd, Nur Azmina Syakirin; Tan, Soon Guan; Bhassu, Subha; Tan, Wen Siang

    2014-09-01

    White tail disease (WTD) kills prawn larvae and causes drastic losses to the freshwater prawn (Macrobrachium rosenbergii) industry. The main causative agent of WTD is Macrobrachium rosenbergii nodavirus (MrNV). The N-terminal end of the MrNV capsid protein is very rich in positively charged amino acids and is postulated to interact with RNA molecules. N-terminal and internal deletion mutagenesis revealed that the RNA-binding region is located at positions 20-29, where 80 % of amino acids are positively charged. Substitution of all these positively charged residues with alanine abolished the RNA binding. Mutants without the RNA-binding region still assembled into virus-like particles, suggesting that this region is not a part of the capsid assembly domain. This paper is, to the best of our knowledge, the first to report the specific RNA-binding region of MrNV capsid protein. © 2014 The Authors.

  1. Robust Optical Richness Estimation with Reduced Scatter

    Energy Technology Data Exchange (ETDEWEB)

    Rykoff, E.S.; /LBL, Berkeley; Koester, B.P.; /Chicago U. /Chicago U., KICP; Rozo, E.; /Chicago U. /Chicago U., KICP; Annis, J.; /Fermilab; Evrard, A.E.; /Michigan U. /Michigan U., MCTP; Hansen, S.M.; /Lick Observ.; Hao, J.; /Fermilab; Johnston, D.E.; /Fermilab; McKay, T.A.; /Michigan U. /Michigan U., MCTP; Wechsler, R.H.; /KIPAC, Menlo Park /SLAC

    2012-06-07

    Reducing the scatter between cluster mass and optical richness is a key goal for cluster cosmology from photometric catalogs. We consider various modifications to the red-sequence matched filter richness estimator of Rozo et al. (2009b), and evaluate their impact on the scatter in X-ray luminosity at fixed richness. Most significantly, we find that deeper luminosity cuts can reduce the recovered scatter, finding that {sigma}{sub ln L{sub X}|{lambda}} = 0.63 {+-} 0.02 for clusters with M{sub 500c} {approx}> 1.6 x 10{sup 14} h{sub 70}{sup -1} M{sub {circle_dot}}. The corresponding scatter in mass at fixed richness is {sigma}{sub ln M|{lambda}} {approx} 0.2-0.3 depending on the richness, comparable to that for total X-ray luminosity. We find that including blue galaxies in the richness estimate increases the scatter, as does weighting galaxies by their optical luminosity. We further demonstrate that our richness estimator is very robust. Specifically, the filter employed when estimating richness can be calibrated directly from the data, without requiring a-priori calibrations of the red-sequence. We also demonstrate that the recovered richness is robust to up to 50% uncertainties in the galaxy background, as well as to the choice of photometric filter employed, so long as the filters span the 4000 {angstrom} break of red-sequence galaxies. Consequently, our richness estimator can be used to compare richness estimates of different clusters, even if they do not share the same photometric data. Appendix A includes 'easy-bake' instructions for implementing our optimal richness estimator, and we are releasing an implementation of the code that works with SDSS data, as well as an augmented maxBCG catalog with the {lambda} richness measured for each cluster.

  2. Reactions with fast radioactive beams of neutron-rich nuclei

    International Nuclear Information System (INIS)

    Aumann, T.

    2005-11-01

    The neutron dripline has presently been reached only for the lightest nuclei up to the element oxygen. In this region of light neutron-rich nuclei, scattering experiments are feasible even for dripline nuclei by utilizing high-energy secondary beams produced by fragmentation. In the present article, reactions of high-energy radioactive beams will be exemplified using recent experimental results mainly derived from measurements of breakup reactions performed at the LAND and FRS facilities at GSI and at the S800 spectrometer at the NSCL. Nuclear and electromagnetically induced reactions allow probing different aspects of nuclear structure at the limits of stability related to the neutron-proton asymmetry and the weak binding close to the dripline. Properties of the valence-neutron wave functions are studied in the one-neutron knockout reaction, revealing the changes of shell structure when going from the beta-stability line to more asymmetric loosely bound neutron-rich systems. The vanishing of the N=8 shell gap for neutron-rich systems like 11 Li and 12 Be, or the new closed N=14, 16 shells for the oxygen isotopes are examples. The continuum of weakly bound nuclei and halo states can be studied by inelastic scattering. The dipole response, for instance, is found to change dramatically when going away from the valley of stability. A redistribution of the dipole strength towards lower excitation energies is observed for neutron-rich nuclei, which partly might be due to a new collective excitation mode related to the neutron-proton asymmetry. Halo nuclei in particular show strong dipole transitions to the continuum at the threshold, being directly related to the ground-state properties of the projectile. Finally, an outlook on future experimental prospects is given. (orig.)

  3. Reactions with fast radioactive beams of neutron-rich nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Aumann, T. [Gesellschaft fuer Schwerionenforschung mbH, Darmstadt (Germany)

    2005-11-01

    The neutron dripline has presently been reached only for the lightest nuclei up to the element oxygen. In this region of light neutron-rich nuclei, scattering experiments are feasible even for dripline nuclei by utilizing high-energy secondary beams produced by fragmentation. In the present article, reactions of high-energy radioactive beams will be exemplified using recent experimental results mainly derived from measurements of breakup reactions performed at the LAND and FRS facilities at GSI and at the S800 spectrometer at the NSCL. Nuclear and electromagnetically induced reactions allow probing different aspects of nuclear structure at the limits of stability related to the neutron-proton asymmetry and the weak binding close to the dripline. Properties of the valence-neutron wave functions are studied in the one-neutron knockout reaction, revealing the changes of shell structure when going from the beta-stability line to more asymmetric loosely bound neutron-rich systems. The vanishing of the N=8 shell gap for neutron-rich systems like {sup 11}Li and {sup 12}Be, or the new closed N=14, 16 shells for the oxygen isotopes are examples. The continuum of weakly bound nuclei and halo states can be studied by inelastic scattering. The dipole response, for instance, is found to change dramatically when going away from the valley of stability. A redistribution of the dipole strength towards lower excitation energies is observed for neutron-rich nuclei, which partly might be due to a new collective excitation mode related to the neutron-proton asymmetry. Halo nuclei in particular show strong dipole transitions to the continuum at the threshold, being directly related to the ground-state properties of the projectile. Finally, an outlook on future experimental prospects is given. (orig.)

  4. Adaptive and Reactive Rich Internet Applications

    OpenAIRE

    Schmidt, Kay-Uwe

    2010-01-01

    In this thesis we present the client-side approach of Adaptive and Reactive Rich Internet Applications as the main result of our research into how to bring in time adaptivity to Rich Internet Applications. Our approach leverages previous work on adaptive hypermedia, event processing and other research disciplines. We present a holistic framework covering the design-time as well as the runtime aspects of Adaptive and Reactive Rich Internet Applications focusing especially on the run-time aspects.

  5. DNA and RNA Quadruplex-Binding Proteins

    Directory of Open Access Journals (Sweden)

    Václav Brázda

    2014-09-01

    Full Text Available Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i-Motifs, minor groove quadruplexes, G-quadruplexes, etc., the best described are G-quadruplexes which are featured by Hoogsteen base-paring. Sequences with the potential to form quadruplexes are widely present in genome of all organisms. They are found often in repetitive sequences such as telomeric ones, and also in promoter regions and 5' non-coding sequences. Recently, many proteins with binding affinity to G-quadruplexes have been identified. One of the initially portrayed G-rich regions, the human telomeric sequence (TTAGGGn, is recognized by many proteins which can modulate telomerase activity. Sequences with the potential to form G-quadruplexes are often located in promoter regions of various oncogenes. The NHE III1 region of the c-MYC promoter has been shown to interact with nucleolin protein as well as other G-quadruplex-binding proteins. A number of G-rich sequences are also present in promoter region of estrogen receptor alpha. In addition to DNA quadruplexes, RNA quadruplexes, which are critical in translational regulation, have also been predicted and observed. For example, the RNA quadruplex formation in telomere-repeat-containing RNA is involved in interaction with TRF2 (telomere repeat binding factor 2 and plays key role in telomere regulation. All these fundamental examples suggest the importance of quadruplex structures in cell processes and their understanding may provide better insight into aging and disease development.

  6. Conservation and Biodiversity of Rich Fens

    DEFF Research Database (Denmark)

    Andersen, Dagmar Kappel

    2014-01-01

    Rich fen is a habitat type dependent on a constant supply of nutrient poor, calcium rich groundwater. A high, stable groundwater table, relatively high pH combined with nutrient poor conditions support a special and very species rich vegetation including many rare and threatened plant species...... of the importance of environmental conditions for the number of typical rich fen species, the species composition within a distinct taxonomic group (the mosses) and for single species (the Fen orchid, Liparis loeselii). In conclusion, especially parameters related to nutrient availability and hydrology are found...

  7. binding protein (HABP1)

    Indian Academy of Sciences (India)

    Unknown

    adsorbed on carbon coated copper grid (400 mesh) for. 5 min at room temperature. The grids were subsequently .... and inhibition by GAGs and DMA were determined on polystyrene wells of microtitre plates (Costar, ... for binding inhibition assays was carried out by mixing equal volumes of the conjugate and the inhibitor at ...

  8. Quarkeosynthesis Binding Energy

    Science.gov (United States)

    Webb, Bill

    2009-05-01

    Quarkeosynthesis shows that the binding energy of a nucleus is the difference between the relativistic kinetic energies of its threesome of Jumbo Quarks and that of its building block quarks from neutrons and protons. There is no involvement of a nuclear strong force or gluon material.

  9. Sequential memory: Binding dynamics

    Science.gov (United States)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  10. binding protein (HABP1)

    Indian Academy of Sciences (India)

    Unknown

    of HA in a concentration-dependent manner, suggesting its multiligand affinity amongst carbohydrates. rHABP1 shows differential affinity ... site is seen to correspond to the carbohydrate-binding site in E-selectin, which has similarity in the ... adsorbed on carbon coated copper grid (400 mesh) for. 5 min at room temperature.

  11. Further biochemical characterization of Mycobacterium leprae laminin-binding proteins

    Directory of Open Access Journals (Sweden)

    M.A.M. Marques

    2001-04-01

    Full Text Available It has been demonstrated that the alpha2 chain of laminin-2 present on the surface of Schwann cells is involved in the process of attachment of Mycobacterium leprae to these cells. Searching for M. leprae laminin-binding molecules, in a previous study we isolated and characterized the cationic proteins histone-like protein (Hlp and ribosomal proteins S4 and S5 as potential adhesins involved in M. leprae-Schwann cell interaction. Hlp was shown to bind alpha2-laminins and to greatly enhance the attachment of mycobacteria to ST88-14 Schwann cells. In the present study, we investigated the laminin-binding capacity of the ribosomal proteins S4 and S5. The genes coding for these proteins were PCR amplified and their recombinant products were shown to bind alpha2-laminins in overlay assays. However, when tested in ELISA-based assays and in adhesion assays with ST88-14 cells, in contrast to Hlp, S4 and S5 failed to bind laminin and act as adhesins. The laminin-binding property and adhesin capacity of two basic host-derived proteins were also tested, and only histones, but not cytochrome c, were able to increase bacterial attachment to ST88-14 cells. Our data suggest that the alanine/lysine-rich sequences shared by Hlp and eukaryotic H1 histones might be involved in the binding of these cationic proteins to laminin.

  12. Accurate prediction of peptide binding sites on protein surfaces.

    Directory of Open Access Journals (Sweden)

    Evangelia Petsalaki

    2009-03-01

    Full Text Available Many important protein-protein interactions are mediated by the binding of a short peptide stretch in one protein to a large globular segment in another. Recent efforts have provided hundreds of examples of new peptides binding to proteins for which a three-dimensional structure is available (either known experimentally or readily modeled but where no structure of the protein-peptide complex is known. To address this gap, we present an approach that can accurately predict peptide binding sites on protein surfaces. For peptides known to bind a particular protein, the method predicts binding sites with great accuracy, and the specificity of the approach means that it can also be used to predict whether or not a putative or predicted peptide partner will bind. We used known protein-peptide complexes to derive preferences, in the form of spatial position specific scoring matrices, which describe the binding-site environment in globular proteins for each type of amino acid in bound peptides. We then scan the surface of a putative binding protein for sites for each of the amino acids present in a peptide partner and search for combinations of high-scoring amino acid sites that satisfy constraints deduced from the peptide sequence. The method performed well in a benchmark and largely agreed with experimental data mapping binding sites for several recently discovered interactions mediated by peptides, including RG-rich proteins with SMN domains, Epstein-Barr virus LMP1 with TRADD domains, DBC1 with Sir2, and the Ago hook with Argonaute PIWI domain. The method, and associated statistics, is an excellent tool for predicting and studying binding sites for newly discovered peptides mediating critical events in biology.

  13. Optical transitions in Ge/SiGe multiple quantum wells with Ge-rich barriers

    Science.gov (United States)

    Bonfanti, M.; Grilli, E.; Guzzi, M.; Virgilio, M.; Grosso, G.; Chrastina, D.; Isella, G.; von Känel, H.; Neels, A.

    2008-07-01

    Direct-gap and indirect-gap transitions in strain-compensated Ge/SiGe multiple quantum wells with Ge-rich SiGe barriers have been studied by optical transmission spectroscopy and photoluminescence experiments. An sp3d5s∗ tight-binding model has been adopted to interpret the experimental results. Photoluminescence spectra and their comparison with theoretical calculations prove the existence of type-I band alignment in compressively strained Ge quantum wells grown on relaxed Ge-rich SiGe buffers. The high quality of the transmission spectra opens up other perspectives for application of these structures in near-infrared optical modulators.

  14. Characterization of vanadium-binding sites of the vanadium-binding protein Vanabin2 by site-directed mutagenesis.

    Science.gov (United States)

    Ueki, Tatsuya; Kawakami, Norifumi; Toshishige, Masaaki; Matsuo, Koichi; Gekko, Kunihiko; Michibata, Hitoshi

    2009-10-01

    Vanabins are a unique protein family of vanadium-binding proteins with nine disulfide bonds. Possible binding sites for VO2+ in Vanabin2 from a vanadium-rich ascidian Ascidia sydneiensis samea have been detected by nuclear magnetic resonance study, but the metal selectivity and metal-binding ability of each site was not examined. In order to reveal functional contribution of each binding site, we prepared several mutants of Vanabin2 by in vitro site-directed mutagenesis and analyzed their metal selectivity and affinity by immobilized metal-ion affinity chromatography and Hummel Dreyer method. Mutation at K10/R60 (site 1) markedly reduced the affinity for VO2+. Mutation at K24/K38/R41/R42 (site 2) decreased the maximum binding number, but only slightly increased the overall affinity for VO2+. Secondary structure of both mutants was the same as that of the wild type as assessed by circular dichroism spectroscopy. Mutation in disulfide bonds near the site 1 did not affect its high affinity binding capacity, while those near the site 2 decreased the overall affinity for VO2+. These results suggested that the site 1 is a high affinity binding site for VO2+, while the site 2 composes a moderate affinity site for multiple VO2+.

  15. LHCb RICH1 Engineering Design Review Report

    CERN Document Server

    Brook, N; Metlica, F; Muir, A; Phillips, A; Buckley, A; Gibson, V; Harrison, K; Jones, C R; Katvars, S G; Lazzeroni, C; Storey, J; Ward, CP; Wotton, S; Alemi, M; Arnabaldi, C; Bellunato, T F; Calvi, M; Matteuzzi, C; Musy, M; Negri, P; Perego, D L; Pessina, G; Chamonal, R; Eisenhardt, S; Lawrence, J; McCarron, J; Muheim, F; Playfer, S; Walker, A; Cuneo, S; Fontanelli, F; Gracco, Valerio; Mini, G; Musico, P; Petrolini, A; Sannino, M; Bates, A; MacGregor, A; O'Shea, V; Parkes, C; Paterson, S; Petrie, D; Pickford, A; Rahman, M; Soler, F; Allebone, L; Barber, J H; Cameron, W; Clark, D; Dornan, Peter John; Duane, A; Egede, U; Hallam, R; Howard, A; Plackett, R; Price, D; Savidge, T; Vidal-Sitjes, G; Websdale, D M; Adinolfi, M; Bibby, J H; Cioffi, C; Gligorov, Vladimir V; Harnew, N; Harris, F; McArthur, I A; Newby, C; Ottewell, B; Rademacker, J; Senanayake, R; Somerville, L P; Soroko, A; Smale, N J; Topp-Jørgensen, S; Wilkinson, G; Yang, S; Benayoun, M; Khmelnikov, V A; Obraztsov, V F; Densham, C J; Easo, S; Franek, B; Kuznetsov, G; Loveridge, P W; Morrow, D; Morris, JV; Papanestis, A; Patrick, G N; Woodward, M L; Aglieri-Rinella, G; Albrecht, A; Braem, André; Campbell, M; D'Ambrosio, C; Forty, R W; Frei, C; Gys, Thierry; Jamet, O; Kanaya, N; Losasso, M; Moritz, M; Patel, M; Piedigrossi, D; Snoeys, W; Ullaland, O; Van Lysebetten, A; Wyllie, K

    2005-01-01

    This document describes the concepts of the engineering design to be adopted for the upstream Ring Imaging Cherenkov detector (RICH1) of the reoptimized LHCb detector. Our aim is to ensure that coherent solutions for the engineering design and integration for all components of RICH1 are available, before proceeding with the detailed design of these components.

  16. Particle Identification with the LHCb RICH System

    CERN Document Server

    Harnew, Neville

    2005-01-01

    The LHCb experiment uses a Ring Imaging Cherenkov (RICH) system to provide particle identification over the momentum range 2-100 GeV/c. Two RICH detectors are employed. The upstream detector, RICH1, utilizes both aerogel and C$_4$F$_{10}$ gas radiators whilst the downstream RICH2 uses a CF$_4$ gas radiator. The RICH2 detector has been fabricated and is installed in the LHCb interaction region; RICH1 has a programme of phased design and construction. Novel Hybrid Photon Detectors (HPDs) have been developed in collaboration with industry to detect the Cherenkov photons in the wavelength range 200-600 nm. The HPDs are enclosed in iron shielding and Mumetal cylinders to allow operation in magnetic fields up to 50mT. The performance of pre-series HPDs and the results obtained from a particle test beam using the full LHCb readout chain is presented. The production of a total of 484 HPDs required for the two RICH detectors has recently commenced. The expected performance of the LHCb RICH system, obtained from real...

  17. Particle identification with the LHCb RICH system

    Science.gov (United States)

    Harnew, Neville

    2006-07-01

    The LHCb experiment uses a Ring Imaging Cherenkov (RICH) system to provide particle identification over the momentum range 2- 100 GeV/c. Two RICH detectors are employed. The upstream detector, RICH 1, utilizes both aerogel and C4F10 gas radiators whilst the downstream RICH 2 uses a CF4 gas radiator. The RICH 2 detector has been fabricated and is installed in the LHCb interaction region; RICH 1 has a programme of phased design and construction. Novel Hybrid Photon Detectors (HPDs) have been developed in collaboration with industry to detect the Cherenkov photons in the wavelength range 200-600 nm. The HPDs are enclosed in iron shielding and Mumetal cylinders to allow operation in magnetic fields up to 50 mT. The performance of pre-series HPDs and the results obtained from a particle test beam using the full LHCb readout chain is presented. The production of a total of 484 HPDs required for the two RICH detectors has recently commenced. The expected performance of the LHCb RICH system, obtained from realistic simulation, is described.

  18. Dissociation Dynamics of Nitrogen Rich Cyclic Compounds

    Science.gov (United States)

    2010-05-17

    Arlington, VA 2220 Abstract The photophysics and photochemistry of the nitrogen-rich compounds diazomethane and diazirine were studied both...experimentally and theoretically following excitation in the ultraviolet . These molecules are locally stable on their ground potential energy surfaces, but they...ABSTRACT The photophysics and photochemistry of the nitrogen-rich compounds diazomethane and diazirine were studied both experimentally and

  19. Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles.

    Science.gov (United States)

    Kuznetsov, Vladimir A

    2017-01-01

    The shape of the experimental frequency distributions (EFD) of diverse molecular interaction events quantifying genome-wide binding is often skewed to the rare but abundant quantities. Such distributions are systematically deviated from standard power-law functions proposed by scale-free network models suggesting that more explanatory and predictive probabilistic model(s) are needed. Identification of the mechanism-based data-driven statistical distributions that provide an estimation and prediction of binding properties of transcription factors from genome-wide binding profiles is the goal of this analytical survey. Here, we review and develop an analytical framework for modeling, analysis, and prediction of transcription factor (TF) DNA binding properties detected at the genome scale. We introduce a mixture probabilistic model of binding avidity function that includes nonspecific and specific binding events. A method for decomposition of specific and nonspecific TF-DNA binding events is proposed. We show that the Kolmogorov-Waring (KW) probability function (PF), modeling the steady state TF binding-dissociation stochastic process, fits well with the EFD for diverse TF-DNA binding datasets. Furthermore, this distribution predicts total number of TF-DNA binding sites (BSs), estimating specificity and sensitivity as well as other basic statistical features of DNA-TF binding when the experimental datasets are noise-rich and essentially incomplete. The KW distribution fits equally well to TF-DNA binding activity for different TFs including ERE, CREB, STAT1, Nanog, and Oct4. Our analysis reveals that the KW distribution and its generalized form provides the family of power-law-like distributions given in terms of hypergeometric series functions, including standard and generalized Pareto and Waring distributions, providing flexible and common skewed forms of the transcription factor binding site (TFBS) avidity distribution function. We suggest that the skewed binding

  20. Platelet-rich plasma in otolaryngology.

    Science.gov (United States)

    Stavrakas, M; Karkos, P D; Markou, K; Grigoriadis, N

    2016-12-01

    Platelet-rich plasma is a novel material that is being used more frequently in many surgical specialties. A literature review on the current and potential uses of platelet-rich plasma in otolaryngology was performed. There is limited evidence on the use of platelet-rich plasma in otolaryngology compared with other specialties: only 11 studies on various subspecialties (otology, rhinology and laryngology) were included in the final review. Based on the limited number of studies, we cannot draw safe conclusions about the value of platelet-rich plasma in otolaryngology. Nevertheless, the available literature suggests that platelet-rich plasma holds promise for future research and may have a number of clinical applications.

  1. Biophysical characterization of the basic cluster in the transcription repression domain of human MeCP2 with AT-rich DNA.

    Science.gov (United States)

    Mushtaq, Ameeq Ul; Lee, Yejin; Hwang, Eunha; Bang, Jeong Kyu; Hong, Eunmi; Byun, Youngjoo; Song, Ji-Joon; Jeon, Young Ho

    2018-01-01

    MeCP2 is a chromatin associated protein which is highly expressed in brain and relevant with Rett syndrome (RTT). There are AT-hook motifs in MeCP2 which can bind with AT-rich DNA, suggesting a role in chromatin binding. Here, we report the identification and characterization of another AT-rich DNA binding motif (residues 295 to 313) from the C-terminal transcription repression domain of MeCP2 by nuclear magnetic resonance (NMR) and isothermal calorimetry (ITC). This motif shows a micromolar affinity to AT-rich DNA, and it binds to the minor groove of DNA like AT-hook motifs. Together with the previous studies, our results provide an insight into a critical role of this motif in chromatin structure and function. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Binding of dinitrogen to an iron-sulfur-carbon site

    Science.gov (United States)

    Čorić, Ilija; Mercado, Brandon Q.; Bill, Eckhard; Vinyard, David J.; Holland, Patrick L.

    2015-10-01

    Nitrogenases are the enzymes by which certain microorganisms convert atmospheric dinitrogen (N2) to ammonia, thereby providing essential nitrogen atoms for higher organisms. The most common nitrogenases reduce atmospheric N2 at the FeMo cofactor, a sulfur-rich iron-molybdenum cluster (FeMoco). The central iron sites that are coordinated to sulfur and carbon atoms in FeMoco have been proposed to be the substrate binding sites, on the basis of kinetic and spectroscopic studies. In the resting state, the central iron sites each have bonds to three sulfur atoms and one carbon atom. Addition of electrons to the resting state causes the FeMoco to react with N2, but the geometry and bonding environment of N2-bound species remain unknown. Here we describe a synthetic complex with a sulfur-rich coordination sphere that, upon reduction, breaks an Fe-S bond and binds N2. The product is the first synthetic Fe-N2 complex in which iron has bonds to sulfur and carbon atoms, providing a model for N2 coordination in the FeMoco. Our results demonstrate that breaking an Fe-S bond is a chemically reasonable route to N2 binding in the FeMoco, and show structural and spectroscopic details for weakened N2 on a sulfur-rich iron site.

  3. Megalin binds and mediates cellular internalization of folate binding protein

    DEFF Research Database (Denmark)

    Birn, Henrik; Zhai, Xiaoyue; Holm, Jan

    2005-01-01

    to express high levels of megalin, is inhibitable by excess unlabeled FBP and by receptor associated protein, a known inhibitor of binding to megalin. Immortalized rat yolk sac cells, representing an established model for studying megalin-mediated uptake, reveal (125)I-labeled FBP uptake which is inhibited...... to bind and mediate cellular uptake of FBP. Surface plasmon resonance analysis shows binding of bovine and human milk FBP to immobilized megalin, but not to low density lipoprotein receptor related protein. Binding of (125)I-labeled folate binding protein (FBP) to sections of kidney proximal tubule, known...

  4. Tree species richness of upper Amazonian forests

    OpenAIRE

    Gentry, Alwyn H.

    1988-01-01

    Upper Amazonian data for tree species richness in 1-hectare plots are reported. All plants ≥10 cm diameter were censused and identified in six plots in Amazonian Peru and one on the Venezuela-Brazil border. The two plots from the everwet forests near Iquitos, Peru, are the most species-rich in the world, with ≈300 species ≥10 cm diameter in single hectares; all of the Peruvian plots are among the most species-rich ever reported. Contrary to accepted opinion, upper Amazonian forest, and perhap...

  5. Firm size diversity, functional richness, and resilience

    Science.gov (United States)

    Garmestani, A.S.; Allen, Craig R.; Mittelstaedt, J.D.; Stow, C.A.; Ward, W.A.

    2006-01-01

    This paper applies recent advances in ecology to our understanding of firm development, sustainability, and economic development. The ecological literature indicates that the greater the functional richness of species in a system, the greater its resilience - that is, its ability to persist in the face of substantial changes in the environment. This paper focuses on the effects of functional richness across firm size on the ability of industries to survive in the face of economic change. Our results indicate that industries with a richness of industrial functions are more resilient to employment volatility. ?? 2006 Cambridge University Press.

  6. Binding matrix: a novel approach for binding site recognition.

    Science.gov (United States)

    Kim, Jan T; Gewehr, Jan E; Martinetz, Thomas

    2004-06-01

    Recognition of protein-DNA binding sites in genomic sequences is a crucial step for discovering biological functions of genomic sequences. Explosive growth in availability of sequence information has resulted in a demand for binding site detection methods with high specificity. The motivation of the work presented here is to address this demand by a systematic approach based on Maximum Likelihood Estimation. A general framework is developed in which a large class of binding site detection methods can be described in a uniform and consistent way. Protein-DNA binding is determined by binding energy, which is an approximately linear function within the space of sequence words. All matrix based binding word detectors can be regarded as different linear classifiers which attempt to estimate the linear separation implied by the binding energy function. The standard approaches of consensus sequences and profile matrices are described using this framework. A maximum likelihood approach for determining this linear separation leads to a novel matrix type, called the binding matrix. The binding matrix is the most specific matrix based classifier which is consistent with the input set of known binding words. It achieves significant improvements in specificity compared to other matrices. This is demonstrated using 95 sets of experimentally determined binding words provided by the TRANSFAC database.

  7. Persimmon fruit tannin-rich fiber reduces cholesterol levels in humans.

    Science.gov (United States)

    Gato, Nobuki; Kadowaki, Akio; Hashimoto, Natsumi; Yokoyama, Shin-ichiro; Matsumoto, Kenji

    2013-01-01

    Bile acid-binding agents are known to lower blood cholesterol levels and have been clinically used for the treatment of hypercholesterolemia. We previously showed that tannin-rich fiber from young persimmon (Diospyros kaki) fruits had bile acid-binding properties. In this study, we performed a randomized, double-blind, placebo-controlled trial to investigate the hypocholesterolemic effects of tannin-rich fiber in humans. The subjects (n = 40, plasma total cholesterol levels 180-259 mg/dl) were divided into 3 groups and ingested cookie bars containing 0 g (placebo group, n = 14), 3 g (low-dose group, n = 13), or 5 g (high-dose group, n = 13) of tannin-rich fiber 3 times daily before meals for 12 weeks. Plasma total cholesterol levels decreased significantly in the low-dose (12 weeks, p < 0.005) and high-dose (6 weeks, p < 0.05; 12 weeks, p < 0.001) groups. In addition, plasma low-density lipoprotein cholesterol levels decreased significantly in the high-dose group (6 weeks, p < 0.05; 12 weeks, p < 0.001). These improvements were not accompanied by changes in plasma high-density lipoprotein cholesterol or plasma triglyceride levels. Our findings indicate that tannin-rich fiber from young persimmon fruits is a useful food material for treating hypercholesterolemia. Copyright © 2012 S. Karger AG, Basel.

  8. Evaluating Media Richness in Organizational Learning

    DEFF Research Database (Denmark)

    Evaluating Media Richness in Organizational Learning is an essential reference source for the latest scholarly research on the application of computational tools for knowledge management frameworks and strategies in organizations. Featuring a broad range of coverage on topics and perspectives...

  9. Carboplatin binding to histidine

    Energy Technology Data Exchange (ETDEWEB)

    Tanley, Simon W. M. [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom); Diederichs, Kay [University of Konstanz, D-78457 Konstanz (Germany); Kroon-Batenburg, Loes M. J. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Levy, Colin [University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom); Schreurs, Antoine M. M. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Helliwell, John R., E-mail: john.helliwell@manchester.ac.uk [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom)

    2014-08-29

    An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.

  10. Optical Binding of Nanowires

    Czech Academy of Sciences Publication Activity Database

    Simpson, Stephen Hugh; Zemánek, Pavel; Marago, O.M.; Jones, P.H.; Hanna, S.

    2017-01-01

    Roč. 17, č. 6 (2017), s. 3485-3492 ISSN 1530-6984 R&D Projects: GA ČR GB14-36681G Grant - others:AV ČR(CZ) CNR-16-12 Program:Bilaterální spolupráce Institutional support: RVO:68081731 Keywords : optical binding nanowires * Brownian motion * self -organization * non-equilibrium thermodynamics * non-equilibrium steady state * spin-orbit coupling * emergent phenomena Subject RIV: BH - Optics, Masers, Lasers OBOR OECD: Optics (including laser optics and quantum optics) Impact factor: 12.712, year: 2016

  11. Species richness, area and climate correlates

    DEFF Research Database (Denmark)

    Nogues, David Bravo; Bastos Araujo, Miguel

    2006-01-01

    Aim Species richness-area theory predicts that more species should be found if one samples a larger area. To avoid biases from comparing species richness in areas of very different sizes, area is often controlled by counting the numbers of co-occupying species in near-equal area grid cells...... affects: (1) the selection of climate variables entering a species richness model; and (2) the accuracy of models in predicting species richness in unsampled grid cells. Location Western Europe. Methods Models are developed for European plant, breeding bird, mammal and herptile species richness using...... seven climate variables. Generalized additive models are used to relate species richness, climate and area. Results We found that variation in the grid cell area was large (50 × 50 km: 8-3311 km2; 220 × 220: 193-55,100 km2), but this did not affect the selection of variables in the models. Similarly...

  12. IGF binding proteins.

    Science.gov (United States)

    Bach, Leon A

    2017-12-18

    Insulin-like growth factor binding proteins (IGFBPs) 1-6 bind IGFs but not insulin with high affinity. They were initially identified as serum carriers and passive inhibitors of IGF actions. However, subsequent studies showed that, although IGFBPs inhibit IGF actions in many circumstances, they may also potentiate these actions. IGFBPs are widely expressed in most tissues, and they are flexible endocrine and autocrine/paracrine regulators of IGF activity, which is essential for this important physiological system. More recently, individual IGFBPs have been shown to have IGF-independent actions. Mechanisms underlying these actions include (i) interaction with non-IGF proteins in compartments including the extracellular space and matrix, the cell surface and intracellularly; (ii) interaction with and modulation of other growth factor pathways including EGF, TGF- and VEGF; and (iii) direct or indirect transcriptional effects following nuclear entry of IGFBPs. Through these IGF-dependent and IGF-independent actions, IGFBPs modulate essential cellular processes including proliferation, survival, migration, senescence, autophagy and angiogenesis. They have been implicated in a range of disorders including malignant, metabolic, neurological and immune diseases. A more complete understanding of their cellular roles may lead to the development of novel IGFBP-based therapeutic opportunities.

  13. Molecular evolution and expression of oxygen transport genes in livebearing fishes (Poeciliidae) from hydrogen sulfide rich springs.

    Science.gov (United States)

    Barts, Nicholas; Greenway, Ryan; Passow, Courtney N; Arias-Rodriguez, Lenin; Kelley, Joanna L; Tobler, Michael

    2018-04-01

    Hydrogen sulfide (H 2 S) is a natural toxicant in some aquatic environments that has diverse molecular targets. It binds to oxygen transport proteins, rendering them non-functional by reducing oxygen-binding affinity. Hence, organisms permanently inhabiting H 2 S-rich environments are predicted to exhibit adaptive modifications to compensate for the reduced capacity to transport oxygen. We investigated 10 lineages of fish of the family Poeciliidae that have colonized freshwater springs rich in H 2 S-along with related lineages from non-sulfidic environments-to test hypotheses about the expression and evolution of oxygen transport genes in a phylogenetic context. We predicted shifts in the expression of and signatures of positive selection on oxygen transport genes upon colonization of H 2 S-rich habitats. Our analyses indicated significant shifts in gene expression for multiple hemoglobin genes in lineages that have colonized H 2 S-rich environments, and three hemoglobin genes exhibited relaxed selection in sulfidic compared to non-sulfidic lineages. However, neither changes in gene expression nor signatures of selection were consistent among all lineages in H 2 S-rich environments. Oxygen transport genes may consequently be predictable targets of selection during adaptation to sulfidic environments, but changes in gene expression and molecular evolution of oxygen transport genes in H 2 S-rich environments are not necessarily repeatable across replicated lineages.

  14. A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT.

    Directory of Open Access Journals (Sweden)

    Pengfei Ding

    2015-06-01

    Full Text Available Bacterial xenogeneic silencing proteins selectively bind to and silence expression from many AT rich regions of the chromosome. They serve as master regulators of horizontally acquired DNA, including a large number of virulence genes. To date, three distinct families of xenogeneic silencers have been identified: H-NS of Proteobacteria, Lsr2 of the Actinomycetes, and MvaT of Pseudomonas sp. Although H-NS and Lsr2 family proteins are structurally different, they all recognize the AT-rich DNA minor groove through a common AT-hook-like motif, which is absent in the MvaT family. Thus, the DNA binding mechanism of MvaT has not been determined. Here, we report the characteristics of DNA sequences targeted by MvaT with protein binding microarrays, which indicates that MvaT prefers binding flexible DNA sequences with multiple TpA steps. We demonstrate that there are clear differences in sequence preferences between MvaT and the other two xenogeneic silencer families. We also determined the structure of the DNA-binding domain of MvaT in complex with a high affinity DNA dodecamer using solution NMR. This is the first experimental structure of a xenogeneic silencer in complex with DNA, which reveals that MvaT recognizes the AT-rich DNA both through base readout by an "AT-pincer" motif inserted into the minor groove and through shape readout by multiple lysine side chains interacting with the DNA sugar-phosphate backbone. Mutations of key MvaT residues for DNA binding confirm their importance with both in vitro and in vivo assays. This novel DNA binding mode enables MvaT to better tolerate GC-base pair interruptions in the binding site and less prefer A tract DNA when compared to H-NS and Lsr2. Comparison of MvaT with other bacterial xenogeneic silencers provides a clear picture that nature has evolved unique solutions for different bacterial genera to distinguish foreign from self DNA.

  15. Dystrophin contains multiple independent membrane-binding domains.

    Science.gov (United States)

    Zhao, Junling; Kodippili, Kasun; Yue, Yongping; Hakim, Chady H; Wasala, Lakmini; Pan, Xiufang; Zhang, Keqing; Yang, Nora N; Duan, Dongsheng; Lai, Yi

    2016-09-01

    Dystrophin is a large sub-sarcolemmal protein. Its absence leads to Duchenne muscular dystrophy (DMD). Binding to the sarcolemma is essential for dystrophin to protect muscle from contraction-induced injury. It has long been thought that membrane binding of dystrophin depends on its cysteine-rich (CR) domain. Here, we provide in vivo evidence suggesting that dystrophin contains three additional membrane-binding domains including spectrin-like repeats (R)1-3, R10-12 and C-terminus (CT). To systematically study dystrophin membrane binding, we split full-length dystrophin into ten fragments and examined subcellular localizations of each fragment by adeno-associated virus-mediated gene transfer. In skeletal muscle, R1-3, CR domain and CT were exclusively localized at the sarcolemma. R10-12 showed both cytosolic and sarcolemmal localization. Importantly, the CR-independent membrane binding was conserved in murine and canine muscles. A critical function of the CR-mediated membrane interaction is the assembly of the dystrophin-associated glycoprotein complex (DGC). While R1-3 and R10-12 did not restore the DGC, surprisingly, CT alone was sufficient to establish the DGC at the sarcolemma. Additional studies suggest that R1-3 and CT also bind to the sarcolemma in the heart, though relatively weak. Taken together, our study provides the first conclusive in vivo evidence that dystrophin contains multiple independent membrane-binding domains. These structurally and functionally distinctive membrane-binding domains provide a molecular framework for dystrophin to function as a shock absorber and signaling hub. Our results not only shed critical light on dystrophin biology and DMD pathogenesis, but also provide a foundation for rationally engineering minimized dystrophins for DMD gene therapy. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  16. LITHIUM-RICH GIANTS IN GLOBULAR CLUSTERS

    Energy Technology Data Exchange (ETDEWEB)

    Kirby, Evan N.; Cohen, Judith G. [California Institute of Technology, 1200 E. California Boulevard, MC 249-17, Pasadena, CA 91125 (United States); Guhathakurta, Puragra [UCO/Lick Observatory and Department of Astronomy and Astrophysics, University of California, 1156 High Street, Santa Cruz, CA 95064 (United States); Zhang, Andrew J. [The Harker School, 500 Saratoga Avenue, San Jose, CA 95129 (United States); Hong, Jerry [Palo Alto High School, 50 Embarcadero Road, Palo Alto, CA, 94301 (United States); Guo, Michelle [Stanford University, 450 Serra Mall, Stanford, CA 94305 (United States); Guo, Rachel [Irvington High School, 41800 Blacow Road, Fremont, CA 94538 (United States); Cunha, Katia [Observatório Nacional, São Cristóvão Rio de Janeiro (Brazil)

    2016-03-10

    Although red giants deplete lithium on their surfaces, some giants are Li-rich. Intermediate-mass asymptotic giant branch (AGB) stars can generate Li through the Cameron–Fowler conveyor, but the existence of Li-rich, low-mass red giant branch (RGB) stars is puzzling. Globular clusters are the best sites to examine this phenomenon because it is straightforward to determine membership in the cluster and to identify the evolutionary state of each star. In 72 hours of Keck/DEIMOS exposures in 25 clusters, we found four Li-rich RGB and two Li-rich AGB stars. There were 1696 RGB and 125 AGB stars with measurements or upper limits consistent with normal abundances of Li. Hence, the frequency of Li-richness in globular clusters is (0.2 ± 0.1)% for the RGB, (1.6 ± 1.1)% for the AGB, and (0.3 ± 0.1)% for all giants. Because the Li-rich RGB stars are on the lower RGB, Li self-generation mechanisms proposed to occur at the luminosity function bump or He core flash cannot explain these four lower RGB stars. We propose the following origin for Li enrichment: (1) All luminous giants experience a brief phase of Li enrichment at the He core flash. (2) All post-RGB stars with binary companions on the lower RGB will engage in mass transfer. This scenario predicts that 0.1% of lower RGB stars will appear Li-rich due to mass transfer from a recently Li-enhanced companion. This frequency is at the lower end of our confidence interval.

  17. Characterization of salivary alpha-amylase binding to Streptococcus sanguis

    Energy Technology Data Exchange (ETDEWEB)

    Scannapieco, F.A.; Bergey, E.J.; Reddy, M.S.; Levine, M.J. (State Univ. of New York, Buffalo (USA))

    1989-09-01

    The purpose of this study was to identify the major salivary components which interact with oral bacteria and to determine the mechanism(s) responsible for their binding to the bacterial surface. Strains of Streptococcus sanguis, Streptococcus mitis, Streptococcus mutans, and Actinomyces viscosus were incubated for 2 h in freshly collected human submandibular-sublingual saliva (HSMSL) or parotid saliva (HPS), and bound salivary components were eluted with 2% sodium dodecyl sulfate. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western transfer, alpha-amylase was the prominent salivary component eluted from S. sanguis. Studies with {sup 125}I-labeled HSMSL or {sup 125}I-labeled HPS also demonstrated a component with an electrophoretic mobility identical to that of alpha-amylase which bound to S. sanguis. Purified alpha-amylase from human parotid saliva was radiolabeled and found to bind to strains of S. sanguis genotypes 1 and 3 and S. mitis genotype 2, but not to strains of other species of oral bacteria. Binding of ({sup 125}I)alpha-amylase to streptococci was saturable, calcium independent, and inhibitable by excess unlabeled alpha-amylases from a variety of sources, but not by secretory immunoglobulin A and the proline-rich glycoprotein from HPS. Reduced and alkylated alpha-amylase lost enzymatic and bacterial binding activities. Binding was inhibited by incubation with maltotriose, maltooligosaccharides, limit dextrins, and starch.

  18. Mycobacterium smegmatis Ku binds DNA without free ends.

    Science.gov (United States)

    Kushwaha, Ambuj K; Grove, Anne

    2013-12-01

    Ku is central to the non-homologous end-joining pathway of double-strand-break repair in all three major domains of life, with eukaryotic homologues being associated with more diversified roles compared with prokaryotic and archaeal homologues. Ku has a conserved central 'ring-shaped' core domain. While prokaryotic homologues lack the N- and C-terminal domains that impart functional diversity to eukaryotic Ku, analyses of Ku from certain prokaryotes such as Pseudomonas aeruginosa and Mycobacterium smegmatis have revealed the presence of distinct C-terminal extensions that modulate DNA-binding properties. We report in the present paper that the lysine-rich C-terminal extension of M. smegmatis Ku contacts the core protein domain as evidenced by an increase in DNA-binding affinity and a decrease in thermal stability and intrinsic tryptophan fluorescence upon its deletion. Ku deleted for this C-terminus requires free DNA ends for binding, but translocates to internal DNA sites. In contrast, full-length Ku can directly bind DNA without free ends, suggesting that this property is conferred by its C-terminus. Such binding to internal DNA sites may facilitate recruitment to sites of DNA damage. The results of the present study also suggest that extensions beyond the shared core domain may have independently evolved to expand Ku function.

  19. Decorin binds myostatin and modulates its activity to muscle cells

    International Nuclear Information System (INIS)

    Miura, Takayuki; Kishioka, Yasuhiro; Wakamatsu, Jun-ichi; Hattori, Akihito; Hennebry, Alex; Berry, Carole J.; Sharma, Mridula; Kambadur, Ravi; Nishimura, Takanori

    2006-01-01

    Myostatin, a member of TGF-β superfamily of growth factors, acts as a negative regulator of skeletal muscle mass. The mechanism whereby myostatin controls the proliferation and differentiation of myogenic cells is mostly clarified. However, the regulation of myostatin activity to myogenic cells after its secretion in the extracellular matrix (ECM) is still unknown. Decorin, a small leucine-rich proteoglycan, binds TGF-β and regulates its activity in the ECM. Thus, we hypothesized that decorin could also bind to myostatin and participate in modulation of its activity to myogenic cells. In order to test the hypothesis, we investigated the interaction between myostatin and decorin by surface plasmon assay. Decorin interacted with mature myostatin in the presence of concentrations of Zn 2+ greater than 10 μM, but not in the absence of Zn 2+ . Kinetic analysis with a 1:1 binding model resulted in dissociation constants (K D ) of 2.02 x 10 -8 M and 9.36 x 10 -9 M for decorin and the core protein of decorin, respectively. Removal of the glycosaminoglycan chain by chondroitinase ABC digestion did not affect binding, suggesting that decorin could bind to myostatin with its core protein. Furthermore, we demonstrated that immobilized decorin could rescue the inhibitory effect of myostatin on myoblast proliferation in vitro. These results suggest that decorin could trap myostatin and modulate its activity to myogenic cells in the ECM

  20. Dynamics of TBP binding to the TATA box

    Science.gov (United States)

    Schluesche, Peter; Heiss, Gregor; Meisterernst, Michael; Lamb, Don C.

    2008-02-01

    Gene expression is highly controlled and regulated in living cells. One of the first steps in gene transcription is recognition of the promoter site by the TATA box Binding Protein (TBP). TBP recruits other transcriptions factors and eventually the RNA polymerase II to transcribe the DNA in mRNA. We developed a single pair Förster Resonance Energy Transfer (spFRET) assay to investigate the mechanism of gene regulation. Here, we apply this assay to investigate the initial binding process of TBP to the adenovirus major late (AdML) promoter site. From the spFRET measurements, we were able to identify two conformations of the TBP-DNA complex that correspond to TBP bound in the correct and the opposite orientation. Increased incubation times or the presence of the transcription factor TFIIA improved the alignment of TBP on the promoter site. Binding of TBP to the TATA box shows a rich dynamics with abrupt transitions between multiple FRET states. A frame-wise histogram analysis revealed the presence of at least six discrete states, showing that TBP binding is more complicated than previously thought. Hence, the spFRET assay is very sensitive to the conformation of the TBP-DNA complex and is very promising tool for investigating the pathway of TBP binding in detail.

  1. Characterization of salivary alpha-amylase binding to Streptococcus sanguis

    International Nuclear Information System (INIS)

    Scannapieco, F.A.; Bergey, E.J.; Reddy, M.S.; Levine, M.J.

    1989-01-01

    The purpose of this study was to identify the major salivary components which interact with oral bacteria and to determine the mechanism(s) responsible for their binding to the bacterial surface. Strains of Streptococcus sanguis, Streptococcus mitis, Streptococcus mutans, and Actinomyces viscosus were incubated for 2 h in freshly collected human submandibular-sublingual saliva (HSMSL) or parotid saliva (HPS), and bound salivary components were eluted with 2% sodium dodecyl sulfate. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western transfer, alpha-amylase was the prominent salivary component eluted from S. sanguis. Studies with 125 I-labeled HSMSL or 125 I-labeled HPS also demonstrated a component with an electrophoretic mobility identical to that of alpha-amylase which bound to S. sanguis. Purified alpha-amylase from human parotid saliva was radiolabeled and found to bind to strains of S. sanguis genotypes 1 and 3 and S. mitis genotype 2, but not to strains of other species of oral bacteria. Binding of [ 125 I]alpha-amylase to streptococci was saturable, calcium independent, and inhibitable by excess unlabeled alpha-amylases from a variety of sources, but not by secretory immunoglobulin A and the proline-rich glycoprotein from HPS. Reduced and alkylated alpha-amylase lost enzymatic and bacterial binding activities. Binding was inhibited by incubation with maltotriose, maltooligosaccharides, limit dextrins, and starch

  2. Platelet-Rich Plasma Increases Pigmentation.

    Science.gov (United States)

    Uysal, Cagri A; Ertas, Nilgun Markal

    2017-11-01

    Platelet-rich plasma (PRP) is an autologous solution of plasma containing 4 to 7 times the baseline concentration of human platelets. Platelet-rich plasma has been widely popular in facial rejuvenation to attenuate wrinkles and has been practically used. The authors have been encountering various patients of increased hiperpigmentation following PRP applications that were performed to attenuate the postinflammatory hiperpigmentation especially after laser treatment. The authors have been using PRP for facial rejuvenation in selected patients and in 1 patient the authors have encountered increased pigmentation over the pigmented skin lesions that were present before the application. The authors recommend that the PRP might increase pigmentation especially in the face region and precautions might be taken before and after the application. Platelet-rich plasma should not be used for the treatment of post inflammatory hiperpigmentation.

  3. Origin of the latitudinal richness gradient

    DEFF Research Database (Denmark)

    Engemann, Kristine; Sandel, Brody Steven; Enquist, Brian J.

    2015-01-01

    predictions for the phylogenetic structure of communities. We test these hypotheses by comparing centers of species richness and phylogenetic clustering for vascular plants in the New World. Range maps for 88,417 plant species were extracted from the Botanical Information and Ecology Network (BIEN) database...... and combined with the BIEN mega phylogeny of >80,000 species. We calculated the Phylogenetic Diversity Index (PDI) and Net Relatedness Index (NRI) for each cell in a 100×100 km grid using a new computationally efficient algorithm. Species richness patterns were compared to patterns of PDI and NRI. We found...... that, for all vascular plants, high species richness is associated with high phylogenetic clustering, supporting a “cradle” model of biodiversity hotspots. However, there is marked variation across plant families, which may be explained by variation in lifespans and growth forms....

  4. On the nature of the Cu-rich aggregates in brain astrocytes

    Energy Technology Data Exchange (ETDEWEB)

    Sullivan, Brendan; Robison, Gregory; Osborn, Jenna; Kay, Martin; Thompson, Peter; Davis, Katherine; Zakharova, Taisiya; Antipova, Olga; Pushkar, Yulia

    2017-04-01

    Fulfilling a bevy of biological roles, copper is an essential metal for healthy brain function. Cu dyshomeostasis has been demonstrated to be involved in some neurological conditions including Menkes and Alzheimer’s diseases. We have previously reported localized Cu-rich aggregates in astrocytes of the subventricular zone (SVZ) in rodent brains with Cu concentrations in the hundreds of millimolar. Metallothionein, a cysteine-rich protein critical to metal homeostasis and known to participate in a variety of neuroprotective and neuroregenerative processes, was proposed as a binding protein. Here, we present an analysis of metallothionein(1,2) knockout (MTKO) mice and age-matched controls using X-ray fluorescence microscopy. In large structures such as the corpus callosum, cortex, and striatum, there is no significant difference in Cu, Fe, or Zn concentrations in MTKO mice compared to age-matched controls. In the astrocyte-rich subventricular zone where Cu-rich aggregates reside, approximately 1/3 as many Cu-rich aggregates persist in MTKO mice resulting in a decrease in periventricular Cu concentration. Aggregates in both wild-type and MTKO mice show XANES spectra characteristic of CuxSy multimetallic clusters and have similar [S]/[Cu] ratios. Consistent with assignment as a CuxSy multimetallic cluster, the astrocyte-rich SVZ of both MTKO and wild-type mice exhibit autofluorescent bodies, though MTKO mice exhibit fewer. Furthermore, XRF imaging of Au-labeled lysosomes and ubiquitin demonstrates a lack of co-localization with Cu-rich aggregates suggesting they are not involved in a degradation pathway. Overall, these data suggest that Cu in aggregates is bound by either metallothionein-3 or a yet unknown protein similar to metallothionein.

  5. Cloning, expression, and characterization of the TATA-binding protein (TBP) promoter binding factor, a transcription activator of the Acanthamoeba TBP gene.

    Science.gov (United States)

    Huang, W; Bateman, E

    1995-12-01

    TATA-binding protein (TBP) gene promoter binding factor (TPBF) is a transactivator which binds to the TBP promoter element (TPE) sequence of the Acanthamoeba TBP gene promoter and stimulates transcription in vitro. We have isolated a cDNA clone encoding TPBF. TPBF is a polypeptide of 327 amino acids with a calculated molecular mass of 37 kDa. The predicted amino acid sequence of TPBF shows no significant homology to other proteins. TPBF has two potential coiled-coil regions, a basic region, a proline-rich region, a histidine-rich N terminus, and a nuclear targeting sequence. The recombinant protein has an apparent molecular mass of 50 kDa, identical with that of TPBF purified from Acanthamoeba. Recombinant TPBF is able to bind DNA and activate transcription with the same specificity as natural Acanthamoeba TPBF, demonstrating the authenticity of the clone. Mobility shift assays of co-translated TPBF polypeptides and chemical cross-linking demonstrate that TPBF is tetrameric in solution and when bound to DNA. Analyses of TPBF mutants show that Coiled-coil II is essential for DNA binding, but Coiled-coil I and the basic region are also involved. TPBF is thus a novel DNA-binding protein with functional similarity to the tumor suppressor protein p53.

  6. Fast Photon Detection for COMPASS RICH1

    CERN Document Server

    Abbon, P; Angerer, H; Apollonio, M; Birsa, R; Bordalo, P; Bradamante, F; Bressan, A; Busso, L; Chiosso, M; Ciliberti, P; Colantoni, M L; Costa, S; Dibiase, N; Dafni, T; Dalla Torre, S; Diaz, V; Duic, v; Delagnes, E; Deschamps, H; Eyrich, W; Faso, D; Ferrero, A; Finger, M; Finger, M Jr; Fischer, H; Gerassimov, S; Giorgi, M; Gobbo, B; Hagemann, R; Von Harrach, D; Heinsius, F H; Joosten, R; Ketzer, B; Königsmann, K; Kolosov, V N; Konorov, I; Kramer, D; Kunne, F; Levorato, S; Maggiora, A; Magnon, A; Mann, A; Martin, A; Menon, G; Mutter, A; Nähle, O; Neyret, D; Nerling, F; Pagano, P; Paul, S; Panebianco, S; Panzieri, D; Pesaro, G; Pizzolotto, C; Polak, J; Rebourgeard, P; Rocco, E; Robinet, F; Schiavon, P; Schill, C; Schoenmeier, P; Silva, L; Slunecka, M; Steiger, L; Sozzi, F; Sulc, M; Svec, M; Tessarotto, F; Teufel, A; Wollny, H

    2006-01-01

    The new photon detection system for COMPASS RICH-1 has been designed to cope with the demanding requests of operation at high beam intensity and at high trigger rates. The detection technique in the central region of RICH-1 has been changed with a system based on multianode photomultipliers coupled to individual fused silica lens telescopes and to a fast, almost dead time free readout system based on the MAD-4 amplifier-discriminator and the F1 TDC-chip. The new photon detection system design and construction are described, as well as its first response in the experiment.

  7. NMR studies of DNA oligomers and their interactions with minor groove binding ligands

    Energy Technology Data Exchange (ETDEWEB)

    Fagan, Patricia A. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1996-05-01

    The cationic peptide ligands distamycin and netropsin bind noncovalently to the minor groove of DNA. The binding site, orientation, stoichiometry, and qualitative affinity of distamycin binding to several short DNA oligomers were investigated by NMR spectroscopy. The oligomers studied contain A,T-rich or I,C-rich binding sites, where I = 2-desaminodeoxyguanosine. I•C base pairs are functional analogs of A•T base pairs in the minor groove. The different behaviors exhibited by distamycin and netropsin binding to various DNA sequences suggested that these ligands are sensitive probes of DNA structure. For sites of five or more base pairs, distamycin can form 1:1 or 2:1 ligand:DNA complexes. Cooperativity in distamycin binding is low in sites such as AAAAA which has narrow minor grooves, and is higher in sites with wider minor grooves such as ATATAT. The distamycin binding and base pair opening lifetimes of I,C-containing DNA oligomers suggest that the I,C minor groove is structurally different from the A,T minor groove. Molecules which direct chemistry to a specific DNA sequence could be used as antiviral compounds, diagnostic probes, or molecular biology tools. The author studied two ligands in which reactive groups were tethered to a distamycin to increase the sequence specificity of the reactive agent.

  8. Differential sensitivity of [3H]nitrendipine binding to cations of toxicological interest in various rat brain areas

    International Nuclear Information System (INIS)

    Rius, R.A.; Govoni, S.; Battaini, F.

    1985-01-01

    [ 3 H]Nitrendipine ([ 3 H]NTP) is a radiolabelled calcium antagonist which can be used to study neuronal calcium (Ca 2+ ) channels. The interaction of Mn 2+ , Zn 2+ , Pb 2+ and La 3+ on [ 3 H]NTP binding was studied in 3 brain areas particularly rich in [ 3 H]NTP binding sites. Differences were observed in the brain regional distribution of [ 3 H]NTP binding as well as in their sensitivity to the metal ions Pb, Mn and Zn. The binding data suggest that neuronal Ca 2+ channels in different brain areas display distinct sensitivity to selected divalent cations. (Auth.)

  9. Pictorial binding: endeavor to classify

    Directory of Open Access Journals (Sweden)

    Zinchenko S.

    2015-01-01

    Full Text Available The article is devoted to the classification of bindings of the 1-19th centuries with a unique and untypical book binding decoration technique (encaustic, tempera and oil paintings. Analysis of design features, materials and techniques of art decoration made it possible to identify them as a separate type - pictorial bindings and divide them into four groups. The first group consists of Coptic bindings, decorated with icon-painting images in encaustic technique. The second group is made up of leather Western bindings of the 13-14th centuries, which have the decoration and technique of ornamentation close to iconography. The third group involves parchment bindings, ornamentation technique of which is closer to the miniature. The last group comprises bindings of East Slavic origin of the 15-19th centuries, decorated with icon-painting pictures made in the technique of tempera or oil painting. The proposed classification requires further basic research as several specific kinds of bindings have not yet been investigated

  10. Thermodynamic and spectroscopic investigations of TMPyP4 association with guanine- and cytosine-rich DNA and RNA repeats of C9orf72.

    Science.gov (United States)

    Alniss, Hasan; Zamiri, Bita; Khalaj, Melisa; Pearson, Christopher E; Macgregor, Robert B

    2018-01-22

    An expansion of the hexanucleotide repeat (GGGGCC)n·(GGCCCC)n in the C9orf72 promoter has been shown to be the cause of Amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). The C9orf72 repeat can form four-stranded structures; the cationic porphyrin (TMPyP4) binds and distorts these structures. Isothermal titration calorimetry (ITC), and circular dichroism (CD) were used to study the binding of TMPyP4 to the C-rich and G-rich DNA and RNA oligos containing the hexanucleotide repeat at pH 7.5 and 0.1 M K + . The CD spectra of G-rich DNA and RNA TMPyP4 complexes showed features of antiparallel and parallel G-quadruplexes, respectively. The shoulder at 260 nm in the CD spectrum becomes more intense upon formation of complexes between TMPyP4 and the C-rich DNA. The peak at 290 nm becomes more intense in the c-rich RNA molecules, suggesting induction of an i-motif structure. The ITC data showed that TMPyP4 binds at two independent sites for all DNA and RNA molecules. For DNA, the data are consistent with TMPyP4 stacking on the terminal tetrads and intercalation. For RNA, the thermodynamics of the two binding modes are consistent with groove binding and intercalation. In both cases, intercalation is the weaker binding mode. These findings are considered with respect to the structural differences of the folded DNA and RNA molecules and the energetics of the processes that drive site-specific recognition by TMPyP4; these data will be helpful in efforts to optimize the specificity and affinity of the binding of porphyrin-like molecules. Copyright © 2018 Elsevier Inc. All rights reserved.

  11. Experiments with neutron-rich isomeric beams

    International Nuclear Information System (INIS)

    Rykaczewski, K.; Lewitowicz, M.; Pfuetzner, M.

    1998-01-01

    A review of experimental results obtained on microsecond-isomeric states in neutron-rich nuclei produced in fragmentation reactions and studied with SISSI-Alpha-LISE3 spectrometer system at GANIL Caen is given. The perspectives of experiments based on secondary reactions with isomeric beams are presented

  12. Origin of the latitudinal richness gradient

    DEFF Research Database (Denmark)

    Engemann, Kristine; Sandel, Brody Steven; Enquist, Brian J.

    2015-01-01

    and combined with the BIEN mega phylogeny of >80,000 species. We calculated the Phylogenetic Diversity Index (PDI) and Net Relatedness Index (NRI) for each cell in a 100×100 km grid using a new computationally efficient algorithm. Species richness patterns were compared to patterns of PDI and NRI. We found...

  13. Proximity focusing RICH with TOF capabilities

    International Nuclear Information System (INIS)

    Korpar, S.; Adachi, I.; Fujita, K.; Fukushima, T.; Gorisek, A.; Hayashi, D.; Iijima, T.; Ikado, T.; Ishikawa, T.; Kawai, H.; Kozakai, Y.; Krizan, P.; Kuratani, A.; Mazuka, Y.; Nakagawa, T.; Nishida, S.; Ogawa, S.; Pestotnik, R.; Seki, T.; Sumiyoshi, T.; Tabata, M.; Unno, Y.

    2007-01-01

    A proximity focusing RICH counter with a multi-channel micro-channel plate (MCP) PMT was tested as a time-of-flight counter. Cherenkov photons emitted in the radiator medium as well as in the entrance window of the PMT were used for the time-of-flight measurement, and an excellent performance of the counter could be demonstrated

  14. Power Divider for Waveforms Rich in Harmonics

    Science.gov (United States)

    Sims, William Herbert, III

    2005-01-01

    A method for dividing the power of an electronic signal rich in harmonics involves the use of an improved divider topology. A divider designed with this topology could be used, for example, to propagate a square-wave signal in an amplifier designed with a push-pull configuration to enable the generation of more power than could be generated in another configuration.

  15. Leveraging data rich environments using marketing analytics

    NARCIS (Netherlands)

    Holtrop, Niels

    2017-01-01

    With the onset of what is popularly known as “big data”, increased attention is being paid to creating value from these data rich environments. Within the field of marketing, the analysis of customer and market data supported by models is known as marketing analytics. The goal of these analyses is

  16. PREPARATION OF NOVOLACS USING PHENOLIC RICH ...

    African Journals Online (AJOL)

    Preferred Customer

    ABSTRACT. The possibility of using phenolic rich components (water insoluble fraction) from biomass pyrolysis oil as partial substitute of phenol in synthesis of high-ortho phenolic novolac under the catalyst of. HCl/Zn(AC)2 has been proved using differential scanning calorimetry (DSC) and Fourier transformed infrared.

  17. Metal binding by food components

    DEFF Research Database (Denmark)

    Tang, Ning

    For calcium binding: Electrochemical method (calcium ion selective electrode) combined with quantum mechanical calculations (density functional theory) were used to investigate the calcium binding affinity of the amino acids and small glycine peptides. The effects of the ionic strength and p......, synergistic effect in calcium binding was found for the small glycine peptide rather than amino acids mixtures with the enhanced driving force up to -6 kJ/mol. Such study provides useful information for the future development of calcium supplements. For zinc binding: Isothermal titration calorimetry...... titration calorimetry and quantum mechanical calculations. This is due to the zinc binding affinity of the relatively softer ligands (investigated food components) will become much stronger than citrate or phytate when they present together in aqueous solution. This mechanism indicates these food components...

  18. Multispectroscopic studies of paeoniflorin binding to calf thymus DNA in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Guowen, E-mail: gwzhang@ncu.edu.cn [State Key Laboratory of Food Science and Technology, Nanchang University, No. 235, Nanjing East Road, Nanchang, Jiangxi 330047 (China); Fu, Peng; Pan, Junhui [State Key Laboratory of Food Science and Technology, Nanchang University, No. 235, Nanjing East Road, Nanchang, Jiangxi 330047 (China)

    2013-02-15

    The mechanism of paeoniflorin binding to calf thymus DNA in physiological buffer (pH 7.4) was investigated by multispectroscopic methods including UV-vis absorption, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy, coupled with viscosity measurements and DNA melting techniques. The results suggested that paeoniflorin molecules could bind to DNA via groove binding mode as evidenced by no significant change in iodide quenching effect, increase in single-stranded DNA (ssDNA) quenching effect, and almost unchanged relative viscosity and melting temperature of DNA. The observed changes in CD signals revealed that DNA remains in the B-conformation. Further, the displacement experiments with Hoechst 33258 probe and the results of FT-IR spectra indicated that paeoniflorin mainly binds in the region of rich A-T base pairs of DNA. The thermodynamic parameters, enthalpy change ({Delta}H Degree-Sign ) and entropy change ({Delta}S Degree-Sign ) were calculated to be -30.09{+-}0.18 kJ mol{sup -1} and -14.07{+-}0.61 J mol{sup -1} K{sup -1} by the van't Hoff equation, suggesting that hydrogen bond and van der Waals forces play a predominant role in the binding of paeoniflorin to DNA. - Highlights: Black-Right-Pointing-Pointer The binding mode of paeoniflorin to calf thymus DNA is the minor groove binding. Black-Right-Pointing-Pointer Paeoniflorin mainly binds in the region of rich A-T base pairs of DNA. Black-Right-Pointing-Pointer The binding does not alter the native B-conformation of DNA. Black-Right-Pointing-Pointer The binding is driven mainly by hydrogen bonds and van der Waals forces.

  19. Localization of tachykinin binding sites (NK1, NK2, NK3 ligands) in the rat brain

    Energy Technology Data Exchange (ETDEWEB)

    Saffroy, M.; Beaujouan, J.C.; Torrens, Y.; Besseyre, J.; Bergstroem, L.G.; Glowinski, J.

    1988-03-01

    A comparative autoradiographic analysis of the distribution of tachykinin binding sites was made on brain serial sections using several ligands. (1) /sup 3/H-SP, /sup 125/I-BHSP and /sup 3/H-physalaemin labeled identical binding sites (NK1 type). (2) /sup 3/H-NKB, /sup 125/I-BHE and /sup 3/H-eledoisin also labeled identical sites (NK3 type). (3) /sup 125/I-BHNKA preferentially labeled NK3 binding sites, the distribution of /sup 125/I-BHNKA binding sites being identical to that of /sup 3/H-NKB or /sup 125/I-BHE binding sites. (4) The distributions of /sup 3/H-SP and /sup 3/H-NKB binding sites were markedly different. (5) A very low density of labeling was found with /sup 3/H-NKA or /sup 125/I-NKA, and these binding sites were distributed only in areas rich in either /sup 3/H-SP or /sup 3/H-NKB binding sites. (6) Particular efforts were made to look for the presence of tachykinin binding sites in the substantia nigra, since this structure is particularly rich in SP and NKA and contains functional tachykinin receptors of the NK1 and NK2 types as suggested by physiological studies. Confirming previous reports, low or very low labeling was observed in the substantia nigra with /sup 3/H-SP or /sup 125/I-BHSP and /sup 3/H-NKB or /sup 125/I-BHE. Similar results were found with /sup 3/H-NKA, /sup 125/I-NKA or /sup 125/I-BHNKA. In conclusion, our data do not provide evidence yet for the existence of NK2 binding sites in the rat brain.

  20. A peek into tropomyosin binding and unfolding on the actin filament.

    Directory of Open Access Journals (Sweden)

    Abhishek Singh

    Full Text Available BACKGROUND: Tropomyosin is a prototypical coiled coil along its length with subtle variations in structure that allow interactions with actin and other proteins. Actin binding globally stabilizes tropomyosin. Tropomyosin-actin interaction occurs periodically along the length of tropomyosin. However, it is not well understood how tropomyosin binds actin. PRINCIPAL FINDINGS: Tropomyosin's periodic binding sites make differential contributions to two components of actin binding, cooperativity and affinity, and can be classified as primary or secondary sites. We show through mutagenesis and analysis of recombinant striated muscle alpha-tropomyosins that primary actin binding sites have a destabilizing coiled-coil interface, typically alanine-rich, embedded within a non-interface recognition sequence. Introduction of an Ala cluster in place of the native, more stable interface in period 2 and/or period 3 sites (of seven increased the affinity or cooperativity of actin binding, analysed by cosedimentation and differential scanning calorimetry. Replacement of period 3 with period 5 sequence, an unstable region of known importance for cooperative actin binding, increased the cooperativity of binding. Introduction of the fluorescent probe, pyrene, near the mutation sites in periods 2 and 3 reported local instability, stabilization by actin binding, and local unfolding before or coincident with dissociation from actin (measured using light scattering, and chain dissociation (analyzed using circular dichroism. CONCLUSIONS: This, and previous work, suggests that regions of tropomyosin involved in binding actin have non-interface residues specific for interaction with actin and an unstable interface that is locally stabilized upon binding. The destabilized interface allows residues on the coiled-coil surface to obtain an optimal conformation for interaction with actin by increasing the number of local substates that the side chains can sample. We suggest

  1. Screening nitrogen-rich bases and oxygen-rich acids by theoretical calculations for forming highly stable salts.

    Science.gov (United States)

    Zhang, Xueli; Gong, Xuedong

    2014-08-04

    Nitrogen-rich heterocyclic bases and oxygen-rich acids react to produce energetic salts with potential application in the field of composite explosives and propellants. In this study, 12 salts formed by the reaction of the bases 4-amino-1,2,4-trizole (A), 1-amino-1,2,4-trizole (B), and 5-aminotetrazole (C), upon reaction with the acids HNO3 (I), HN(NO2 )2 (II), HClO4 (III), and HC(NO2 )3 (IV), are studied using DFT calculations at the B97-D/6-311++G** level of theory. For the reactions with the same base, those of HClO4 are the most exothermic and spontaneous, and the most negative Δr Gm in the formation reaction also corresponds to the highest decomposition temperature of the resulting salt. The ability of anions and cations to form hydrogen bonds decreases in the order NO3 (-) >N(NO2 )2 (-) >ClO4 (-) >C(NO2 )3 (-) , and C(+) >B(+) >A(+) . In particular, those different cation abilities are mainly due to their different conformations and charge distributions. For the salts with the same anion, the larger total hydrogen-bond energy (EH,tot ) leads to a higher melting point. The order of cations and anions on charge transfer (q), second-order perturbation energy (E2 ), and binding energy (Eb ) are the same to that of EH,tot , so larger q leads to larger E2 , Eb , and EH,tot . All salts have similar frontier orbitals distributions, and their HOMO and LUMO are derived from the anion and the cation, respectively. The molecular orbital shapes are kept as the ions form a salt. To produce energetic salts, 5-aminotetrazole and HClO4 are the preferred base and acid, respectively. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Calcium-binding proteins from human platelets

    International Nuclear Information System (INIS)

    Gogstad, G.O.; Krutnes, M.B.; Solum, N.O.

    1983-01-01

    Calcium-binding platelet proteins were examined by crossed immunoelectrophoresis of solubilized platelets against antibodies to whole platelets followed by incubation of the immunoplates with 45 Ca 2 + and autoradiography. When the immunoplates had been pretreated with EDTA at pH 9.0 in order to remove divalent cations, three immunoprecipitates were markedly labelled with 45 Ca 2 + . These corresponded to the glycoprotein IIb-IIIa complex, glycoprotein Ia and a presently unidentified antigen termed G18. These antigens were membrane-bound and surface-oriented. When an excess of EDTA was introduced in the incubation media the results revealed that the glycoprotein IIb-IIIa complex and antigen G18, but not glycoprotein Ia, contained sites with a stronger affinity for calcium than has EDTA at pH 7.4 Immunoprecipitates of the separate glycoproteins IIb and IIIa both bound calcium in the same manner as the glycoprotein IIb-IIIa complex. As another approach, platelet-rich plasma was incubated with 45 Ca 2 + prior to crossed immunoelectrophoresis of the solubilized platelets. A single immunoprecipitate was wekly labelled. This did not correspond to any of the immunoprecipitates which were visible after staining with Coomassie blue. The labelling of this antigen was markedly increased when the platelt-rich plasma had been preincubated with EDTA and in this case a weak labelling of the glycoprotein IIB-IIIa precipitate also became apparent. No increased incorporation of calcium occured in any of these immunoprecipitates when the platelets were aggregated with ADP in the presence of 45 Ca 2 + . (orig.)

  3. Pro DNS and BIND 10

    CERN Document Server

    Aitchison, Ron

    2011-01-01

    Pro DNS and BIND 10 guides you through the challenging array of features surrounding DNS with a special focus on the latest release of BIND, the world's most popular DNS implementation. This book unravels the mysteries of DNS, offering insight into origins, evolution, and key concepts like domain names and zone files. This book focuses on running DNS systems based on BIND 10, the first stable release that includes support for the latest DNSSEC standards. Whether you administer a DNS system, are thinking about running one, or you simply want to understand the DNS system, then this book for you.

  4. Protein binding of psychotropic agents

    International Nuclear Information System (INIS)

    Hassan, H.A.

    1990-01-01

    Based upon fluorescence measurements, protein binding of some psychotropic agents (chlorpromazine, promethazine, and trifluoperazine) to human IgG and HSA was studied in aqueous cacodylate buffer, PH7. The interaction parameters determined from emission quenching of the proteins. The interaction parameters determined include the equilibrium constant (K), calculated from equations derived by Borazan and coworkers, the number of binding sites (n) available to the monomer molecules on a single protein molecule. The results revealed a high level of affinity, as reflected by high values of K, and the existence of specific binding sites, since a limited number of n values are obtained. 39 tabs.; 37 figs.; 83 refs

  5. The HADES-RICH upgrade using Hamamatsu H12700 MAPMTs with DiRICH FEE + Readout

    Science.gov (United States)

    Patel, V.; Traxler, M.

    2018-03-01

    The High Acceptance Di-Electron Spectrometer (HADES) is operational since the year 2000 and uses a hadron blind RICH detector for electron identification. The RICH photon detector is currently replaced by Hamamatsu H12700 MAPMTs with a readout system based on the DiRICH front-end module. The electronic readout chain is being developed as a joint effort of the HADES-, CBM- and PANDA collaborations and will also be used in the photon detectors for the upcoming Compressed Baryonic Matter (CBM) and PANDA experiments at FAIR . This article gives a brief overview on the photomultipliers and their quality assurance test measurements, as well as first measurements of the new DiRICH front-end module in final configurations.

  6. Heavy metals binding properties of esterified lemon

    International Nuclear Information System (INIS)

    Arslanoglu, Hasan; Altundogan, Hamdi Soner; Tumen, Fikret

    2009-01-01

    Sorption of Cd 2+ , Cr 3+ , Cu 2+ , Ni 2+ , Pb 2+ and Zn 2+ onto a carboxyl groups-rich material prepared from lemon was investigated in batch systems. The results revealed that the sorption is highly pH dependent. Sorption kinetic data indicated that the equilibrium was achieved in the range of 30-240 min for different metal ions and sorption kinetics followed the pseudo-second-order model for all metals studied. Relative sorption rate of various metal cations was found to be in the general order of Ni 2+ > Cd 2+ > Cu 2+ > Pb 2+ > Zn 2+ > Cr 3+ . The binding characteristics of the sorbent for heavy metal ions were analyzed under various conditions and isotherm data was accurately fitted to the Langmuir equation. The metal binding capacity order calculated from Langmuir isotherm was Pb 2+ > Cu 2+ > Ni 2+ > Cd 2+ > Zn 2+ > Cr 3+ . The mean free energy of metal sorption process calculated from Dubinin-Radushkevich parameter and the Polanyi potential was found to be in the range of 8-11 kJ mol -1 for the metals studied showing that the main mechanism governing the sorption process seems to be ion exchange. The basic thermodynamic parameters of metals ion sorption process were calculated by using the Langmuir constants obtained from equilibration study. The ΔG o and ΔH o values for metals ion sorption on the lemon sorbent showed the process to be spontaneous and exothermic in nature. Relatively low ΔH o values revealed that physical adsorption significantly contributed to the mechanism.

  7. Heavy metals binding properties of esterified lemon.

    Science.gov (United States)

    Arslanoglu, Hasan; Altundogan, Hamdi Soner; Tumen, Fikret

    2009-05-30

    Sorption of Cd(2+), Cr(3+), Cu(2+), Ni(2+), Pb(2+) and Zn(2+) onto a carboxyl groups-rich material prepared from lemon was investigated in batch systems. The results revealed that the sorption is highly pH dependent. Sorption kinetic data indicated that the equilibrium was achieved in the range of 30-240 min for different metal ions and sorption kinetics followed the pseudo-second-order model for all metals studied. Relative sorption rate of various metal cations was found to be in the general order of Ni(2+)>Cd(2+)>Cu(2+)>Pb(2+)>Zn(2+)>Cr(3+). The binding characteristics of the sorbent for heavy metal ions were analyzed under various conditions and isotherm data was accurately fitted to the Langmuir equation. The metal binding capacity order calculated from Langmuir isotherm was Pb(2+)>Cu(2+)>Ni(2+)>Cd(2+)>Zn(2+)>Cr(3+). The mean free energy of metal sorption process calculated from Dubinin-Radushkevich parameter and the Polanyi potential was found to be in the range of 8-11 kJ mol(-1) for the metals studied showing that the main mechanism governing the sorption process seems to be ion exchange. The basic thermodynamic parameters of metals ion sorption process were calculated by using the Langmuir constants obtained from equilibration study. The DeltaG degrees and DeltaH degrees values for metals ion sorption on the lemon sorbent showed the process to be spontaneous and exothermic in nature. Relatively low DeltaH degrees values revealed that physical adsorption significantly contributed to the mechanism.

  8. Heavy metals binding properties of esterified lemon

    Energy Technology Data Exchange (ETDEWEB)

    Arslanoglu, Hasan; Altundogan, Hamdi Soner [Department of Chemical Engineering, Firat University, 23279 Elazig (Turkey); Tumen, Fikret, E-mail: ftumen@firat.edu.tr [Department of Chemical Engineering, Firat University, 23279 Elazig (Turkey)

    2009-05-30

    Sorption of Cd{sup 2+}, Cr{sup 3+}, Cu{sup 2+}, Ni{sup 2+}, Pb{sup 2+} and Zn{sup 2+} onto a carboxyl groups-rich material prepared from lemon was investigated in batch systems. The results revealed that the sorption is highly pH dependent. Sorption kinetic data indicated that the equilibrium was achieved in the range of 30-240 min for different metal ions and sorption kinetics followed the pseudo-second-order model for all metals studied. Relative sorption rate of various metal cations was found to be in the general order of Ni{sup 2+} > Cd{sup 2+} > Cu{sup 2+} > Pb{sup 2+} > Zn{sup 2+} > Cr{sup 3+}. The binding characteristics of the sorbent for heavy metal ions were analyzed under various conditions and isotherm data was accurately fitted to the Langmuir equation. The metal binding capacity order calculated from Langmuir isotherm was Pb{sup 2+} > Cu{sup 2+} > Ni{sup 2+} > Cd{sup 2+} > Zn{sup 2+} > Cr{sup 3+}. The mean free energy of metal sorption process calculated from Dubinin-Radushkevich parameter and the Polanyi potential was found to be in the range of 8-11 kJ mol{sup -1} for the metals studied showing that the main mechanism governing the sorption process seems to be ion exchange. The basic thermodynamic parameters of metals ion sorption process were calculated by using the Langmuir constants obtained from equilibration study. The {Delta}G{sup o} and {Delta}H{sup o} values for metals ion sorption on the lemon sorbent showed the process to be spontaneous and exothermic in nature. Relatively low {Delta}H{sup o} values revealed that physical adsorption significantly contributed to the mechanism.

  9. Chromatin immunoprecipitation to analyze DNA binding sites of HMGA2.

    Directory of Open Access Journals (Sweden)

    Nina Winter

    Full Text Available BACKGROUND: HMGA2 is an architectonic transcription factor abundantly expressed during embryonic and fetal development and it is associated with the progression of malignant tumors. The protein harbours three basically charged DNA binding domains and an acidic protein binding C-terminal domain. DNA binding induces changes of DNA conformation and hence results in global overall change of gene expression patterns. Recently, using a PCR-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment procedure two consensus sequences for HMGA2 binding have been identified. METHODOLOGY/PRINCIPAL FINDINGS: In this investigation chromatin immunoprecipitation (ChIP experiments and bioinformatic methods were used to analyze if these binding sequences can be verified on chromatin of living cells as well. CONCLUSION: After quantification of HMGA2 protein in different cell lines the colon cancer derived cell line HCT116 was chosen for further ChIP experiments because of its 3.4-fold higher HMGA2 protein level. 49 DNA fragments were obtained by ChIP. These fragments containing HMGA2 binding sites have been analyzed for their AT-content, location in the human genome and similarities to sequences generated by a SELEX study. The sequences show a significantly higher AT-content than the average of the human genome. The artificially generated SELEX sequences and short BLAST alignments (11 and 12 bp of the ChIP fragments from living cells show similarities in their organization. The flanking regions are AT-rich, whereas a lower conservation is present in the center of the sequences.

  10. Nucleic acid binding and other biomedical properties of artificial oligolysines

    Directory of Open Access Journals (Sweden)

    Roviello GN

    2016-11-01

    Full Text Available Giovanni N Roviello,1 Caterina Vicidomini,1 Vincenzo Costanzo,1 Valentina Roviello2 1CNR Istituto di Biostrutture e Bioimmagini, Via Mezzocannone site and Headquarters, 2Centro Regionale di Competenza (CRdC Tecnologie, Via Nuova Agnano, Napoli, Italy Abstract: In the present study, we report the interaction of an artificial oligolysine (referred to as AOL realized in our laboratory with targets of biomedical importance. These included polyinosinic acid (poly rI and its complex with polycytidylic acid (poly I:C, RNAs with well-known interferon-inducing ability, and double-stranded (ds DNA. The ability of the peptide to bind both single-stranded poly rI and ds poly I:C RNAs emerged from our circular dichroism (CD and ultraviolet (UV studies. In addition, we found that AOL forms complexes with dsDNA, as shown by spectroscopic binding assays and UV thermal denaturation experiments. These findings are encouraging for the possible use of AOL in biomedicine for nucleic acid targeting and oligonucleotide condensation, with the latter being a key step preceding their clinical application. Moreover, we tested the ability of AOL to bind to proteins, using serum albumin as a model protein. We demonstrated the oligolysine–protein binding by CD experiments which suggested that AOL, positively charged under physiological conditions, binds to the protein regions rich in anionic residues. Finally, the morphology characterization of the solid oligolysine, performed by scanning electron microscopy, showed different crystal forms including cubic-shaped crystals confirming the high purity of AOL. Keywords: nucleic acid binding, polyinosinic acid, double-stranded nucleic acids, oligolysine, circular dichroism

  11. Development of the RICH detectors in LHCb

    CERN Document Server

    Easo, S

    2003-01-01

    For particle identification, LHCb plans to use two RICH detectors, one covering the charged particle momentum range 1-65 GeV/c using aerogel and C//4F//1//0 radiators and the other covering up to 150 Ge V/c using CF//4 radiator. Hybrid photo diodes (HPD) with 80 mm photocathode diameter are being developed to detect the Cherenkov photons in the wavelength range 200-600 nm. The HPDs encapsulate silicon pixel anodes bump bonded to binary readout chips processed using 0.25 mum CMOS technology. Results obtained with prototype radiators and HPDs in test beams will be presented and the design and development of these RICH detectors will be reviewed.

  12. RICH upgrade: Current status and future perspectives

    CERN Document Server

    Pistone, A

    2016-01-01

    The LHCb experiment is dedicated to precision measurements of CP violation and rare decays of B hadrons at the Large Hadron Collider (LHC) at CERN (Geneva). The second long shutdown of the LHC is currently scheduled to begin in 2018. During this period the LHCb experiment with all its sub-detectors will be upgraded in order to run at an instantaneous luminosity of 2×10$^{33}$ cm$^{−2}$s$^{−1}$ and to read out data at a rate of 40MHz into a flexible software-based trigger. The Ring Imaging CHerenkov (RICH) system will require new photon detectors and modifications of the optics of the upstream detector. Tests of the prototype of the smallest constituent of the new RICH system have been performed during testbeam sessions at the Test Beam Facility SPS North Area (CERN) in Autumn 2014.

  13. The RICH detector of the CBM experiment

    Science.gov (United States)

    Adamczewski-Musch, J.; Akishin, P.; Becker, K.-H.; Belogurov, S.; Bendarouach, J.; Boldyreva, N.; Deveaux, C.; Dobyrn, V.; Dürr, M.; Eschke, J.; Förtsch, J.; Heep, J.; Höhne, C.; Kampert, K.-H.; Kochenda, L.; Kopfer, J.; Kravtsov, P.; Kres, I.; Lebedev, S.; Lebedeva, E.; Leonova, E.; Linev, S.; Mahmoud, T.; Michel, J.; Miftakhov, N.; Niebur, W.; Ovcharenko, E.; Patel, V.; Pauly, C.; Pfeifer, D.; Querchfeld, S.; Rautenberg, J.; Reinecke, S.; Riabov, Y.; Roshchin, E.; Samsonov, V.; Schetinin, V.; Tarasenkova, O.; Traxler, M.; Ugur, C.; Vznuzdaev, E.; Vznuzdaev, M.

    2017-12-01

    The CBM-RICH detector is designed to identify electrons with momenta up to 8 GeV/c and high purity as this is essential for the CBM physics program. The detector consist of a CO2-gaseous radiator, a spherical mirror system, and Multi-Anode PhotoMultiplier Tubes (MAPMT) of type H12700 from Hamamatsu as photon detectors. The detector concept was verified through R&D studies and a laterally scaled prototype. The results were summarized in a TDR, in which open issues were defined concerning the readout electronics, the shielding of the magnetic stray field in the MAPMT region, the radiation hardness of the MAPMT sensors, and the mechanical holding structure of the mirror system. In this article an overview is given on the CBM RICH development with focus on those open issues.

  14. Binding of Lysozyme to Spherical Poly(styrenesulfonate Gels

    Directory of Open Access Journals (Sweden)

    Martin Andersson

    2018-01-01

    Full Text Available Polyelectrolyte gels are useful as carriers of proteins and other biomacromolecules in, e.g., drug delivery. The rational design of such systems requires knowledge about how the binding and release are affected by electrostatic and hydrophobic interactions between the components. To this end we have investigated the uptake of lysozyme by weakly crosslinked spherical poly(styrenesulfonate (PSS microgels and macrogels by means of micromanipulator assisted light microscopy and small angle X-ray scattering (SAXS in an aqueous environment. The results show that the binding process is an order of magnitude slower than for cytochrome c and for lysozyme binding to sodium polyacrylate gels under the same conditions. This is attributed to the formation of very dense protein-rich shells in the outer layers of the microgels with low permeability to the protein. The shells in macrogels contain 60 wt % water and nearly charge stoichiometric amounts of lysozyme and PSS in the form of dense complexes of radius 8 nm comprising 30–60 lysozyme molecules. With support from kinetic modelling results we propose that the rate of protein binding and the relaxation rate of the microgel are controlled by the protein mass transport through the shell, which is strongly affected by hydrophobic and electrostatic interactions. The mechanism explains, in turn, an observed dependence of the diffusion rate on the apparent degree of crosslinking of the networks.

  15. Proton radioactivity from proton-rich nuclei

    International Nuclear Information System (INIS)

    Guzman, F.; Goncalves, M.; Tavares, O.A.P.; Duarte, S.B.; Garcia, F.; Rodriguez, O.

    1999-03-01

    Half-lives for proton emission from proton-rich nuclei have been calculated by using the effective liquid drop model of heavy-particle decay of nuclei. It is shown that this model is able to offer results or spontaneous proton-emission half-life-values in excellent agreement with the existing experimental data. Predictions of half-life-values for other possible proton-emission cases are present for null orbital angular momentum. (author)

  16. Sulfur rich microporous polymer enables rapid and efficient removal of mercury(II) from water.

    Science.gov (United States)

    Xu, Dan; Wu, Winston Duo; Qi, Hao-Jun; Yang, Rui-Xia; Deng, Wei-Qiao

    2018-04-01

    Design and synthesis of adsorbents for efficient decontamination of hazardous contaminants Hg 2+ from wastewater, based on a facile and economical strategy, is an attractive target. Here, a novel sulfur rich microporous polymer (sulfur content of 31.4 wt %) with high surface area as well as densely populated sulfur atom with fast accessibility was reported to remove mercury (II) from water. The as prepared polymer (SMP) exhibited high binding affinity, high adsorption capacities, rapid adsorption kinetics, and good recyclability for Hg 2+ . The adsorption capacity of SMP was 595.2 mg g -1 . Furthermore, SMP could reduce trace concentrations of Hg 2+ from 200 p. p. b. to a level below drinking water standards (2 p. p. b.) within 3 min. This work allows large-scale production of sulfur rich porous materials for the practical application in water treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. The COMPASS RICH-1 detector upgrade

    CERN Document Server

    Abbon, P; Angerer, H; Apollonio, M; Birsa, R; Bordalo, P; Bradamante, F; Bressan, A; Busso, L; Chiosso, M; Ciliberti, P; Colantoni, M L; Costa, S; Dalla Torre, S; Dafni, T; Delagnes, E; Deschamps, H; Díaz, V; Dibiase, N; Duic, V; Eyrich, W; Faso, D; Ferrero, A; Finger, M; Finger, M Jr; Fischer, H; Gerassimov, S; Giorgi, M; Gobbo, B; Hagemann, R; Von Harrach, D; Heinsius, F H; Joosten, R; Ketzer, B; Königsmann, K C; Kolosov, V N; Konorov, I; Kramer, Daniel; Kunne, F; Lehmann, A; Levorato, S; Maggiora, A; Magnon, A; Mann, A; Martin, A; Menon, G; Mutter, A; Nähle, O; Nerling, F; Neyret, D; Pagano, P; Panebianco, S; Panzieri, D; Paul, S; Pesaro, G; Polak, J; Rebourgeard, P; Robinet, F; Rocco, E; Schiavon, P; Schill, C; Schröder, W; Silva, L; Slunecka, M; Sozzi, F; Steiger, L; Sulc, M; Svec, M; Tessarotto, F; Teufel, A; Wollny, H

    2008-01-01

    The COMPASS experiment at CERN provides hadron identification in a wide momentum range employing a large size gaseous Ring Imaging CHerenkov detector (RICH). The presence of large uncorrelated background in the COMPASS environment was limiting the efficiency of COMPASS RICH-1 in the very forward regime. A major upgrade of RICH-1 required a new technique for Cherenkov photon detection at count rates of several 10$^{6}$/s per channel in the central detector part, and a read-out system allowing for trigger rates of up to 100 kHz. To cope with these requirements, the photon detectors of the central region have been replaced with a fast photon detection system described here, while, in the peripheral regions, the existing multi-wire proportional chambers with CsI photo-cathodes have been equipped with a new read-out system based on APV preamplifiers and flash ADC chips. The new system consists of multi-anode photomultiplier tubes (MAPMTs) coupled to individual fused silica lens telescopes, and fast read-out electr...

  18. SHBG (Sex Hormone Binding Globulin)

    Science.gov (United States)

    ... and Iron-binding Capacity (TIBC, UIBC) Trichomonas Testing Triglycerides Troponin Tryptase Tumor Markers Uric Acid Urinalysis Urine ... Syndrome CME. Medscape From Nature Clinical Practice Endocrinology & Metabolism [On-line information]. Available online at http://www. ...

  19. Role of the serine-rich surface glycoprotein Srr1 of Streptococcus agalactiae in the pathogenesis of infective endocarditis.

    Directory of Open Access Journals (Sweden)

    Ho Seong Seo

    Full Text Available The binding of bacteria to fibrinogen and platelets are important events in the pathogenesis of infective endocarditis. Srr1 is a serine-rich repeat glycoprotein of Streptococcus agalactiae that binds directly to the Aα chain of human fibrinogen. To assess the impact of Srr1 on the pathogenesis of endocarditis due to S. agalactiae, we first examined the binding of this organism to immobilized human platelets. Strains expressing Srr1 had significantly higher levels of binding to human platelets in vitro, as compared with isogenic Δsrr1 mutants. In addition, platelet binding was inhibited by pretreatment with anti-fibrinogen IgG or purified Srr1 binding region. To assess the contribution of Srr1 to pathogenicity, we compared the relative virulence of S. agalactiae NCTC 10/84 strain and its Δsrr1 mutant in a rat model of endocarditis, where animals were co-infected with the WT and the mutant strains at a 1:1 ratio. At 72 h post-infection, bacterial densities (CFU/g of the WT strain within vegetations, kidneys, and spleens were significantly higher, as compared with the Δsrr1 mutant. These results indicate that Srr1 contributes to the pathogenesis of endocarditis due to S. agalactiae, at least in part through its role in fibrinogen-mediated platelet binding.

  20. Asymmetric cation-binding catalysis

    DEFF Research Database (Denmark)

    Oliveira, Maria Teresa; Lee, Jiwoong

    2017-01-01

    solvents, thus increasing their applicability in synthesis. The expansion of this concept to chiral polyethers led to the emergence of asymmetric cation-binding catalysis, where chiral counter anions are generated from metal salts, particularly using BINOL-based polyethers. Alkali metal salts, namely KF...... and KCN, are selectively bound to the catalyst, providing exceptionally high enantioselectivities for kinetic resolutions, elimination reactions (fluoride base), and Strecker synthesis (cyanide nucleophile). Asymmetric cation-binding catalysis was recently expanded to silicon-based reagents, enabling...

  1. LRRK2 kinase activity is dependent on LRRK2 GTP binding capacity but independent of LRRK2 GTP binding.

    Directory of Open Access Journals (Sweden)

    Jean-Marc Taymans

    Full Text Available Leucine rich repeat kinase 2 (LRRK2 is a Parkinson's disease (PD gene that encodes a large multidomain protein including both a GTPase and a kinase domain. GTPases often regulate kinases within signal transduction cascades, where GTPases act as molecular switches cycling between a GTP bound "on" state and a GDP bound "off" state. It has been proposed that LRRK2 kinase activity may be increased upon GTP binding at the LRRK2 Ras of complex proteins (ROC GTPase domain. Here we extensively test this hypothesis by measuring LRRK2 phosphorylation activity under influence of GDP, GTP or non-hydrolyzable GTP analogues GTPγS or GMPPCP. We show that autophosphorylation and lrrktide phosphorylation activity of recombinant LRRK2 protein is unaltered by guanine nucleotides, when co-incubated with LRRK2 during phosphorylation reactions. Also phosphorylation activity of LRRK2 is unchanged when the LRRK2 guanine nucleotide binding pocket is previously saturated with various nucleotides, in contrast to the greatly reduced activity measured for the guanine nucleotide binding site mutant T1348N. Interestingly, when nucleotides were incubated with cell lysates prior to purification of LRRK2, kinase activity was slightly enhanced by GTPγS or GMPPCP compared to GDP, pointing to an upstream guanine nucleotide binding protein that may activate LRRK2 in a GTP-dependent manner. Using metabolic labeling, we also found that cellular phosphorylation of LRRK2 was not significantly modulated by nucleotides, although labeling is significantly reduced by guanine nucleotide binding site mutants. We conclude that while kinase activity of LRRK2 requires an intact ROC-GTPase domain, it is independent of GDP or GTP binding to ROC.

  2. Ginkgotides: Proline-Rich Hevein-Like Peptides from Gymnosperm Ginkgo biloba

    OpenAIRE

    Wong, Ka H.; Tan, Wei Liang; Serra, Aida; Xiao, Tianshu; Sze, Siu Kwan; Yang, Daiwen; Tam, James P.

    2016-01-01

    Hevein and hevein-like peptides belong to the family of chitin-binding cysteine-rich peptides. They are classified into three subfamilies, the prototypic 8C- and the 6C- and 10C-hevein-like peptides. Thus far, only five 8C-hevein-like peptides have been characterized from three angiosperms and none from gymnosperm. To determine their occurrence and distribution in the gymnosperm, Ginkgo biloba leaves were examined. Here, we report the discovery and characterization of eleven novel 8C-hevein-l...

  3. Determination of Disulfide Bond Connectivity of Cysteine-rich Peptide IpTx{sub a}

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Chul Won; Kim, Jim Il [Chonnam National Univ., Gwangju (Korea, Republic of); Sato, Kazuki [Fukuoka Women' s Univ., Fukuoka (Japan)

    2013-06-15

    Cysteine-rich peptides stabilized by intramolecular disulfide bonds have often been isolated from venoms of microbes, animals and plants. These peptides typically have much higher stability and improved biopharmaceutical properties compared to their linear counterparts. Therefore the correct disulfide bond formation of small proteins and peptides has been extensively studied for a better understanding of their folding mechanism and achieving efficient generation of the naturally occurring biologically active product. Imperatoxin A (IpTx{sub a}), a peptide toxin containing 6 cysteine residues, was isolated from the venom of scorpion Pandinus imperator, selectively binds the ryanodine receptors and activates Ca{sup 2+} release from sarcoplasmic reticulum (SR). IpTx{sub a} increases the binding of ryanodine to ryanodine receptors (RyRs) and encourages reconstituted single channel to induce subconductance states.

  4. Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport.

    Science.gov (United States)

    Falconi, Mattia; Oteri, Francesco; Di Palma, Francesco; Pandey, Saurabh; Battistoni, Andrea; Desideri, Alessandro

    2011-02-01

    Comparative homology modelling techniques have been used to model the protein ZnuA from Salmonella enterica serovar Typhimurium using the 3D structure of the homologous protein from Escherichia coli. These two-domain proteins bind one Zn(2+) atom, with high affinity, in the inter-domain cleft and possess a histidine-rich loop in the N-terminal domain. Alternative structures of the ZnuA histidine-rich loop, never resolved by the X-ray diffraction method, have been modelled. A model of the apo form, one with the histidine-rich loop deleted and two alternative structures with a second zinc ion bound to the histidine-rich loop, have been generated. In all the modelled proteins, investigated through molecular dynamics simulation, the histidine-rich loop is highly mobile and its fluctuations are correlated to the ligand stability observed in the zinc sites. Based on the plasticity of the histidine-rich loop and its significant effects on protein mobility a possible role in the capture and/or transfer of the zinc ions has been suggested.

  5. Principles for computational design of binding antibodies.

    Science.gov (United States)

    Baran, Dror; Pszolla, M Gabriele; Lapidoth, Gideon D; Norn, Christoffer; Dym, Orly; Unger, Tamar; Albeck, Shira; Tyka, Michael D; Fleishman, Sarel J

    2017-10-10

    Natural proteins must both fold into a stable conformation and exert their molecular function. To date, computational design has successfully produced stable and atomically accurate proteins by using so-called "ideal" folds rich in regular secondary structures and almost devoid of loops and destabilizing elements, such as cavities. Molecular function, such as binding and catalysis, however, often demands nonideal features, including large and irregular loops and buried polar interaction networks, which have remained challenging for fold design. Through five design/experiment cycles, we learned principles for designing stable and functional antibody variable fragments (Fvs). Specifically, we ( i ) used sequence-design constraints derived from antibody multiple-sequence alignments, and ( ii ) during backbone design, maintained stabilizing interactions observed in natural antibodies between the framework and loops of complementarity-determining regions (CDRs) 1 and 2. Designed Fvs bound their ligands with midnanomolar affinities and were as stable as natural antibodies, despite having >30 mutations from mammalian antibody germlines. Furthermore, crystallographic analysis demonstrated atomic accuracy throughout the framework and in four of six CDRs in one design and atomic accuracy in the entire Fv in another. The principles we learned are general, and can be implemented to design other nonideal folds, generating stable, specific, and precise antibodies and enzymes.

  6. Salivary proline-rich protein may reduce tannin-iron chelation: a systematic narrative review.

    Science.gov (United States)

    Delimont, Nicole M; Rosenkranz, Sara K; Haub, Mark D; Lindshield, Brian L

    2017-01-01

    Tannins are often cited for antinutritional effects, including chelation of non-heme iron. Despite this, studies exploring non-heme iron bioavailability inhibition with long-term consumption have reported mixed results. Salivary proline-rich proteins (PRPs) may mediate tannin-antinutritional effects on non-heme iron bioavailability. To review evidence regarding biochemical binding mechanisms and affinity states between PRPs and tannins, as well as effects of PRPs on non-heme iron bioavailability with tannin consumption in vivo. Narrative systematic review and meta-analysis. Common themes in biochemical modeling and affinity studies were collated for summary and synthesis; data were extracted from in vivo experiments for meta-analysis. Thirty-two studies were included in analysis. Common themes that positively influenced tannin-PRP binding included specificity of tannin-PRP binding, PRP and tannin stereochemistry. Hydrolyzable tannins have different affinities than condensed tannins when binding to PRPs. In vivo, hepatic iron stores and non-heme iron absorption are not significantly affected by tannin consumption ( d  = -0.64-1.84; -2.7-0.13 respectively), and PRP expression may increase non-heme iron bioavailability with tannin consumption. In vitro modeling suggests that tannins favor PRP binding over iron chelation throughout digestion. Hydrolyzable tannins are not representative of tannin impact on non-heme iron bioavailability in food tannins because of their unique structural properties and PRP affinities. With tannin consumption, PRP production is increased, and may be an initial line of defense against tannin-non-heme iron chelation in vivo . More research is needed to compare competitive binding of tannin-PRP to tannin-non-heme iron complexes, and elucidate PRPs' role in adaption to non-heme iron bioavailability in vivo.

  7. The COMPASS RICH-1 detector upgrade

    International Nuclear Information System (INIS)

    Colantoni, M.L.; Panzieri, D.; Joosten, R.; Naehle, O.; Kolosov, V.N.; Eyrich, W.; Lehmann, A.; Schroeder, W.; Teufel, A.; Fischer, H.; Hagemann, R.; Heinsius, F.H.; Konigsmann, K.; Mutter, A.; Nerling, F.; Schill, C.; Wollny, H.; Kramer, D.; Polak, J.; Sulc, M.; Svec, M.; Silva, L.; Von Harrach, D.; Angerer, H.; Gerassimov, S.; Ketzer, B.; Konorov, I.; Mann, A.; Paul, S.; Finger, M.; Finger, M. Jr.; Slunecka, M.; Steiger, L.; Finger, M.; Finger, M. Jr.; Slunecka, M.; Steiger, L.; Abbon, P.; Dafni, T.; Delagnes, E.; Deschamps, H.; Kunne, F.; Magnon, A.; Neyret, D.; Panebianco, S.; Rebourgeard, P.; Robinet, F.; Alekseev, M.; Busso, L.; Chiosso, M.; Costa, S.; Dibiase, N.; Faso, D.; Ferrero, A.; Maggiora, A.; Alekseev, M.; Busso, L.; Chiosso, M.; Costa, S.; Dibiase, N.; Faso, D.; Ferrero, A.; Maggiora, A.; Apollonio, M.; Birsa, R.; Bradamante, F.; Bressan, A.; Ciliberti, P.; Torre, S. Dalla; Diaz, V.; Duic, V.; Giorgi, M.; Gobbo, B.; Levorato, S.; Martin, A.; Menon, G.; Pagano, P.; Pesaro, G.; Rocco, E.; Schiavon, P.; Sozzi, F.; Tessarotto, F.; Apollonio, M.; Birsa, R.; Bradamante, F.; Bressan, A.; Ciliberti, P.; Torre, S. Dalla; Diaz, V.; Duic, V.; Giorgi, M.; Gobbo, B.; Levorato, S.; Martin, A.; Menon, G.; Pagano, P.; Pesaro, G.; Rocco, E.; Schiavon, P.; Sozzi, F.; Tessarotto, F.

    2008-01-01

    The COMPASS experiment at CERN provides hadron identification in a wide momentum range employing a large size gaseous Ring Imaging Cherenkov detector (RICH). The presence of large uncorrelated background in the COMPASS environment was limiting the efficiency of COMPASS RICH-1 in the very forward regime. A major upgrade of RICH-1 required a new technique for Cherenkov photon detection at count rates of several 10 6 /s per channel in the central detector part, and a read-out system allowing for trigger rates of up to 100 kHz. To cope with these requirements, the photon detectors of the central region have been replaced with a fast photon detection system described here, while, in the peripheral regions, the existing multi-wire proportional chambers with CsI photo-cathodes have been equipped with a new read-out system based on APV preamplifiers and flash ADC chips. The new system consists of multi-anode photo-multiplier tubes (MAPMTs) coupled to individual fused silica lens telescopes, and fast read-out electronics based on the MAD4 amplifier-discriminator and the dead-time free F1 TDC chip. The project was completely designed and implemented in less than two years: The upgraded detector is in operation since the 2006 CERN SPS run. We present the photon detection design, constructive aspects and test studies to characterise the single photon response of the MAPMTs coupled to the read-out system as well as the detector performance based on the 2006 data. (authors)

  8. Reconstruction and calibration strategies for the LHCb RICH detector

    CERN Multimedia

    2006-01-01

    - LHCb particle identification - LHCb ring pattern recognition algorithm requirements - RICH pattern recognition - Cherenkov angle reconstruction online - Online PID - Hough transform - Metropolis- Hastings Markov chains - PID online: physics performances - Rich PID Callibration

  9. UStore: A Distributed Storage With Rich Semantics

    OpenAIRE

    Dinh, Anh; Wang, Ji; Wang, Sheng; Chen, Gang; Chin, Wei-Ngan; Lin, Qian; Ooi, Beng Chin; Ruan, Pingcheng; Tan, Kian-Lee; Xie, Zhongle; Zhang, Hao; Zhang, Meihui

    2017-01-01

    Today's storage systems expose abstractions which are either too low-level (e.g., key-value store, raw-block store) that they require developers to re-invent the wheels, or too high-level (e.g., relational databases, Git) that they lack generality to support many classes of applications. In this work, we propose and implement a general distributed data storage system, called UStore, which has rich semantics. UStore delivers three key properties, namely immutability, sharing and security, whic...

  10. Mars: A water-rich planet

    Science.gov (United States)

    Carr, Michael H.

    1987-01-01

    Good geomorphic evidence is presented for a planet that was once water rich, and that a lower limit on the amount of water available for a given Martian watershed may be estimated by assuming that the volume of material eroded was equal to the volume of water available. This estimate, coupled with high latitude water estimates of 50 to 100 m gives a global inventory of about 500 m total water in the subsurface. It was emphasized that this is a lower limit as considerable water may be bound in weathered debris and in primary minerals.

  11. A Water Rich Mars Surface Mission Scenario

    Science.gov (United States)

    Hoffman, Stephen J.; Andrews, Alida; Joosten, B. Kent; Watts, Kevin

    2017-01-01

    In an on-going effort to make human Mars missions more affordable and sustainable, NASA continues to investigate the innovative leveraging of technological advances in conjunction with the use of accessible Martian resources directly applicable to these missions. One of the resources with the broadest utility for human missions is water. Many past studies of human Mars missions assumed a complete lack of water derivable from local sources. However, recent advances in our understanding of the Martian environment provides growing evidence that Mars may be more "water rich" than previously suspected. This is based on data indicating that substantial quantities of water are mixed with surface regolith, bound in minerals located at or near the surface, and buried in large glacier-like forms. This paper describes an assessment of what could be done in a "water rich" human Mars mission scenario. A description of what is meant by "water rich" in this context is provided, including a quantification of the water that would be used by crews in this scenario. The different types of potential feedstock that could be used to generate these quantities of water are described, drawing on the most recently available assessments of data being returned from Mars. This paper specifically focuses on sources that appear to be buried quantities of water ice. (An assessment of other potential feedstock materials is documented in another paper.) Technologies and processes currently used in terrestrial Polar Regions are reviewed. One process with a long history of use on Earth and with potential application on Mars - the Rodriguez Well - is described and results of an analysis simulating the performance of such a well on Mars are presented. These results indicate that a Rodriguez Well capable of producing the quantities of water identified for a "water rich" human mission are within the capabilities assumed to be available on the Martian surface, as envisioned in other comparable Evolvable

  12. How countries become rich and reduce poverty

    DEFF Research Database (Denmark)

    Whitfield, Lindsay

    2012-01-01

    For the sake of less developed countries, it is time to adjust the discussion of international development assistance on poverty reduction. This article attempts to do so by reviewing new and old literature explaining why some countries are rich and others are poor. History has repeatedly shown...... that building up capabilities in manufacturing and improving the productivity of agriculture are the keys to wealth creation and long-term sustained poverty reduction. Furthermore, industrialisation and increased agricultural productivity are interdependent processes. Discussion about ending world poverty needs...

  13. ACHILLES TENDON RUPTURE AND PLATELET RICH PLASMA

    Directory of Open Access Journals (Sweden)

    Pietro Zedde

    2012-03-01

    Full Text Available Achilles tendon rupture is currently one of the most frequent injuries in athletes. Such rupture may be caused by a sudden dorsiflexion of the ankle, pushing off with the weight bearing forefoot while extending the knee or violent dorsiflexion of a plantar flexed foot. The treatment goal consists of restoring the normal tendon length and tension, as well as the function and strength of the gastrocnemius-soleus complex. The biological repair process can be enhanced in all stages of recovery with the use of PRP (Platelet Rich Plasma without any side effects.

  14. Un contenu riche et diversifié

    Directory of Open Access Journals (Sweden)

    Esther Cloutier

    2010-05-01

    Full Text Available Bonjour,Nous sommes très heureux de vous convier à lire ce nouveau numéro de notre revue. Son contenu est riche et diversifié. Plusieurs thèmes sont abordés : la santé et la sécurité du travail dans les petites entreprises, l’autoévaluation du stress au travail, une démarche ergonomique de transformation du contexte d’intervention, les risques routiers professionnels des conducteurs de travaux, un outil de gestion du sommeil, ainsi que les facteurs socioculturels et TMS. En premier lieu, un a...

  15. HTML5 Designing Rich Internet Applications

    CERN Document Server

    David, Matthew

    2010-01-01

    Implement the powerful new multimedia and interactive capabilities offered by HTML5, including style control tools, illustration tools, video, audio, and rich media solutions. Understand how HTML5 is changing the Web development game with this full-color, project-based treatment that shows you-not just tells you-what HTML5 can do for your Web sites. Reinforce your practical understanding of the new standard with demo applications and tutorials, so that execution is one short step away. The companion website, visualizetheweb.com, is packed full of extra information, online code libraries, and

  16. COMPASS mirror wall of RICH 1

    CERN Document Server

    Patrice Loïez

    2001-01-01

    The COMPASS experiment uses ring imaging Cherenkov (RICH) counters to identify particles produced in high-energy muon collisions, to better understand the spin structure of the nucleon. Charged particles moving faster than the speed of light in the medium through which they are travelling emit a cone of Cherenkov radiation in the direction of their motion. The light in this cone is reflected from these mirrors onto a photo detector so that the size of the cone can be measured, which gives the energy of the particle.

  17. Modeling a neutron rich nuclei source

    International Nuclear Information System (INIS)

    Mirea, M.; Bajeat, O.; Clapier, F.; Ibrahim, F.; Mueller, A.C.; Pauwels, N.; Proust, J.; Mirea, M.

    2000-01-01

    The deuteron break-up process in a suitable converter gives rise to intense neutron beams. A source of neutron rich nuclei based on the neutron induced fission can be realised using these beams. A theoretical optimization of such a facility as a function of the incident deuteron energy is reported. The model used to determine the fission products takes into account the excitation energy of the target nucleus and the evaporation of prompt neutrons. Results are presented in connection with a converter-target specific geometry. (authors)

  18. Structure of neutron-rich nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Nazarewicz, W. [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Physics]|[Oak Ridge National Lab., TN (United States). Physics Div.]|[Warsaw Univ. (Poland). Inst. of Theoretical Physics

    1997-11-01

    One of the frontiers of today`s nuclear science is the ``journey to the limits``: of atomic charge and nuclear mass, of neutron-to-proton ratio, and of angular momentum. The new data on exotic nuclei are expected to bring qualitatively new information about the fundamental properties of the nucleonic many-body system, the nature of the nuclear interaction, and nucleonic correlations at various energy-distance scales. In this talk, current developments in nuclear structure of neutron-rich nuclei are discussed from a theoretical perspective.

  19. Mars: a water-rich planet

    International Nuclear Information System (INIS)

    Carr, M.H.

    1987-01-01

    Good geomorphic evidence is presented for a planet that was once water rich, and that a lower limit on the amount of water available for a given Martian watershed may be estimated by assuming that the volume of material eroded was equal to the volume of water available. This estimate, coupled with high latitude water estimates of 50 to 100 m gives a global inventory of about 500 m total water in the subsurface. It was emphasized that this is a lower limit as considerable water may be bound in weathered debris and in primary minerals

  20. Development of a Rich Picture editor

    DEFF Research Database (Denmark)

    Valente, Andrea; Marchetti, Emanuela

    2010-01-01

    rich picture practice into software proved difficult, therefore, we decided to follow a user-centered approach: design and implement a prototype with basic functionalities, then run a usability test with a few students and professionals. The feedback collected in the test validated our hypothesis circa...... us in the design of the tool next version. At a more general level we realized that modern object-oriented development methodologies, such as agile methods, are informed by design, hence they sometimes assume design skills that programmers do not have or do not value....

  1. Structure of neutron-rich nuclei

    International Nuclear Information System (INIS)

    Nazarewicz, W.; Oak Ridge National Lab., TN; Warsaw Univ.

    1997-11-01

    One of the frontiers of today's nuclear science is the ''journey to the limits'': of atomic charge and nuclear mass, of neutron-to-proton ratio, and of angular momentum. The new data on exotic nuclei are expected to bring qualitatively new information about the fundamental properties of the nucleonic many-body system, the nature of the nuclear interaction, and nucleonic correlations at various energy-distance scales. In this talk, current developments in nuclear structure of neutron-rich nuclei are discussed from a theoretical perspective

  2. Water binding in legume seeds

    Science.gov (United States)

    Vertucci, C. W.; Leopold, A. C.

    1987-01-01

    The physical status of water in seeds has a pivotal role in determining the physiological reactions that can take place in the dry state. Using water sorption isotherms from cotyledon and axis tissue of five leguminous seeds, the strength of water binding and the numbers of binding sites have been estimated using van't Hoff analyses and the D'Arcy/Watt equation. These parameters of water sorption are calculated for each of the three regions of water binding and for a range of temperatures. Water sorption characteristics are reflective of the chemical composition of the biological materials as well as the temperature at which hydration takes place. Changes in the sorption characteristics with temperature and hydration level may suggest hydration-induced structural changes in cellular components.

  3. Domain walls collision in Fe-rich and Co-rich glass covered microwires

    Directory of Open Access Journals (Sweden)

    Gonzalez J.

    2013-01-01

    Full Text Available We report the results of the investigation of domain walls propagation in Fe-rich and Co-rich microwires performed using Sixtus-Tonks and magneto-optical Kerr effect techniques. It was found that under certain experimental conditions we are able to create the regime of the motion of two domain walls moving to opposite directions which terminates by the collision of the domain walls. Also the domain walls collision was visualized using magneto-optical Kerr effect microscope when the surface giant Barkhausen jump induced by circular magnetic field has been observed.

  4. Sports medicine applications of platelet rich plasma.

    Science.gov (United States)

    Mishra, Allan; Harmon, Kimberly; Woodall, James; Vieira, Amy

    2012-06-01

    Platelet rich plasma (PRP) is a powerful new biologic tool in sports medicine. PRP is a fraction of autologous whole blood containing and increased number of platelets and a wide variety of cytokines such as platelet derived growth factor (PDGF), vascular endothelial growth factor (VEGF) and transforming growth factor beta-1 (TGF-B1), fibroblast growth factor (FGF), Insulin-like growth factor-1 (IGF-1) among many others. Worldwide interest in this biologic technology has recently risen sharply. Basic science and preclinical data support the use of PRP for a variety of sports related injuries and disorders. The published, peer reviewed, human data on PRP is limited. Although the scientific evaluation of clinical efficacy is in the early stages, elite and recreational athletes already use PRP in the treatment of sports related injuries. Many questions remain to be answered regarding the use of PRP including optimal formulation, including of leukocytes, dosage and rehabilitation protocols. In this review, a classification for platelet rich plasma is proposed and the in-vitro, preclinical and human investigations of PRP applications in sports medicine will be reviewed as well as a discussion of rehabilitation after a PRP procedure. The regulation of PRP by the World Anti-Doping Agency will also be discussed. PRP is a promising technology in sports medicine; however, it will require more vigorous study in order to better understand how to apply it most effectively.

  5. Magnesium-rich Basalts on Mercury

    Science.gov (United States)

    Martel, L. M. V.

    2013-05-01

    X-ray and gamma-ray spectrometers on NASA's MESSENGER spacecraft are making key measurements regarding the composition and properties of the surface of Mercury, allowing researchers to more clearly decipher the planet's formation and geologic history. The origin of the igneous rocks in the crust of Mercury is the focus of recent research by Karen Stockstill-Cahill and Tim McCoy (National Museum of Natural History, Smithsonian Institution), along with Larry Nittler and Shoshana Weider (Carnegie Institution of Washington) and Steven Hauck II (Case Western Reserve University). Using the well-known MELTS computer code Stockstill-Cahill and coauthors worked with MESSENGER-derived and rock-analog compositions to constrain petrologic models of the lavas that erupted on the surface of Mercury. Rock analogs included a partial melt of the Indarch meteorite and a range of Mg-rich terrestrial rocks. Their work shows the lavas on Mercury are most similar to terrestrial magnesian basalt (with lowered FeO content). The implications of the modeling are that Mg-rich lavas came from high-temperature sources in Mercury's mantle and erupted at high temperature with exceptionally low viscosity into thinly bedded and laterally extensive flows, concepts open to further evaluation by laboratory experiments and by geologic mapping of Mercury's surface using MESSENGER's imaging system and laser altimeter to document flow features and dimensions.

  6. Conversion of glycerol to hydrogen rich gas.

    Science.gov (United States)

    Tran, Nguyen H; Kannangara, G S Kamali

    2013-12-21

    Presently there is a glut of glycerol as the by-product of biofuel production and it will grow as production increases. The conundrum is how we can consume this material and convert it into a more useful product. One potential route is to reform glycerol to hydrogen rich gas including synthesis gas (CO + H2) and hydrogen. However, there is recent literature on various reforming techniques which may have a bearing on the efficiency of such a process. Hence in this review reforming of glycerol at room temperature (normally photo-catalytic), catalysis at moderate and high temperature and a non-catalytic pyrolysis process are presented. The high temperature processes allow the generation of synthesis gas with the hydrogen to carbon monoxide ratios being suitable for synthesis of dimethyl ether, methanol and for the Fischer-Tropsch process using established catalysts. Efficient conversion of synthesis gas to hydrogen involves additional catalysts that assist the water gas shift reaction, or involves in situ capture of carbon dioxide and hydrogen. Reforming at reduced temperatures including photo-reforming offers the opportunity of producing synthesis gas or hydrogen using single catalysts. Together, these processes will assist in overcoming the worldwide glut of glycerol, increasing the competitiveness of the biofuel production and reducing our dependency on the fossil based, hydrogen rich gas.

  7. Platelet rich plasma in ocular surface.

    Science.gov (United States)

    Riestra, A C; Alonso-Herreros, J M; Merayo-Lloves, J

    2016-10-01

    The use of platelet-rich preparations has experienced a significant increase in recent years due to its role in tissue-repair and regeneration. The aim of this study is to examine the available evidence regarding the application of plasma rich in growth factors, and its variations, on the ocular surface. A review is also presented on the effects of platelet-derived growth factors, the implications of the preparation methods, and the existing literature on the safety and efficacy of these therapies in ocular surface diseases. Despite the widespread use of platelet preparations there is no consensus on the most appropriate preparation method, and growth factors concentration vary with different systems. These preparations have been used in the treatment of ocular surface diseases, such as dry eye or persistent epithelial defects, among others, with good safety and efficacy profiles, but further studies are needed to compare to the currently available alternatives. Copyright © 2016 Sociedad Española de Oftalmología. Published by Elsevier España, S.L.U. All rights reserved.

  8. Bioaccumulation of copper ions by Escherichia coli expressing vanabin genes from the vanadium-rich ascidian Ascidia sydneiensis samea.

    Science.gov (United States)

    Ueki, Tatsuya; Sakamoto, Yasuhisa; Yamaguchi, Nobuo; Michibata, Hitoshi

    2003-11-01

    The genes encoding two vanadium-binding proteins, vanabin1 and vanabin2, from a vanadium-rich ascidian, Ascidia sydneiensis samea, were recently identified and cloned (T. Ueki, T. Adachi, S. Kawano, M. Aoshima, N. Yamaguchi, K. Kanamori, and H. Michibata, Biochim. Biophys. Acta 1626:43-50, 2003). The vanabins were found to bind vanadium(IV), and an excess of copper(II) ions inhibited the binding of vanadium(IV) to the vanabins in vitro. In this study, we constructed Escherichia coli strains that expressed vanabin1 or vanabin2 fused to maltose-binding protein (MBP) in the periplasmic space. We found that both strains accumulated about twenty times more copper(II) ions than the control BL21 strain, while no significant accumulation of vanadium was observed. The strains expressing either MBP-vanabin1 or MBP-vanabin2 absorbed approximately 70% of the copper ions in the medium to which 10 micro M copper (II) ions were initially added. The MBP-vanabin1 and MBP-vanabin2 protein expressed in the periplasm bound to copper ions at a copper:protein molar ratio of 8:1 and 5:1, respectively, but MBP did not bind to copper ions. These data showed that the metal-binding proteins vanabin1 and vanabin2 bound copper ions directly and enhanced the bioaccumulation of copper ions by E. coli.

  9. Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach

    DEFF Research Database (Denmark)

    Buus, S; Lauemøller, S L; Worning, P

    2003-01-01

    We have generated Artificial Neural Networks (ANN) capable of performing sensitive, quantitative predictions of peptide binding to the MHC class I molecule, HLA-A*0204. We have shown that such quantitative ANN are superior to conventional classification ANN, that have been trained to predict...... binding vs non-binding peptides. Furthermore, quantitative ANN allowed a straightforward application of a 'Query by Committee' (QBC) principle whereby particularly information-rich peptides could be identified and subsequently tested experimentally. Iterative training based on QBC-selected peptides...

  10. Arginine-rich histones have strong antiviral activity for influenza A viruses.

    Science.gov (United States)

    Hoeksema, Marloes; Tripathi, Shweta; White, Mitchell; Qi, Li; Taubenberger, Jeffery; van Eijk, Martin; Haagsman, Henk; Hartshorn, Kevan L

    2015-10-01

    While histones are best known for DNA binding and transcription-regulating properties, they also have antimicrobial activity against a broad range of potentially pathogenic organisms. Histones are abundant in neutrophil extracellular traps, where they play an important role in NET-mediated antimicrobial killing. Here, we show anti-influenza activity of histones against both seasonal H3N2 and H1N1, but not pandemic H1N1. The arginine rich histones, H3 and H4, had greater neutralizing and viral aggregating activity than the lysine rich histones, H2A and H2B. Of all core histones, histone H4 is most potent in neutralizing IAV, and incubation with IAV with histone H4 results in a decrease in uptake and viral replication by epithelial cells when measured by qRT-PCR. The antiviral activity of histone H4 is mediated principally by direct effects on viral particles. Histone H4 binds to IAV as assessed by ELISA and co-sedimentation of H4 with IAV. H4 also induces aggregation, as assessed by confocal microscopy and light transmission assays. Despite strong antiviral activity against the seasonal IAV strains, H4 was inactive against pandemic H1N1. These findings indicate a possible role for histones in the innate immune response against IAV. © The Author(s) 2015.

  11. A DNA-binding protein from Candida albicans that binds to the RPG box of Saccharomyces cerevisiae and the telomeric repeat sequence of C. albicans.

    Science.gov (United States)

    Ishii, N; Yamamoto, M; Lahm, H W; Iizumi, S; Yoshihara, F; Nakayama, H; Arisawa, M; Aoki, Y

    1997-02-01

    Electromobility shift assays with a DNA probe containing the Saccharomyces cerevisiae ENO1 RPG box identified a specific DNA-binding protein in total protein extracts of Candida albicans. The protein, named Rbf1p (RPG-box-binding protein 1), bound to other S. cerevisiae RPG boxes, although the nucleotide recognition profile was not completely the same as that of S. cerevisiae Rap 1p (repressor-activator protein 1), an RPG-box-binding protein. The repetitive sequence of the C. albicans chromosomal telomere also competed with RPG-box binding to Rbf1p. For further analysis, we purified Rbf1p 57,600-fold from C. albicans total protein extracts, raised mAbs against the purified protein and immunologically cloned the gene, whose ORF specified a protein of 527 aa. The bacterially expressed protein showed RPG-box-binding activity with the same profile as that of the purified one. The Rbf1p, containing two glutamine-rich regions that are found in many transcription factors, showed transcriptional activation capability in S. cerevisiae and was predominantly observed in nuclei. These results suggest that Rbf1p is a transcription factor with telomere-binding activity in C. albicans.

  12. Species richness of arbuscular mycorrhizal fungi: associations with grassland plant richness and biomass

    Czech Academy of Sciences Publication Activity Database

    Hiiesalu, Inga; Pärtel, M.; Davison, J.; Gerhold, P.; Metsis, M.; Moora, M.; Öpik, M.; Vasar, M.; Zobel, M.; Wilson, S. D.

    2014-01-01

    Roč. 203, č. 1 (2014), s. 233-244 ISSN 1469-8137 R&D Projects: GA MŠk EE2.3.30.0048 Institutional research plan: CEZ:AV0Z60050516 Institutional support: RVO:67985939 Keywords : belowground plant richness * diversity * productivity Subject RIV: EH - Ecology, Behaviour Impact factor: 6.545, year: 2013

  13. Is torrefaction of polysaccharides-rich biomass equivalent to carbonization of lignin-rich biomass?

    Science.gov (United States)

    Bilgic, E; Yaman, S; Haykiri-Acma, H; Kucukbayrak, S

    2016-01-01

    Waste biomass species such as lignin-rich hazelnut shell (HS) and polysaccharides-rich sunflower seed shell (SSS) were subjected to torrefaction at 300°C and carbonization at 600°C under nitrogen. The structural variations in torrefied and carbonized biomasses were compared. Also, the burning characteristics under dry air and pure oxygen (oxy-combustion) conditions were investigated. It was concluded that the effects of carbonization on HS are almost comparable with the effects of torrefaction on SSS in terms of devolatilization and deoxygenation potentials and the increases in carbon content and the heating value. Consequently, it can be proposed that torrefaction does not provide efficient devolatilization from the lignin-rich biomass while it is relatively more efficient for polysaccharides-rich biomass. Heat-induced variations in biomass led to significant changes in the burning characteristics under both burning conditions. That is, low temperature reactivity of biomass reduced considerably and the burning shifted to higher temperatures with very high burning rates. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Silica-Rich Soil in Gusev Crater

    Science.gov (United States)

    2007-01-01

    NASA's Mars Exploration Rover Spirit has found a patch of bright-toned soil so rich in silica that scientists propose water must have been involved in concentrating it. The silica-rich patch, informally named 'Gertrude Weise' after a player in the All-American Girls Professional Baseball League, was exposed when Spirit drove over it during the 1,150th Martian day, or sol, of Spirit's Mars surface mission (March 29, 2007). One of Spirit's six wheels no longer rotates, so it leaves a deep track as it drags through soil. Most patches of disturbed, bright soil that Spirit had investigated previously are rich in sulfur, but this one has very little sulfur and is about 90 percent silica. Spirit's panoramic camera imaged the bright patch through various filters on Sol 1,158 (April 6). This approximately true-color image combines images taken through three different filters. The track of disturbed soil is roughly 20 centimeters (8 inches) wide. Spirit's miniature thermal emission spectrometer, which can assess a target's mineral composition from a distance, examined the Gertrude Weise patch on Sol 1,172 (April 20). The indications it found for silica in the overturned soil prompted a decision to drive Spirit close enough to touch the soil with the alpha particle X-ray spectrometer, a chemical analyzer at the end of Spirit's robotic arm. The alpha particle X-ray spectrometer collected data about this target on sols 1,189 and 1,190 (May 8 and May 9) and produced the finding of approximately 90 percent silica. Silica is silicon dioxide. On Earth, it commonly occurs as the crystalline mineral quartz and is the main ingredient in window glass. The Martian silica at Gertrude Weise is non-crystalline, with no detectable quartz. In most cases, water is required to produce such a concentrated deposit of silica, according to members of the rover science team. One possible origin for the silica could have been interaction of soil with acidic steam produced by volcanic activity

  15. Silica-Rich Soil Found by Spirit

    Science.gov (United States)

    2007-01-01

    NASA's Mars Exploration Rover Spirit has found a patch of bright-toned soil so rich in silica that scientists propose water must have been involved in concentrating it. The silica-rich patch, informally named 'Gertrude Weise' after a player in the All-American Girls Professional Baseball League, was exposed when Spirit drove over it during the 1,150th Martian day, or sol, of Spirit's Mars surface mission (March 29, 2007). One of Spirit's six wheels no longer rotates, so it leaves a deep track as it drags through soil. Most patches of disturbed, bright soil that Spirit had investigated previously are rich in sulfur, but this one has very little sulfur and is about 90 percent silica. This image is a approximately true-color composite of three images taken through different filters by Spirit's panoramic camera on Sol 1,187 (May 6). The track of disturbed soil is roughly 20 centimeters (8 inches) wide. Spirit's miniature thermal emission spectrometer, which can assess a target's mineral composition from a distance, examined the Gertrude Weise patch on Sol 1,172 (April 20). The indications it found for silica in the overturned soil prompted a decision to drive Spirit close enough to touch the soil with the alpha particle X-ray spectrometer, a chemical analyzer at the end of Spirit's robotic arm. The alpha particle X-ray spectrometer collected data about this target on sols 1,189 and 1,190 (May 8 and May 9) and produced the finding of approximately 90 percent silica. Silica is silicon dioxide. On Earth, it commonly occurs as the crystalline mineral quartz and is the main ingredient in window glass. The Martian silica at Gertrude Weise is non-crystalline, with no detectable quartz. In most cases, water is required to produce such a concentrated deposit of silica, according to members of the rover science team. One possible origin for the silica could have been interaction of soil with acidic steam produced by volcanic activity. Another could have been from water in a hot

  16. Multifunctional G-rich and RRM-containing domains of TbRGG2 perform separate yet essential functions in trypanosome RNA editing.

    Science.gov (United States)

    Foda, Bardees M; Downey, Kurtis M; Fisk, John C; Read, Laurie K

    2012-09-01

    Efficient editing of Trypanosoma brucei mitochondrial RNAs involves the actions of multiple accessory factors. T. brucei RGG2 (TbRGG2) is an essential protein crucial for initiation and 3'-to-5' progression of editing. TbRGG2 comprises an N-terminal G-rich region containing GWG and RG repeats and a C-terminal RNA recognition motif (RRM)-containing domain. Here, we perform in vitro and in vivo separation-of-function studies to interrogate the mechanism of TbRGG2 action in RNA editing. TbRGG2 preferentially binds preedited mRNA in vitro with high affinity attributable to its G-rich region. RNA-annealing and -melting activities are separable, carried out primarily by the G-rich and RRM domains, respectively. In vivo, the G-rich domain partially complements TbRGG2 knockdown, but the RRM domain is also required. Notably, TbRGG2's RNA-melting activity is dispensable for RNA editing in vivo. Interactions between TbRGG2 and MRB1 complex proteins are mediated by both G-rich and RRM-containing domains, depending on the binding partner. Overall, our results are consistent with a model in which the high-affinity RNA binding and RNA-annealing activities of the G-rich domain are essential for RNA editing in vivo. The RRM domain may have key functions involving interactions with the MRB1 complex and/or regulation of the activities of the G-rich domain.

  17. When is protein binding important?

    Science.gov (United States)

    Heuberger, Jules; Schmidt, Stephan; Derendorf, Hartmut

    2013-09-01

    The present paper is an ode to a classic citation by Benet and Hoener (2002. Clin Pharm Ther 71(3):115-121). The now classic paper had a huge impact on drug development and the way the issue of protein binding is perceived and interpreted. Although the authors very clearly pointed out the limitations and underlying assumptions for their delineations, these are too often overlooked and the classic paper's message is misinterpreted by broadening to cases that were not intended. Some members of the scientific community concluded from the paper that protein binding is not important. This was clearly not intended by the authors, as they finished their paper with a paragraph entitled: "When is protein binding important?" Misinterpretation of the underlying assumptions in the classic work can result in major pitfalls in drug development. Therefore, we revisit the topic of protein binding with the intention of clarifying when clinically relevant changes should be considered during drug development. Copyright © 2013 Wiley Periodicals, Inc.

  18. Minor-Groove Binding Drugs: Where Is the Second Hoechst 33258 Molecule?

    KAUST Repository

    Fornander, Louise H.

    2013-05-16

    Hoechst 33258 binds with high affinity into the minor groove of AT-rich sequences of double-helical DNA. Despite extensive studies of this and analogous DNA binding molecules, there still remains uncertainty concerning the interactions when multiple ligand molecules are accommodated within close distance. Albeit not of direct concern for most biomedical applications, which are at low drug concentrations, interaction studies for higher drug binding are important as they can give fundamental insight into binding mechanisms and specificity, including drug self-stacking interactions that can provide base-sequence specificity. Using circular dichroism (CD), isothermal titration calorimetry (ITC), and proton nuclear magnetic resonance (1H NMR), we examine the binding of Hoechst 33258 to three oligonucleotide duplexes containing AT regions of different lengths: [d(CGCGAATTCGCG)]2 (A2T2), [d(CGCAAATTTGCG)]2 (A3T 3), and [d(CGAAAATTTTCG)]2 (A4T4). We find similar binding geometries in the minor groove for all oligonucleotides when the ligand-to-duplex ratio is less than 1:1. At higher ratios, a second ligand can be accommodated in the minor groove of A4T4 but not A2T2 or A3T3. We conclude that the binding of the second Hoechst to A4T4 is not cooperative and that the molecules are sitting with a small separation apart, one after the other, and not in a sandwich structure as previously proposed. © 2013 American Chemical Society.

  19. Self-assembled FUS binds active chromatin and regulates gene transcription

    Science.gov (United States)

    Yang, Liuqing; Gal, Jozsef; Chen, Jing; Zhu, Haining

    2014-01-01

    Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease. Fused in sarcoma (FUS) is a DNA/RNA binding protein and mutations in FUS cause a subset of familial ALS. Most ALS mutations are clustered in the C-terminal nuclear localization sequence of FUS and consequently lead to the accumulation of protein inclusions in the cytoplasm. It remains debatable whether loss of FUS normal function in the nucleus or gain of toxic function in the cytoplasm plays a more critical role in the ALS etiology. Moreover, the physiological function of FUS in the nucleus remains to be fully understood. In this study, we found that a significant portion of nuclear FUS was bound to active chromatin and that the ALS mutations dramatically decreased FUS chromatin binding ability. Functionally, the chromatin binding is required for FUS transcription activation, but not for alternative splicing regulation. The N-terminal QGSY (glutamine-glycine-serine-tyrosine)-rich region (amino acids 1–164) mediates FUS self-assembly in the nucleus of mammalian cells and the self-assembly is essential for its chromatin binding and transcription activation. In addition, RNA binding is also required for FUS self-assembly and chromatin binding. Together, our results suggest a functional assembly of FUS in the nucleus under physiological conditions, which is different from the cytoplasmic inclusions. The ALS mutations can cause loss of function in the nucleus by disrupting this assembly and chromatin binding. PMID:25453086

  20. A Universal Stress Protein (USP) in Mycobacteria Binds cAMP

    Science.gov (United States)

    Banerjee, Arka; Adolph, Ramona S.; Gopalakrishnapai, Jayashree; Kleinboelting, Silke; Emmerich, Christiane; Steegborn, Clemens; Visweswariah, Sandhya S.

    2015-01-01

    Mycobacteria are endowed with rich and diverse machinery for the synthesis, utilization, and degradation of cAMP. The actions of cyclic nucleotides are generally mediated by binding of cAMP to conserved and well characterized cyclic nucleotide binding domains or structurally distinct cGMP-specific and -regulated cyclic nucleotide phosphodiesterase, adenylyl cyclase, and E. coli transcription factor FhlA (GAF) domain-containing proteins. Proteins with cyclic nucleotide binding and GAF domains can be identified in the genome of mycobacterial species, and some of them have been characterized. Here, we show that a significant fraction of intracellular cAMP is bound to protein in mycobacterial species, and by using affinity chromatography techniques, we identify specific universal stress proteins (USP) as abundantly expressed cAMP-binding proteins in slow growing as well as fast growing mycobacteria. We have characterized the biochemical and thermodynamic parameters for binding of cAMP, and we show that these USPs bind cAMP with a higher affinity than ATP, an established ligand for other USPs. We determined the structure of the USP MSMEG_3811 bound to cAMP, and we confirmed through structure-guided mutagenesis, the residues important for cAMP binding. This family of USPs is conserved in all mycobacteria, and we suggest that they serve as “sinks” for cAMP, making this second messenger available for downstream effectors as and when ATP levels are altered in the cell. PMID:25802331

  1. Effects of single-stranded DNA binding proteins on primer extension by telomerase.

    Science.gov (United States)

    Cohen, Shlomit; Jacob, Eyal; Manor, Haim

    2004-08-12

    We present a biochemical analysis of the effects of three single-stranded DNA binding proteins on extension of oligonucleotide primers by the Tetrahymena telomerase. One of them, a human protein designated translin, which was shown to specifically bind the G-rich Tetrahymena and human telomeric repeats, slightly stimulated the primer extension reactions at molar ratios of translin/primer of primers, rather than by a direct interaction of this protein with telomerase. A second protein, the general human single-stranded DNA binding protein Replication Protein A (RPA), similarly affected the primer extension by telomerase, even though its mode of binding to DNA differs from that of translin. A third protein, the E. coli single-stranded DNA binding protein (SSB), whose binding to DNA is highly cooperative, caused more substantial stimulation and inhibition at the lower and the higher molar ratios of SSB/primer, respectively. Both telomere-specific and general single-stranded DNA binding proteins are found in living cells in telomeric complexes. Based on our data, we propose that these proteins may exert either stimulatory or inhibitory effects on intracellular telomerases, depending on their local concentrations. Copyright 2004 Elsevier B.V.

  2. The conserved Tarp actin binding domain is important for chlamydial invasion.

    Directory of Open Access Journals (Sweden)

    Travis J Jewett

    2010-07-01

    Full Text Available The translocated actin recruiting phosphoprotein (Tarp is conserved among all pathogenic chlamydial species. Previous reports identified single C. trachomatis Tarp actin binding and proline rich domains required for Tarp mediated actin nucleation. A peptide antiserum specific for the Tarp actin binding domain was generated and inhibited actin polymerization in vitro and C. trachomatis entry in vivo, indicating an essential role for Tarp in chlamydial pathogenesis. Sequence analysis of Tarp orthologs from additional chlamydial species and C. trachomatis serovars indicated multiple putative actin binding sites. In order to determine whether the identified actin binding domains are functionally conserved, GST-Tarp fusions from multiple chlamydial species were examined for their ability to bind and nucleate actin. Chlamydial Tarps harbored variable numbers of actin binding sites and promoted actin nucleation as determined by in vitro polymerization assays. Our findings indicate that Tarp mediated actin binding and nucleation is a conserved feature among diverse chlamydial species and this function plays a critical role in bacterial invasion of host cells.

  3. Targeted binding of the M13 bacteriophage to thiamethoxam organic crystals.

    Science.gov (United States)

    Cho, Whirang; Fowler, Jeffrey D; Furst, Eric M

    2012-04-10

    Phage display screening with a combinatorial library was used to identify M13-type bacteriophages that express peptides with selective binding to organic crystals of thiamethoxam. The six most strongly binding phages exhibit at least 1000 times the binding affinity of wild-type M13 and express heptapeptide sequences that are rich in hydrophobic, hydrogen-bonding amino acids and proline. Among the peptide sequences identified, M13 displaying the pIII domain heptapeptide ASTLPKA exhibits the strongest binding to thiamethoxam in competitive binding assays. Electron and confocal microscopy confirm the specific binding affinity of ASTLPKA to thiamethoxam. Using atomic force microscope (AFM) probes functionalized with ASTLPKA expressing phage, we found that the average adhesion force between the bacteriophage and a thiamethoxam surface is 1.47 ± 0.80 nN whereas the adhesion force of wild-type M13KE phage is 0.18 ± 0.07 nN. Such a strongly binding bacteriophage could be used to modify the surface chemistry of thiamethoxam crystals and other organic solids with a high degree of specificity. © 2012 American Chemical Society

  4. Reduction of starch granule size by expression of an engineered tandem starch-binding domain in potato plants

    NARCIS (Netherlands)

    Ji, Q.; Oomen, R.J.F.J.; Vincken, J.P.; Bolam, D.N.; Gilbert, H.J.; Suurs, L.C.J.M.; Visser, R.G.F.

    2004-01-01

    Granule size is an important parameter when using starch in industrial applications. An artificial tandem repeat of a family 20 starch-binding domain (SBD2) was engineered by two copies of the SBD derived from Bacillus circulans cyclodextrin glycosyltransferase via the Pro-Thr-rich linker peptice

  5. LHCb RICH 2 engineering design review report

    CERN Document Server

    Adinolfi, M; Allebone, L R; Ameri, M; Barber, G J; Barczyk, A; Bellunato, T F; Benayoun, M; Bibby, J; Braem, André; Brew, C A J; Brook, N; Buckley, A; Calvi, M; Campbell, M; Chamonal, R; Cole, J; Cuneo, S; D'Ambrosio, C; Damerell, G; Densham, C J; Dornan, Peter John; Duane, A; Easo, S; Egede, U; Eisenhardt, S; Flavell, AJ; Fontanelli, F; Forty, R W; Franek, B J; Frei, C; George, K; Gibson, V; Girone, M; Gracco, Valerio; Guy, J; Gys, Thierry; Harnew, N; Head, R; Hill, R; Jolly, S; Jones, C; Katvars, S G; Khan, A; Laub, M; Lawrence, J; Libby, J; Lidbury, J A; Losasso, M; MacGregor, A; Matteuzzi, C; Mini, G; Morris, J V; Muheim, F; Musico, P; Musy, M; Negri, P; Newby, C; O'Shea, V; Papanestis, A; Parkes, CJ; Patrick, G N; Petrolini, A; Phillips, A; Piazzoni, C; Pickford, A N; Piedigrossi, D; Playfer, S; Presland, A; Price, D R; Radermacker, J; Sannino, M; Savage, P; Shepherd-Themistocleous, C H; Smale, N J; Snoeys, W; Soler, F J P; Temple, S A; Topp-Jørgensen, S; Ullaland, O; Ward, C P; Websdale, D M; White, R; Wilkinson, G; Wilson, F; Woodward, M L; Wotton, S A; Wyllie, Ken H

    2002-01-01

    The LHCb detector is a single arm spectrometer designed to exploit the large number of b-hadrons produced at the LHC in order to make precision studies of CP asymmetries and of rare decays in the B-meson system. It is therefore essential for the experiment that the detector configuration includes a particle identification system with high separation power between kaons and pions. We will present in this note the engineering solutions for the lightweight, high precision Ring Imaging Cherenkov detector, RICH2, of the spectrometer. The design is built around a large space frame used as a high stability support for the optical system and as a supporting structure for the magnetic shielding needed for the photon detectors. All material not essential for the operation of the detector is located outside the acceptance of the spectrometer. The space frame also defines the Cherenkov gas volume.

  6. Graphics performance in rich Internet applications.

    Science.gov (United States)

    Hoetzlein, Rama C

    2012-01-01

    Rendering performance for rich Internet applications (RIAs) has recently focused on the debate between using Flash and HTML5 for streaming video and gaming on mobile devices. A key area not widely explored, however, is the scalability of raw bitmap graphics performance for RIAs. Does Flash render animated sprites faster than HTML5? How much faster is WebGL than Flash? Answers to these questions are essential for developing large-scale data visualizations, online games, and truly dynamic websites. A new test methodology analyzes graphics performance across RIA frameworks and browsers, revealing specific performance outliers in existing frameworks. The results point toward a future in which all online experiences might be GPU accelerated.

  7. Platelet Rich Plasma and Knee Surgery

    Directory of Open Access Journals (Sweden)

    Mikel Sánchez

    2014-01-01

    Full Text Available In orthopaedic surgery and sports medicine, the knee joint has traditionally been considered the workhorse. The reconstruction of every damaged element in this joint is crucial in achieving the surgeon’s goal to restore the knee function and prevent degeneration towards osteoarthritis. In the last fifteen years, the field of regenerative medicine is witnessing a boost of autologous blood-derived platelet rich plasma products (PRPs application to effectively mimic and accelerate the tissue healing process. The scientific rationale behind PRPs is the delivery of growth factors, cytokines, and adhesive proteins present in platelets and plasma, as well as other biologically active proteins conveyed by the plasma such as fibrinogen, prothrombin, and fibronectin; with this biological engineering approach, new perspectives in knee surgery were opened. This work describes the use of PRP to construct and repair every single anatomical structure involved in knee surgery, detailing the process conducted in ligament, meniscal, and chondral surgery.

  8. Platelet-rich plasma: applications in dermatology.

    Science.gov (United States)

    Conde Montero, E; Fernández Santos, M E; Suárez Fernández, R

    2015-03-01

    In recent years, the use of platelet-rich plasma has increased notably in a range of diseases and settings. Uses of these products now go beyond skin rejuvenation therapy in patients with facial ageing. Good outcomes for other dermatological indications such as skin ulcers and, more recently, alopecia have been reported in case series and controlled studies. However, these indications are not currently included in the labeling given that stronger scientific evidence is required to support their real benefits. With the increased use of these products, dermatologists need to become familiar with the underlying biological principles and able to critically assess the quality and outcomes of the studies of these products in different skin diseases. Copyright © 2013 Elsevier España, S.L.U. and AEDV. All rights reserved.

  9. Platelet-rich plasma for osteoarthritis treatment

    Directory of Open Access Journals (Sweden)

    Eduardo Knop

    2016-04-01

    Full Text Available ABSTRACT We conducted a comprehensive and systematic search of the literature on the use of platelet-rich plasma (PRP in the treatment of osteoarthritis, using the Medline, Lilacs, Cochrane and SciELO databases, from May 2012 to October 2013. A total of 23 studies were selected, with nine being controlled trials and, of these, seven randomized, which included 725 patients. In this series, the group receiving PRP showed improvement in pain and joint function compared to placebo and hyaluronic acid. The response lasted up to two years and was better in milder cases. However it was found that there is no standardization in the PRP production method, neither in the number, timing, and volume of applications. Furthermore, the populations studied were not clearly described in many studies. Thus, these results should be analyzed with caution, and further studies with more standardized methods would be necessary for a more consistent conclusion about the PRP role in osteoarthritis.

  10. RICH High Voltages & PDF Analysis @ LHCb

    CERN Multimedia

    Fanchini, E

    2009-01-01

    In the LHCb experiment an important issue is the identification of the hadrons of the final states of the B mesons decays. Two RICH subdetectors are devoted to this task, and the Hybrid Photon Detectors (HPDs) are the photodetectors used to detect Cherenkov light. In this poster there is a description of how the very high voltage (-18 KV) supply stability used to power the HPDs is monitored. It is also presented the basics of a study which can be done with the first collision data: the analysis of the dimuons from the Drell-Yan process. This process is well known and the acceptance of the LHCb detector in terms of pseudorapidity will be very useful to improve the knowledge of the proton structure functions or, alternatively, try to estimate the luminosity from it.

  11. The neutrino opacity of neutron rich matter

    Science.gov (United States)

    Alcain, P. N.; Dorso, C. O.

    2017-05-01

    The study of neutron rich matter, present in neutron star, proto-neutron stars and core-collapse supernovae, can lead to further understanding of the behavior of nuclear matter in highly asymmetric nuclei. Heterogeneous structures are expected to exist in these systems, often referred to as nuclear pasta. We have carried out a systematic study of neutrino opacity for different thermodynamic conditions in order to assess the impact that the structure has on it. We studied the dynamics of the neutrino opacity of the heterogeneous matter at different thermodynamic conditions with semiclassical molecular dynamics model already used to study nuclear multifragmentation. For different densities, proton fractions and temperature, we calculate the very long range opacity and the cluster distribution. The neutrino opacity is of crucial importance for the evolution of the core-collapse supernovae and the neutrino scattering.

  12. The neutrino opacity of neutron rich matter

    Energy Technology Data Exchange (ETDEWEB)

    Alcain, P.N., E-mail: pabloalcain@gmail.com [Departamento de Física, FCEyN, UBA and IFIBA, Conicet, Pabellón 1, Ciudad Universitaria, 1428 Buenos Aires (Argentina); IFIBA-CONICET (Argentina); Dorso, C.O. [Departamento de Física, FCEyN, UBA and IFIBA, Conicet, Pabellón 1, Ciudad Universitaria, 1428 Buenos Aires (Argentina); IFIBA-CONICET (Argentina)

    2017-05-15

    The study of neutron rich matter, present in neutron star, proto-neutron stars and core-collapse supernovae, can lead to further understanding of the behavior of nuclear matter in highly asymmetric nuclei. Heterogeneous structures are expected to exist in these systems, often referred to as nuclear pasta. We have carried out a systematic study of neutrino opacity for different thermodynamic conditions in order to assess the impact that the structure has on it. We studied the dynamics of the neutrino opacity of the heterogeneous matter at different thermodynamic conditions with semiclassical molecular dynamics model already used to study nuclear multifragmentation. For different densities, proton fractions and temperature, we calculate the very long range opacity and the cluster distribution. The neutrino opacity is of crucial importance for the evolution of the core-collapse supernovae and the neutrino scattering.

  13. Evaluation of the In Vivo and Ex Vivo Binding of Novel BC1 Cannabinoid Receptor Radiotracers

    Energy Technology Data Exchange (ETDEWEB)

    Miller, A.; Gatley, J.; Gifford, A.

    2002-01-01

    The primary active ingredient of marijuana, 9-tetrahydrocannabinol, exerts its psychoactive effects by binding to cannabinoid CB1 receptors. These receptors are found throughout the brain with high concentrations in the hippocampus and cerebellum. The current study was conducted to evaluate the binding of a newly developed putative cannabinoid antagonist, AM630, and a classical cannabinoid 8-tetrahydrocannabinol as potential PET and/or SPECT imaging agents for brain CB1 receptors. For both of these ligands in vivo and ex vivo studies in mice were conducted. AM630 showed good overall brain uptake (as measure by %IA/g) and a moderately rapid clearance from the brain with a half-clearance time of approximately 30 minutes. However, AM630 did not show selective binding to CB1 cannabinoid receptors. Ex vivo autoradiography supported the lack of selective binding seen in the in vivo study. Similar to AM630, 8-tetrahydrocanibol also failed to show selective binding to CB1 receptor rich brain areas. The 8-tetrahydrocanibol showed moderate overall brain uptake and relatively slow brain clearance as compared to AM630. Further studies were done with AM2233, a cannabinoid ligand with a similar structure as AM630. These studies were done to develop an ex vivo binding assay to quantify the displacement of [131I]AM2233 binding by other ligands in Swiss-Webster and CB1 receptor knockout mice. By developing this assay we hoped to determine the identity of an unknown binding site for AM2233 present in the hippocampus of CB1 knockout mice. Using an approach based on incubation of brain slices prepared from mice given intravenous [131I]AM2233 in either the presence or absence of AM2233 (unlabelled) it was possible to demonstrate a significant AM2233-displacable binding in the Swiss-Webster mice. Future studies will determine if this assay is appropriate for identifying the unknown binding site for AM2233 in the CB1 knockout mice.

  14. Experimental determination of one- and two-neutron separation energies for neutron-rich copper isotopes

    Science.gov (United States)

    Yu, Mian; Wei, Hui-Ling; Song, Yi-Dan; Ma, Chun-Wang

    2017-09-01

    A method is proposed to determine the one-neutron S n or two-neutron S 2n separation energy of neutron-rich isotopes. Relationships between S n (S 2n) and isotopic cross sections have been deduced from an empirical formula, i.e., the cross section of an isotope exponentially depends on the average binding energy per nucleon B/A. The proposed relationships have been verified using the neutron-rich copper isotopes measured in the 64A MeV 86Kr + 9Be reaction. S n, S 2n, and B/A for the very neutron-rich 77,78,79Cu isotopes are determined from the proposed correlations. It is also proposed that the correlations between S n, S 2n and isotopic cross sections can be used to find the location of neutron drip line isotopes. Supported by Program for Science and Technology Innovation Talents at Universities of Henan Province (13HASTIT046), Natural and Science Foundation in Henan Province (162300410179), Program for the Excellent Youth at Henan Normal University (154100510007) and Y-D Song thanks the support from the Creative Experimental Project of National Undergraduate Students (CEPNU 201510476017)

  15. Long-term music training tunes how the brain temporally binds signals from multiple senses

    OpenAIRE

    Lee, HweeLing; Noppeney, Uta

    2011-01-01

    Practicing a musical instrument is a rich multisensory experience involving the integration of visual, auditory, and tactile inputs with motor responses. This combined psychophysics–fMRI study used the musician's brain to investigate how sensory-motor experience molds temporal binding of auditory and visual signals. Behaviorally, musicians exhibited a narrower temporal integration window than nonmusicians for music but not for speech. At the neural level, musicians showed increased audiovisua...

  16. A PUFA-rich diet improves fat oxidation following saturated fat-rich meal.

    Science.gov (United States)

    Stevenson, Jada L; Miller, Mary K; Skillman, Hannah E; Paton, Chad M; Cooper, Jamie A

    2017-08-01

    To determine substrate oxidation responses to saturated fatty acid (SFA)-rich meals before and after a 7-day polyunsaturated fatty acid (PUFA)-rich diet versus control diet. Twenty-six, normal-weight, adults were randomly assigned to either PUFA or control diet. Following a 3-day lead-in diet, participants completed the pre-diet visit where anthropometrics and resting metabolic rate (RMR) were measured, and two SFA-rich HF meals (breakfast and lunch) were consumed. Indirect calorimetry was used to determine fat oxidation (Fox) and energy expenditure (EE) for 4 h after each meal. Participants then consumed a PUFA-rich diet (50 % carbohydrate, 15 % protein, 35 % fat, of which 21 % of total energy was PUFA) or control diet (50 % carbohydrate, 15 % protein, 35 % fat, of which 7 % of total energy was PUFA) for the next 7 days. Following the 7-day diet, participants completed the post-diet visit. From pre- to post-PUFA-rich diet, there was no change in RMR (16.3 ± 0.8 vs. 16.4 ± 0.8 kcal/20 min) or in incremental area under the curve for EE (118.9 ± 20.6-126.9 ± 14.1 kcal/8h, ns). Fasting respiratory exchange ratio increased from pre- to post-PUFA-rich diet only (0.83 ± 0.1-0.86 ± 0.1, p diet (0.03 ± 0.1-0.23 ± 0.1 g/15 min for cumulative Fox; p diet initiates greater fat oxidation after eating occasional high SFA meals compared to a control diet, an effect achieved in 7 days.

  17. Characterization of little skate (Leucoraja erinacea) recombinant transthyretin: Zinc-dependent 3,3',5-triiodo-l-thyronine binding.

    Science.gov (United States)

    Suzuki, Shunsuke; Kasai, Kentaro; Yamauchi, Kiyoshi

    2015-01-01

    Transthyretin (TTR) diverged from an ancestral 5-hydroxyisourate hydrolase (HIUHase) by gene duplication at some early stage of chordate evolution. To clarify how TTR had participated in the thyroid system as an extracellular thyroid hormone (TH) binding protein, TH binding properties of recombinant little skate Leucoraja erinacea TTR was investigated. At the amino acid level, skate TTR showed 37-46% identities with the other vertebrate TTRs. Because the skate TTR had a unique histidine-rich segment in the N-terminal region, it could be purified by Ni-affinity chromatography. The skate TTR was a 46-kDa homotetramer of 14.5kDa subunits, and had one order of magnitude higher affinity for 3,3',5-triiodo-l-thyronine (T3) and some halogenated phenols than for l-thyroxine. However, the skate TTR had no HIUHase activity. Ethylenediaminetetraacetic acid (EDTA) treatment inhibited [(125)I]T3 binding activity whereas the addition of Zn(2+) to the EDTA-treated TTR recovered [(125)I]T3 binding activity in a Zn(2+) concentration-dependent manner. Scatchard analysis revealed the presence of two classes of binding site for T3, with dissociation constants of 0.24 and 17nM. However, the high-affinity sites were completely abolished with 1mM EDTA, whereas the remaining low-affinity sites decreased binding capacity. The number of zinc per TTR was quantified to be 4.5-6.3. Our results suggest that skate TTR has tight Zn(2+)-binding sites, which are essential for T3 binding to at least the high-affinity sites. Zn(2+) binding to the N-terminal histidine-rich segment may play an important role in acquisition or reinforcement of TH binding ability during early evolution of TTR. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

    Energy Technology Data Exchange (ETDEWEB)

    Stanek, Kimberly A.; Patterson-West, Jennifer; Randolph, Peter S.; Mura, Cameron

    2017-03-31

    The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophileAquifex aeolicus(Aae), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore,AaeHfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures ofAaeHfq were determined in space groupsP1 andP6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U6RNA reveals that the outer rim of theAaeHfq hexamer features a well defined binding pocket that is selective for uracil. ThisAaeHfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.

  19. NMR structure of a biologically active peptide containing the RNA-binding domain of human immunodeficiency virus type 1 Tat.

    Science.gov (United States)

    Mujeeb, A; Bishop, K; Peterlin, B M; Turck, C; Parslow, T G; James, T L

    1994-01-01

    The Tat protein of human immunodeficiency virus type 1 enhances transcription by binding to a specific RNA element on nascent viral transcripts. Binding is mediated by a 10-amino acid basic domain that is rich in arginines and lysines. Here we report the three-dimensional peptide backbone structure of a biologically active 25-mer peptide that contains the human immunodeficiency virus type 1 Tat basic domain linked to the core regulatory domain of another lentiviral Tat--i.e., that from equine infectious anemia virus. Circular dichroism and two-dimensional proton NMR studies of this hybrid peptide indicate that the Tat basic domain forms a stable alpha-helix, whereas the adjacent regulatory sequence is mostly in extended form. These findings suggest that the tendency to form stable alpha-helices may be a common property of arginine- and lysine-rich RNA-binding domains. Images PMID:8058789

  20. Cysteine-Rich Secretory Proteins (CRISP and their role in mammalian fertilization

    Directory of Open Access Journals (Sweden)

    Débora J Cohen

    2011-01-01

    Full Text Available Epididymal protein CRISPI is a member of the CRISP (Cysteine-RIch Secretory proteins family and is involved in sperm-egg fusion through its interaction with complementary sites on the egg surface. Results from our laboratory have shown that this binding ability resides in a 12-amino-acid region corresponding to a highly conserved motif of the CRISP family, named Signature 2 (S2. In addition to this, our results revealed that CRISP1 could also be involved in the previous step of sperm binding to the zona pellucida, identifying a novel role for this protein in fertilization. As another approach to elucidate the participation of CRISP1 in fertilization, a mouse line containing a targeted disruption of CRISP1 was generated. Although CRISP1-deficient mice exhibited normal fertility, CRISP1-defficient sperm presented a decreased level of protein tyrosine phosphorylation during capacitation, and an impaired ability to fertilize both zona-intact and zona-free eggs in vitro, confirming the proposed roles for the protein in fertilization. Evidence obtained in our laboratory indicated that testicular CRISP2 would also be involved in sperm-egg fusion. Competition assays between CRISP1 and CRISP2, as well as the comparison of their corresponding S2 regions, suggest that both proteins bind to common complementary sites in the egg. Together, these results suggest a functional cooperation between CRISP1 and CRISP2 to ensure the success of fertilization.

  1. C-terminal low-complexity sequence repeats of Mycobacterium smegmatis Ku modulate DNA binding.

    Science.gov (United States)

    Kushwaha, Ambuj K; Grove, Anne

    2013-01-24

    Ku protein is an integral component of the NHEJ (non-homologous end-joining) pathway of DSB (double-strand break) repair. Both eukaryotic and prokaryotic Ku homologues have been characterized and shown to bind DNA ends. A unique feature of Mycobacterium smegmatis Ku is its basic C-terminal tail that contains several lysine-rich low-complexity PAKKA repeats that are absent from homologues encoded by obligate parasitic mycobacteria. Such PAKKA repeats are also characteristic of mycobacterial Hlp (histone-like protein) for which they have been shown to confer the ability to appose DNA ends. Unexpectedly, removal of the lysine-rich extension enhances DNA-binding affinity, but an interaction between DNA and the PAKKA repeats is indicated by the observation that only full-length Ku forms multiple complexes with a short stem-loop-containing DNA previously designed to accommodate only one Ku dimer. The C-terminal extension promotes DNA end-joining by T4 DNA ligase, suggesting that the PAKKA repeats also contribute to efficient end-joining. We suggest that low-complexity lysine-rich sequences have evolved repeatedly to modulate the function of unrelated DNA-binding proteins.

  2. Platelet-rich fibrin or platelet-rich plasma – which one is better? an opinion

    Directory of Open Access Journals (Sweden)

    Shweta Bansal

    2017-01-01

    Full Text Available The healing of hard and soft tissue in mediated by a wide range of intracellular and extracellular events that are regulated by signaling proteins. Platelets can play a crucial role in periodontal regeneration as they are the reservoirs of growth factors and cytokines which are the key factors for regeneration of bone and maturation of soft tissue. Platelet-rich plasma (PRP is first generation platelet concentrate. However, the short duration of cytokine release and its poor mechanical properties have resulted in search of new material. Platelet-rich fibrin (PRF is a natural fibrin-based biomaterial prepared from an anticoagulant-free blood harvest without any artificial biochemical modification (no bovine thrombin is required that allows obtaining fibrin membranes enriched with platelets and growth factors. The slow polymerization during centrifugation, fibrin-based structure, ease of preparation, minimal expense makes PRF somewhat superior in some aspect to PRP.

  3. The future of RICH detectors through the light of the LHCb RICH

    Science.gov (United States)

    D'Ambrosio, C.; LHCb RICH Collaboration

    2017-12-01

    The limitations in performance of the present RICH system in the LHCb experiment are given by the natural chromatic dispersion of the gaseous Cherenkov radiator, the aberrations of the optical system and the pixel size of the photon detectors. Moreover, the overall PID performance can be affected by high detector occupancy as the pattern recognition becomes more difficult with high particle multiplicities. This paper shows a way to improve performance by systematically addressing each of the previously mentioned limitations. These ideas are applied in the present and future upgrade phases of the LHCb experiment. Although applied to specific circumstances, they are used as a paradigm on what is achievable in the development and realisation of high precision RICH detectors.

  4. arXiv The Future of RICH Detectors through the Light of the LHCb RICH

    CERN Document Server

    D'Ambrosio, C.; Easo, S.; Petrolini, A.; Ullaland, O.

    2017-12-21

    The limitations in performance of the present RICH system in the LHCb experiment are given by the natural chromatic dispersion of the gaseous Cherenkov radiator, the aberrations of the optical system and the pixel size of the photon detectors. Moreover, the overall PID performance can be affected by high detector occupancy as the pattern recognition becomes more difficult with high particle multiplicities. This paper shows a way to improve performance by systematically addressing each of the previously mentioned limitations. These ideas are applied in the present and future upgrade phases of the LHCb experiment. Although applied to specific circumstances, they are used as a paradigm on what is achievable in the development and realisation of high precision RICH detectors.

  5. Calcium binding by dietary fibre

    International Nuclear Information System (INIS)

    James, W.P.T.; Branch, W.J.; Southgate, D.A.T.

    1978-01-01

    Dietary fibre from plants low in phytate bound calcium in proportion to its uronic-acid content. This binding by the non-cellulosic fraction of fibre reduces the availability of calcium for small-intestinal absorption, but the colonic microbial digestion of uronic acids liberates the calcium. Thus the ability to maintain calcium balance on high-fibre diets may depend on the adaptive capacity on the colon for calcium. (author)

  6. Ligand binding by PDZ domains

    DEFF Research Database (Denmark)

    Chi, Celestine N.; Bach, Anders; Strømgaard, Kristian

    2012-01-01

    The postsynaptic density protein-95/disks large/zonula occludens-1 (PDZ) protein domain family is one of the most common protein-protein interaction modules in mammalian cells, with paralogs present in several hundred human proteins. PDZ domains are found in most cell types, but neuronal proteins...... as pathological conditions have been reviewed recently. In this review, we focus on the molecular details of how PDZ domains bind their protein ligands and their potential as drug targets in this context....

  7. Binding energy of protonium ions

    Science.gov (United States)

    Assad Abdel-Raouf, Mohamed

    2009-11-01

    The goal of the present work is to calculate the binding energy of the protonium ions bar PPe+ and bar PPe- using Rayleigh- Ritz variational method. It is indicated that an employment of 21 components of the trial wavefunction yields -0.08793 eV as the ground state energy of these ions. Our result agrees quite well with recently obtained results based on elaborate Monte Carlo approximations. It confirms the possible formation of these ions in laboratory.

  8. Material Binding Peptides for Nanotechnology

    Directory of Open Access Journals (Sweden)

    Urartu Ozgur Safak Seker

    2011-02-01

    Full Text Available Remarkable progress has been made to date in the discovery of material binding peptides and their utilization in nanotechnology, which has brought new challenges and opportunities. Nowadays phage display is a versatile tool, important for the selection of ligands for proteins and peptides. This combinatorial approach has also been adapted over the past decade to select material-specific peptides. Screening and selection of such phage displayed material binding peptides has attracted great interest, in particular because of their use in nanotechnology. Phage display selected peptides are either synthesized independently or expressed on phage coat protein. Selected phage particles are subsequently utilized in the synthesis of nanoparticles, in the assembly of nanostructures on inorganic surfaces, and oriented protein immobilization as fusion partners of proteins. In this paper, we present an overview on the research conducted on this area. In this review we not only focus on the selection process, but also on molecular binding characterization and utilization of peptides as molecular linkers, molecular assemblers and material synthesizers.

  9. Anion binding in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Feiters, Martin C [Department of Organic Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Meyer-Klaucke, Wolfram [EMBL Hamburg Outstation at DESY, Notkestrasse 85, D-22607 Hamburg (Germany); Kostenko, Alexander V; Soldatov, Alexander V [Faculty of Physics, Southern Federal University, Sorge 5, Rostov-na-Donu, 344090 (Russian Federation); Leblanc, Catherine; Michel, Gurvan; Potin, Philippe [Centre National de la Recherche Scientifique and Universite Pierre et Marie Curie Paris-VI, Station Biologique de Roscoff, Place Georges Teissier, BP 74, F-29682 Roscoff cedex, Bretagne (France); Kuepper, Frithjof C [Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, Scotland (United Kingdom); Hollenstein, Kaspar; Locher, Kaspar P [Institute of Molecular Biology and Biophysics, ETH Zuerich, Schafmattstrasse 20, Zuerich, 8093 (Switzerland); Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R, E-mail: m.feiters@science.ru.n [Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft (Netherlands)

    2009-11-15

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L{sub 3} (2p{sub 3/2}) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  10. Anion binding in biological systems

    International Nuclear Information System (INIS)

    Feiters, Martin C; Meyer-Klaucke, Wolfram; Kostenko, Alexander V; Soldatov, Alexander V; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Kuepper, Frithjof C; Hollenstein, Kaspar; Locher, Kaspar P; Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R

    2009-01-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L 3 (2p 3/2 ) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  11. Anion binding in biological systems

    Science.gov (United States)

    Feiters, Martin C.; Meyer-Klaucke, Wolfram; Kostenko, Alexander V.; Soldatov, Alexander V.; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Küpper, Frithjof C.; Hollenstein, Kaspar; Locher, Kaspar P.; Bevers, Loes E.; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

    2009-11-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L3 (2p3/2) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  12. Outlook of COMPASS RICH1 data handling algorithms

    CERN Document Server

    Finger, Miroslav H

    2003-01-01

    COMPASS is a fixed target experiment at the CERN SPS designed to study hadron spectroscopy with hadron beams and hadron structure with polarized muon beams. This paper is aiming to outlook the COMPASS RICH1 data handling algorithms in order to discuss some of the data analysis methods proposed for the RICH2 detector. The need for improvement and testing of COMPASS real data acquisition for better performance in realistic COMPASS environment is elaborated. The experience of more than 5 years of RICH1 software development and improvements oriented mainly on taking into account RICH1 constructive specifics, promises a similar hard work for RICH2 algorithmists. Its first stage is Monte Carlo simulation of RICH2 data. (14 refs).

  13. Synthesis and study of neutron-rich nuclides

    International Nuclear Information System (INIS)

    Luo Yixiao

    1995-01-01

    During the past few years our understanding of the decay properties and nuclear structure has been extended in a systematic fashion for the neutron-rich nuclei. This review will first sketch the production and identification of the neutron-rich nuclei throughout the whole mass region, and will then discuss the impressive progress in the studies of the exotic decay properties and nuclear structure of neutron-rich nuclei. Their astrophysical implications will also be outlined

  14. Hybrid photon detectors for the LHCb RICH

    CERN Document Server

    Eisenhardt, Stephan

    2006-01-01

    The LHCb Ring Imaging Cherenkov (RICH) counters use the pixel Hybrid Photon Detector (HPD) as a photo-sensitive device. Photo-electrons are produced in semi-transparent multi-alkali photo-cathode (S20) and are accelerated by a voltage of 20 kV onto a pixelated silicon anode. The anode is bump-bonded to the LHCBPIX1 pixel readout chip which amplifies and digitises the anode signals at the LHC speed of 40 MHz. Using a demagnification of five, the effective pixel size at the HPD window is 2.5 x 2.5 mm$^2$. Over the course of 18 months, 550 HPSs will undergo a quality-assurance programme to verify the specifications and to characterise the tubes. The tested parameters include the threshold and noise behaviour of the chip, the response to light emitting diode (LED) light, the demagnification of the electron optics, the leakage current and the depletion of the silicon sensor, the quality of the vacuum, the signal efficiency and the dark count rate. Results of tests of the first nine HPDs of the final design are pr...

  15. Methane rich gasification of wood pellets

    Directory of Open Access Journals (Sweden)

    Joka Magdalena

    2016-01-01

    Full Text Available In the work there are shown the results of experimental studies on methane rich gasification of pinewood pellets in Bio-CONOx technology. The experiment was carried out on a laboratory scale gasifier (5 kW, which design features allow producing a high quality gas with a high methane content. In the results there was identified the impact of the quantity of Bio-CONOx on the amount of flammable gas compounds (methane, hydrogen and carbon monoxide in the synthesis gas and the gas calorific value. The additive was added in 10,20,30 and 50% concentrations to the gasifier chamber. It has been shown that increasing the amount of the additive has a positive effect on the calorific value of the synthesis gas (Fig.1,2. Gas with a high content of methane (and high calorific value was obtained from gasification of biomass with a 50% addition of Bio-CONOx. There was also examined the proportion of blowing air (gasifying medium for which the properties of obtained syngas were the best.

  16. Constructing rich false memories of committing crime.

    Science.gov (United States)

    Shaw, Julia; Porter, Stephen

    2015-03-01

    Memory researchers long have speculated that certain tactics may lead people to recall crimes that never occurred, and thus could potentially lead to false confessions. This is the first study to provide evidence suggesting that full episodic false memories of committing crime can be generated in a controlled experimental setting. With suggestive memory-retrieval techniques, participants were induced to generate criminal and noncriminal emotional false memories, and we compared these false memories with true memories of emotional events. After three interviews, 70% of participants were classified as having false memories of committing a crime (theft, assault, or assault with a weapon) that led to police contact in early adolescence and volunteered a detailed false account. These reported false memories of crime were similar to false memories of noncriminal events and to true memory accounts, having the same kinds of complex descriptive and multisensory components. It appears that in the context of a highly suggestive interview, people can quite readily generate rich false memories of committing crime.

  17. Photoconduction in silicon rich oxide films

    Science.gov (United States)

    Luna-López, J. A.; Aceves-Mijares, M.; Carrillo-López, J.; Morales-Sanchez, A.; Flores-Gracia, F. J.; Garcia-Salgado, G.

    2009-05-01

    Photoconduction of silicon rich oxide (SRO) thin films were studied by current-voltage (I-V) measurements, where ultraviolet (UV) and white (Vis) light illumination were applied. SRO thin films were deposited by low pressure chemical vapour deposition (LPCVD) technique, using SiH4 (silane) and N2O (nitrous oxide) as reactive gases at 700 °. The gas flow ratio, Ro = [N2O]/[SiH4] was used to control the silicon excess. The thickness and refractive index of the SRO films were 72.0 nm, 75.5 nm, 59.1 nm, 73.4 nm and 1.7, 1.5, 1.46, 1.45, corresponding to Ro = 10, 20, 30 and 50, respectively. These results were obtained by null ellipsometry. Si nanoparticles (Si-nps) and defects within SRO films permit to obtain interesting photoelectric properties as a high photocurrent and photoconduction. These effects strongly depend on the silicon excess, thickness and structure type. Two different structures (Al/SRO/Si and Al/SRO/SRO/Si metal-oxide-semiconductor (MOS)-like structures) were fabricated and used as devices. The photocurrent in these structures is dominated by the generation of carriers due to the incident photon energies (~3.0-1.6 eV and 5 eV). These structures showed large photoconductive response at room temperature. Therefore, these structures have potential applications in optoelectronics devices.

  18. Photoconduction in silicon rich oxide films

    Energy Technology Data Exchange (ETDEWEB)

    Luna-Lopez, J A; Carrillo-Lopez, J; Flores-Gracia, F J; Garcia-Salgado, G [CIDS-ICUAP, Benemerita Universidad Autonoma de Puebla. Ed. 103 D and C, col. San Manuel, Puebla, Pue. Mexico 72570 (Mexico); Aceves-Mijares, M; Morales-Sanchez, A, E-mail: jluna@buap.siu.m, E-mail: jluna@inaoep.m [INAOE, Luis Enrique Erro No. 1, Apdo. 51, Tonantzintla, Puebla, Mexico 72000 (Mexico)

    2009-05-01

    Photoconduction of silicon rich oxide (SRO) thin films were studied by current-voltage (I-V) measurements, where ultraviolet (UV) and white (Vis) light illumination were applied. SRO thin films were deposited by low pressure chemical vapour deposition (LPCVD) technique, using SiH{sub 4} (silane) and N{sub 2}O (nitrous oxide) as reactive gases at 700 {sup 0}. The gas flow ratio, Ro = [N{sub 2}O]/[SiH{sub 4}] was used to control the silicon excess. The thickness and refractive index of the SRO films were 72.0 nm, 75.5 nm, 59.1 nm, 73.4 nm and 1.7, 1.5, 1.46, 1.45, corresponding to R{sub o} = 10, 20, 30 and 50, respectively. These results were obtained by null ellipsometry. Si nanoparticles (Si-nps) and defects within SRO films permit to obtain interesting photoelectric properties as a high photocurrent and photoconduction. These effects strongly depend on the silicon excess, thickness and structure type. Two different structures (Al/SRO/Si and Al/SRO/SRO/Si metal-oxide-semiconductor (MOS)-like structures) were fabricated and used as devices. The photocurrent in these structures is dominated by the generation of carriers due to the incident photon energies ({approx}3.0-1.6 eV and 5 eV). These structures showed large photoconductive response at room temperature. Therefore, these structures have potential applications in optoelectronics devices.

  19. The HERMES dual-radiator RICH detector

    CERN Document Server

    Jackson, H E

    2003-01-01

    The HERMES experiment emphasizes measurements of semi-inclusive deep-inelastic scattering. Most of the hadrons produced lie between 2 and 10 GeV, a region in which it had not previously been feasible to separate pions, kaons, and protons with standard particle identification (PID) techniques. The recent development of new clear, large, homogeneous and hydrophobic silica aerogel material with a low index of refraction offered the means to apply RICH PID techniques to this difficult momentum region. The HERMES instrument uses two radiators, C sub 4 F sub 1 sub 0 , a heavy fluorocarbon gas, and a wall of silica aerogel tiles. A lightweight spherical mirror constructed using a newly perfected technique to make resin-coated carbon-fiber surfaces of optical quality provides optical focusing on a photon detector consisting of 1934 photomultiplier tubes (PMT) for each detector half. The PMT array is held in a soft steel matrix to provide shielding against the residual field of the main spectrometer magnet. Ring recon...

  20. A Metadata-Rich File System

    Energy Technology Data Exchange (ETDEWEB)

    Ames, S; Gokhale, M B; Maltzahn, C

    2009-01-07

    Despite continual improvements in the performance and reliability of large scale file systems, the management of file system metadata has changed little in the past decade. The mismatch between the size and complexity of large scale data stores and their ability to organize and query their metadata has led to a de facto standard in which raw data is stored in traditional file systems, while related, application-specific metadata is stored in relational databases. This separation of data and metadata requires considerable effort to maintain consistency and can result in complex, slow, and inflexible system operation. To address these problems, we have developed the Quasar File System (QFS), a metadata-rich file system in which files, metadata, and file relationships are all first class objects. In contrast to hierarchical file systems and relational databases, QFS defines a graph data model composed of files and their relationships. QFS includes Quasar, an XPATH-extended query language for searching the file system. Results from our QFS prototype show the effectiveness of this approach. Compared to the defacto standard, the QFS prototype shows superior ingest performance and comparable query performance on user metadata-intensive operations and superior performance on normal file metadata operations.

  1. Plasma rico en plaquetas Platelet -rich plasma

    Directory of Open Access Journals (Sweden)

    J. González Lagunas

    2006-04-01

    Full Text Available El Plasma Rico en Plaquetas es una suspensión concentrada de la sangre centrifugada que contiene elevadas concentraciones de trombocitos. Durante los últimos años, este producto ha aparecido de forma repetida en publicaciones científicas y en medios de comunicación generales como un producto que por sus características induce la curación y regeneración de los tejidos. La premisa de su uso es que las elevadas concentraciones de plaquetas en el PRP, liberan cantidades significativas de factores de crecimiento. En este artículo se van a recoger las evidencias científicas que se han presentado en la literatura médica con respecto al PRP y a la curación ósea, así como las diferentes aplicaciones clínicas que se han sugerido.Platelet-rich plasma is a by-product of centrifuged whole blood that contains high levels of thrombocytes. In the last decade, scientific and media interest has been generated by this product that apparently has the capacity of inducing and promoting tissue healing and regeneration. The premise of its use is that the large number of platelets in PRP release significant amounts of growth factors. In this paper, a critical review of the medical literature regarding PRP and bone healing will be presented. Also, the suggested clinical applications of the product will be addressed.

  2. Platelet-rich plasma for osteoarthritis treatment.

    Science.gov (United States)

    Knop, Eduardo; Paula, Luiz Eduardo de; Fuller, Ricardo

    2016-01-01

    We conducted a comprehensive and systematic search of the literature on the use of platelet-rich plasma (PRP) in the treatment of osteoarthritis, using the Medline, Lilacs, Cochrane and SciELO databases, from May 2012 to October 2013. A total of 23 studies were selected, with nine being controlled trials and, of these, seven randomized, which included 725 patients. In this series, the group receiving PRP showed improvement in pain and joint function compared to placebo and hyaluronic acid. The response lasted up to two years and was better in milder cases. However it was found that there is no standardization in the PRP production method, neither in the number, timing, and volume of applications. Furthermore, the populations studied were not clearly described in many studies. Thus, these results should be analyzed with caution, and further studies with more standardized methods would be necessary for a more consistent conclusion about the PRP role in osteoarthritis. Copyright © 2015 Elsevier Editora Ltda. All rights reserved.

  3. Fuel-rich, catalytic reaction experimental results

    Science.gov (United States)

    Rollbuhler, R. James

    1991-01-01

    Future aeropropulsion gas turbine combustion requirements call for operating at very high inlet temperatures, pressures, and large temperature rises. At the same time, the combustion process is to have minimum pollution effects on the environment. Aircraft gas turbine engines utilize liquid hydrocarbon fuels which are difficult to uniformly atomize and mix with combustion air. An approach for minimizing fuel related problems is to transform the liquid fuel into gaseous form prior to the completion of the combustion process. Experimentally obtained results are presented for vaporizing and partially oxidizing a liquid hydrocarbon fuel into burnable gaseous components. The presented experimental data show that 1200 to 1300 K reaction product gas, rich in hydrogen, carbon monoxide, and light-end hydrocarbons, is formed when flowing 0.3 to 0.6 fuel to air mixes through a catalyst reactor. The reaction temperatures are kept low enough that nitrogen oxides and carbon particles (soot) do not form. Results are reported for tests using different catalyst types and configurations, mass flowrates, input temperatures, and fuel to air ratios.

  4. Cell-type specificity of ChIP-predicted transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Håndstad Tony

    2012-08-01

    Full Text Available Abstract Background Context-dependent transcription factor (TF binding is one reason for differences in gene expression patterns between different cellular states. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq identifies genome-wide TF binding sites for one particular context—the cells used in the experiment. But can such ChIP-seq data predict TF binding in other cellular contexts and is it possible to distinguish context-dependent from ubiquitous TF binding? Results We compared ChIP-seq data on TF binding for multiple TFs in two different cell types and found that on average only a third of ChIP-seq peak regions are common to both cell types. Expectedly, common peaks occur more frequently in certain genomic contexts, such as CpG-rich promoters, whereas chromatin differences characterize cell-type specific TF binding. We also find, however, that genotype differences between the cell types can explain differences in binding. Moreover, ChIP-seq signal intensity and peak clustering are the strongest predictors of common peaks. Compared with strong peaks located in regions containing peaks for multiple transcription factors, weak and isolated peaks are less common between the cell types and are less associated with data that indicate regulatory activity. Conclusions Together, the results suggest that experimental noise is prevalent among weak peaks, whereas strong and clustered peaks represent high-confidence binding events that often occur in other cellular contexts. Nevertheless, 30-40% of the strongest and most clustered peaks show context-dependent regulation. We show that by combining signal intensity with additional data—ranging from context independent information such as binding site conservation and position weight matrix scores to context dependent chromatin structure—we can predict whether a ChIP-seq peak is likely to be present in other cellular contexts.

  5. Full Length Amelogenin Binds to Cell Surface LAMP-1 on Tooth Root/Periodontium Associated Cells

    Science.gov (United States)

    Zhang, Hai; Tompkins, Kevin; Garrigues, Jacques; Snead, Malcolm L.; Gibson, Carolyn W.; Somerman, Martha J.

    2010-01-01

    Objectives Lysosome-associated membrane protein-1 (LAMP-1) has been suggested to be a cell surface receptor for a specific amelogenin isoform, leucine-rich amelogenin peptide or LRAP. However, it is unclear if LAMP-1 is an amelogenin receptor for dental mesenchymal cells. The goal of this study was to determine if LAMP-1 serves as a cell surface binding site for full length amelogenin on tooth root/periodontium associated mesenchymal cells. Design Murine dental follicle cells and cementoblasts (OCCM-30) were cultured for 2 days followed by addition of full length recombinant mouse amelogenin, rp(H)M180. Dose-response (0 to 100 μg/ml) and time course (0 to 120 minutes) assays were performed to determine the optimal conditions for live cell surface binding using immuno-fluorescent microscopy. A competitive binding assay was performed to determine binding specificity by adding Emdogain (1 mg/ml) to the media. An antibody against LAMP-1 was used to detect the location of LAMP-1 on the cell surface and the pattern was compared to cell surface bound amelogenin. Both amelogenin and cell surface LAMP-1 were immuno-co-localized to compare the amount and distribution pattern. Results Maximum surface binding was achieved with 50 μg/ml of rp(H)M180 for 120 minutes. This binding was specific as demonstrated by competitive inhibition (79% lower) with the addition of Emdogain. The binding pattern for rp(H)M180 was similar to the distribution of surface LAMP-1 on dental follicle cells and cementoblasts. The high co-localization coefficient (0.92) for rp(H)M180 and LAMP-1 supports rp(H)M180 binding to cell surface LAMP-1. Conclusions The data from this study suggest that LAMP-1 can serve as a cell surface binding site for amelogenin on dental follicle cells and cementoblasts. PMID:20382373

  6. Cell binding fragments from a sponge proteoglycan-like aggregation factor.

    Science.gov (United States)

    Misevic, G N; Jumblatt, J E; Burger, M M

    1982-06-25

    The marine sponge Microciona prolifera aggregation factor (MAF) is a 2 X 10(7) dalton proteoglycan. MAF mediates species-specific cell-cell recognition through two functionally different sites: a Ca2+-independent species-specific cell binding site and a Ca2+-dependent MAF-MAF binding site. Dissociation procedures combined with protease treatment were used to produce cell-binding pieces from the large complex. The seven different sized fragments produced were all uronic acid-rich glycoproteins of the apparent molecular weights: 15 X 10(6), 2.5 X 10(5), 1.2 X 10(5), 7 X 10(4), 2.7 X 10(4), 5 X 10(3), and 3.6 X 10(3). Each of the fragments retained species-specific binding to Microciona cells and was also capable of inhibiting MAF-promoted cell aggregation. However, the fragments were unable to bind to MAF-conjugated agarose beads in the presence or absence of CA2+ ions. These three properties are those expected for the cell binding site of MAF. Since the binding affinity decreased linearly with decreasing molecular weight of the fragments, we believe that the cell binding sites in MAF may be highly polyvalent, although to fully support such a concept, a detailed chemical characterization of each of the fragments is needed. A high valency of cell binding sites would overcome a relatively low Ka for the single site and would thereby not only guarantee specificity but also explain the need for the large size of the proteoglycan complex found to mediate species-specific sponge aggregation.

  7. Solute-vacancy binding in aluminum

    International Nuclear Information System (INIS)

    Wolverton, C.

    2007-01-01

    Previous efforts to understand solute-vacancy binding in aluminum alloys have been hampered by a scarcity of reliable, quantitative experimental measurements. Here, we report a large database of solute-vacancy binding energies determined from first-principles density functional calculations. The calculated binding energies agree well with accurate measurements where available, and provide an accurate predictor of solute-vacancy binding in other systems. We find: (i) some common solutes in commercial Al alloys (e.g., Cu and Mg) possess either very weak (Cu), or even repulsive (Mg), binding energies. Hence, we assert that some previously reported large binding energies for these solutes are erroneous. (ii) Large binding energies are found for Sn, Cd and In, confirming the proposed mechanism for the reduced natural aging in Al-Cu alloys containing microalloying additions of these solutes. (iii) In addition, we predict that similar reduction in natural aging should occur with additions of Si, Ge and Au. (iv) Even larger binding energies are found for other solutes (e.g., Pb, Bi, Sr, Ba), but these solutes possess essentially no solubility in Al. (v) We have explored the physical effects controlling solute-vacancy binding in Al. We find that there is a strong correlation between binding energy and solute size, with larger solute atoms possessing a stronger binding with vacancies. (vi) Most transition-metal 3d solutes do not bind strongly with vacancies, and some are even energetically strongly repelled from vacancies, particularly for the early 3d solutes, Ti and V

  8. Lactoferrin binding molecules in human seminal plasma.

    Science.gov (United States)

    Thaler, C J; Vanderpuye, O A; McIntyre, J A; Faulk, W P

    1990-10-01

    During ejaculation, the iron binding protein lactoferrin binds to sperm and forms a major component of sperm-coating antigens. Physicochemical properties of lactoferrin in seminal plasma (SP) and on sperm differ from those of purified lactoferrin. These differences have been attributed to the binding of unknown seminal macromolecules to lactoferrin. We have studied lactoferrin binding molecules in SP. The SP samples were coated onto microtiter plates and tested for binding of biotinylated lactoferrin. SP was found to specifically bind biotinylated lactoferrin. This binding was competitively inhibited by coincubation with unlabeled lactoferrin but was not affected by control incubations done with human IgG or transferrin. Lactoferrin binding molecules in SP were biochemically characterized by using SDS-PAGE and ligand blotting. Biotinylated lactoferrin bound to SP molecules of approximately 120, 60 and 30 kDa. No binding was observed with biotinylated transferrin. The presence of molecules that associate with lactoferrin in SP was further studied by using crossed immunoelectrophoresis. Lactoferrin in SP immunoprecipitated as two peaks, one of which corresponded to purified lactoferrin. These results suggest that some lactoferrin molecules in SP are free and that others are associated with lactoferrin binding molecules. Binding of lactoferrin to lactoferrin binding molecules appears to change its physicochemical properties and thus could influence its biologic activity and its affinity to sperm.

  9. Acyl-coenzyme A binding protein (ACBP)

    DEFF Research Database (Denmark)

    Kragelund, B B; Knudsen, J; Poulsen, F M

    1999-01-01

    Acyl-coenzyme A binding proteins are known from a large group of eukaryote species and to bind a long chain length acyl-CoA ester with very high affinity. Detailed biochemical mapping of ligand binding properties has been obtained as well as in-depth structural studies on the bovine apo-protein a...

  10. Polymeric competitive protein binding adsorbents for radioassay

    International Nuclear Information System (INIS)

    Adams, R.J.

    1976-01-01

    Serum protein comprising specific binding proteins such as antibodies, B 12 intrinsic factor, thyroxin binding globulin and the like may be copolymerized with globulin constituents of serum by the action of ethylchloroformate to form readily packed insoluble precipitates which, following purification as by washing, are eminently suited for employment as competitive binding protein absorbents in radioassay procedures. 10 claims, no drawings

  11. Affinity maturation generates greatly improved xyloglucan-specific carbohydrate binding modules

    Directory of Open Access Journals (Sweden)

    Cicortas Gunnarsson Lavinia

    2009-10-01

    Full Text Available Abstract Background Molecular evolution of carbohydrate binding modules (CBM is a new approach for the generation of glycan-specific molecular probes. To date, the possibility of performing affinity maturation on CBM has not been investigated. In this study we show that binding characteristics such as affinity can be improved for CBM generated from the CBM4-2 scaffold by using random mutagenesis in combination with phage display technology. Results Two modified proteins with greatly improved affinity for xyloglucan, a key polysaccharide abundant in the plant kingdom crucial for providing plant support, were generated. Both improved modules differ from other existing xyloglucan probes by binding to galactose-decorated subunits of xyloglucan. The usefulness of the evolved binders was verified by staining of plant sections, where they performed better than the xyloglucan-binding module from which they had been derived. They discriminated non-fucosylated from fucosylated xyloglucan as shown by their ability to stain only the endosperm, rich in non-fucosylated xyloglucan, but not the integument rich in fucosylated xyloglucan, on tamarind seed sections. Conclusion We conclude that affinity maturation of CBM selected from molecular libraries based on the CBM4-2 scaffold is possible and has the potential to generate new analytical tools for detection of plant carbohydrates.

  12. Leishmania replication protein A-1 binds in vivo single-stranded telomeric DNA

    International Nuclear Information System (INIS)

    Neto, J.L. Siqueira; Lira, C.B.B.; Giardini, M.A.; Khater, L.; Perez, A.M.; Peroni, L.A.; Reis, J.R.R. dos; Freitas-Junior, L.H.; Ramos, C.H.I.; Cano, M.I.N.

    2007-01-01

    Replication protein A (RPA) is a highly conserved heterotrimeric single-stranded DNA-binding protein involved in different events of DNA metabolism. In yeast, subunits 1 (RPA-1) and 2 (RPA-2) work also as telomerase recruiters and, in humans, the complex unfolds G-quartet structures formed by the 3' G-rich telomeric strand. In most eukaryotes, RPA-1 and RPA-2 bind DNA using multiple OB fold domains. In trypanosomatids, including Leishmania, RPA-1 has a canonical OB fold and a truncated RFA-1 structural domain. In Leishmania amazonensis, RPA-1 alone can form a complex in vitro with the telomeric G-rich strand. In this work, we show that LaRPA-1 is a nuclear protein that associates in vivo with Leishmania telomeres. We mapped the boundaries of the OB fold DNA-binding domain using deletion mutants. Since Leishmania and other trypanosomatids lack homologues of known telomere end binding proteins, our results raise questions about the function of RPA-1 in parasite telomeres

  13. Calcium Binding by Ro 60 Multiple Antigenic Peptides on PVDF Membrane.

    Science.gov (United States)

    Kurien, Biji T; Bachmann, Michael P

    2015-01-01

    Antibodies directed against ribonucleoprotein (RNP) particles are observed in systemic lupus erythematosus. Ro RNP particle is one such target. It is composed of a 60 kDa protein (Ro 60 or SS-A) that is non-covalently associated with at least one of the four short uridine-rich RNAs (the hY RNAs). Previously, we showed that multiple antigenic peptides (MAPs) made from the sequence of the Ro 60 autoantigen could be used, using double-immunodiffusion studies, enzyme-linked immunosorbant assay, affinity chromatography, and surface plasmon resonance, to show intramolecular and intermolecular protein-protein interaction within the Ro 60 RNP particle. We also observed that calcium is important in mediating this interaction. We hypothesized, therefore, that 60 kDa Ro is a calcium-binding protein. To investigate this, we electrophoresed 60 kDa Ro MAPs, transferred them to PVDF membrane, and assayed calcium binding using the Quin-2 system. Several Ro 60 MAPs were found to bind calcium using this assay, as well as bovine serum albumin, another calcium-binding protein. However, a MAP constructed from the Sm autoantigen did not bind to calcium. These data, along with our observation regarding the involvement of calcium in protein-protein interaction occurring between Ro 60 antigen and Ro 60 MAPs, makes us propose that Ro 60 antigen is a calcium-binding protein.

  14. A General Aspect of Platelet Rich Plasma

    Directory of Open Access Journals (Sweden)

    Onur ORAL

    2015-08-01

    Full Text Available The aim of this scientific paper is to introduce Platelet Rich Plasma (PRP cure method by people who never heard about it. People can hurt their selves, thus they can have damaged tissue; for instance broken bone, a scar or a wounded area. Furthe rmore damaged tissue can be a cartilage tissue, which takes very long time to heal. Platelets, those exist in the veins as thrombus, come up to repair those damaged tissues. However, platelets would be insufficient to cure damaged area in a short time. At this point PRP cure method give a hand to the healing process. By centrifuging people’s own blood via special kits, platelets can be separated from blood cells as plasma. That plasma’s platelet density is 3 - 5 times greater than that blood’s platelet densit y. Afterwards PRP method is implemented by injection of plasma to the damaged area or tissue. After implementation of 2 - 4 sessions per week, damaged tissue can be regenerated. It is fast healing method because densified platelet plasma is used; and it is s afe because that plasma is obtained from people’s own blood. PRP can be implemented on many areas; for instance on dentistry, sports medicine, different kind of surgeries such as plastic, vascular or orthopedic and so on. When soccer players brake their le gs, their sports life come to the end, but what if their broken legs was healed better and faster than general healing process? To sum up, PRP is very safe and the future of healing process.

  15. Luminescence characterization of a sodium rich feldspar

    Energy Technology Data Exchange (ETDEWEB)

    Correcher, V.; Sanchez M, L. [CIEMAT, Av. Complutense 22, 28040 Madrid (Spain); Garcia G, J. [MNCN-CSIC, c/ J. Gutierrez Abascal 2, Madrid 28006 (Spain); Rivera, T. [CICATA-IPN, Av. Legaria 694, 11500 Mexico D.F. (Mexico)

    2006-07-01

    This paper reports on the radioluminescence (RL) and thermoluminescence (TL) properties of a sodium rich feldspar ((Na,K)[AlSi{sub 3}O{sub 8}]) with a mean molecular composition of orthoclase (Or) and albite (Ab) of Or{sub 1}Ab{sub 99}. Despite the complexity of the luminescence signals of the sample, it is possible to determine six different emission bands at about 300, 380, 420, 460, 550 and 680 nm. The 300 nm emission can be associated to structural defects related to the recombination process in which the Na{sup +} ion diffusion-limited is involved. The UV-blue emission band at (i) 380 nm is characteristic of mineral phases containing SiO{sub 4} tetrahedral and could be related to intrinsic defects in the lattice, (ii) the 420 nm band could be associated to the presence of Cu (II) ions placed next to the hole traps or the recombination on a centre formed from a hole-oxygen atom adjacent to two Al atoms (Al-O-Al) and (iii) the 460 nm waveband could be due to the presence of Ti{sup 4+}. The green and red emissions are respectively associated to the presence of Mn{sup 2+} and Fe{sup 3+} ions. The ratio between the relative intensities, peaked at 290 (the more intense waveband) and 550 nm is about 10:1 in both TL and RL; this fact indicates that the efficiency of recombination centres does no changes regardless on the type of the process. (Author)

  16. Drug binding properties of neonatal albumin

    DEFF Research Database (Denmark)

    Brodersen, R; Honoré, B

    1989-01-01

    Neonatal and adult albumin was isolated by gel chromatography on Sephacryl S-300, from adult and umbilical cord serum, respectively. Binding of monoacetyl-diamino-diphenyl sulfone, warfarin, sulfamethizole, and diazepam was studied by means of equilibrium dialysis and the binding data were analyzed...... by the method of several acceptable fitted curves. It was found that the binding affinity to neonatal albumin is less than to adult albumin for monoacetyl-diamino-diphenyl sulfone and warfarin. Sulfamethizole binding to the neonatal protein is similarly reduced when more than one molecule of the drug is bound...... per albumin molecule, and binding of the first sulfamethizole molecule is possibly reduced as well. Diazepam binds with equal affinity to the fetal and adult proteins. Among the two main albumin drug-binding functions, for warfarin and diazepam, the former is thus compromised in the newborn infant...

  17. Theoretical and Methodological Foundations of Statistical Evaluation of the Rich

    OpenAIRE

    Romanchuk N.

    2013-01-01

    In the paper main approaches of rich people identification are analyzed, the classifications of estimation methods of mentioned social group are given. The method of rich threshold identification with the use of Household Living Conditions Survey Data and System of National Accounts Data by the method of statistical weight calibration is proposed.

  18. Theoretical and Methodological Foundations of Statistical Evaluation of the Rich

    Directory of Open Access Journals (Sweden)

    Romanchuk N.

    2013-01-01

    Full Text Available In the paper main approaches of rich people identification are analyzed, the classifications of estimation methods of mentioned social group are given. The method of rich threshold identification with the use of Household Living Conditions Survey Data and System of National Accounts Data by the method of statistical weight calibration is proposed.

  19. Estimating tree species richness from forest inventory plot data

    Science.gov (United States)

    Ronald E. McRoberts; Dacia M. Meneguzzo

    2007-01-01

    Montreal Process Criterion 1, Conservation of Biological Diversity, expresses species diversity in terms of number of forest dependent species. Species richness, defined as the total number of species present, is a common metric for analyzing species diversity. A crucial difficulty in estimating species richness from sample data obtained from sources such as inventory...

  20. Factors determining plant species richness in Alaskan artic tundra

    NARCIS (Netherlands)

    Welle, van der M.E.W.; Vermeulen, P.J.; Shaver, G.R.; Berendse, F.

    2003-01-01

    We studied the relationship between plant N:P ratio, soil characteristics and species richness in wet sedge and tussock tundra in northern Alaska at seven sites. We also collected data on soil characteristics, above-ground biomass, species richness and composition. The N:P ratio of the vegetation

  1. Climate induced increases in species richness of marine fishes

    NARCIS (Netherlands)

    Hiddink, J.G.; Hofstede, ter R.

    2008-01-01

    Climate change has been predicted to lead to changes in local and regional species richness through species extinctions and latitudinal ranges shifts. Here, we show that species richness of fish in the North Sea, a group of ecological and socio-economical importance, has increased over a 22-year

  2. Rich Man, Poor Man: Developmental Differences in Attributions and Perceptions

    Science.gov (United States)

    Sigelman, Carol K.

    2012-01-01

    In an examination guided by cognitive developmental and attribution theory of how explanations of wealth and poverty and perceptions of rich and poor people change with age and are interrelated, 6-, 10-, and 14-year-olds (N = 88) were asked for their causal attributions and trait judgments concerning a rich man and a poor man. First graders, like…

  3. Small leucine-rich proteoglycans in the aging skeleton

    DEFF Research Database (Denmark)

    Young, M F; Bi, Y; Ameye, L

    2006-01-01

    Small Leucine-Rich Proteoglyans (SLRPs) are major skeletal extracellular matrix (ECM) components that comprise a family of 13 members containing repeats of a leucine-rich motif. To examine SLRP function, we generated mice deficient in one or more member and analyzed them at the tissue, cell and m...

  4. Enhancing Mathematical Learning in a Technology-Rich Environment

    Science.gov (United States)

    Suh, Jennifer M.; Johnston, Christopher J.; Douds, Joshua

    2008-01-01

    This article describes teachers working collaboratively to plan mathematics lessons in a technology-rich environment. Addressing the needs of their diverse students, in particular, English Language Learners and students with special needs, the authors discuss how a technology-rich learning environment influences critical features of the classroom.…

  5. Platelet rich plasma in dermatology and aesthetic medicine

    OpenAIRE

    Neerja Puri

    2015-01-01

    Platelet rich plasma is a promising therapy in dermatology and aesthetic medicine. In this article we will discuss the pros and cons of platelet rich plasma (PRP) and the usage of PRP in aesthetics. PRP is especially used for conditions like facial and neck rejuvenation, fine lines and wrinkles, abdominal striae and facial scarring.

  6. Platelet rich plasma in dermatology and aesthetic medicine

    Directory of Open Access Journals (Sweden)

    Neerja Puri

    2015-04-01

    Full Text Available Platelet rich plasma is a promising therapy in dermatology and aesthetic medicine. In this article we will discuss the pros and cons of platelet rich plasma (PRP and the usage of PRP in aesthetics. PRP is especially used for conditions like facial and neck rejuvenation, fine lines and wrinkles, abdominal striae and facial scarring.

  7. Knowledge and Consumption pattern of Vitamin A rich-foods ...

    African Journals Online (AJOL)

    Due to lack of knowledge, some of the household subject some foods rich in vitamin A to traditional medicine use rather than using them to enrich their meals. Conclusion: Knowledge of the technologies for storage and preservation of vitamin A rich foods is very important in stabilizing price and making the foods available ...

  8. Research Note Herbaceous plant species richness and composition ...

    African Journals Online (AJOL)

    This study investigated the relationship between grazing veld condition and herbaceous plant species richness in the moist Midlands Mistbelt Grassland in KwaZulu-Natal. The observed herbaceous plant species richness and composition of 12 sample plots (50 m x 50 m) was determined in three study sites using quadrat ...

  9. Consumption patterns of iron and vitamin a rich foods and ...

    African Journals Online (AJOL)

    The iron-rich foods most frequently consumed by the respondents were legumes, green leafy vegetables, nuts and seeds which respectively, made 41.9%, 17.1% and 11.2% contributions to iron intakes of the women. Vitamin A-rich foods most frequently consumed by the respondents were palm oil and vegetables which ...

  10. Lexical richness and collocational competence in second-language writing

    NARCIS (Netherlands)

    Vedder, I.; Benigno, V.

    2016-01-01

    In this article we report on an experiment set up to investigate lexical richness and collocational competence in the written production of 39 low-intermediate and intermediate learners of Italian L2. Lexical richness was assessed by means of a lexical profiling method inspired by Laufer and Nation

  11. Synthesis and study of neutron-rich nuclides

    International Nuclear Information System (INIS)

    Luo, Y.X.

    1995-01-01

    During the past few years our understanding of the decay properties and nuclear structure has been extended in a systematic fashion for the neutron-rich nuclei. This review will discuss the impressive progress in the studies of the exotic decay properties and nuclear structure of n-rich nuclei. Their astrophysical implications will also be outlined. ((orig.))

  12. Small leucine-rich proteoglycans in the aging skeleton

    DEFF Research Database (Denmark)

    Young, M F; Bi, Y; Ameye, L

    2006-01-01

    Small Leucine-Rich Proteoglyans (SLRPs) are major skeletal extracellular matrix (ECM) components that comprise a family of 13 members containing repeats of a leucine-rich motif. To examine SLRP function, we generated mice deficient in one or more member and analyzed them at the tissue, cell...

  13. Rich Nations vs. Poor Nations: Baiting the Global Trap.

    Science.gov (United States)

    Strada, Michael J.

    1985-01-01

    The growing differences between rich and poor nations effects the world's poor more immediately, but rich countries are vulnerable to resultant problems. This article faults American educational systems for not adequately addressing the nature of global dilemmas or their solutions. (DF)

  14. The Lack of Mutagenic Potential of a Guanine-Rich Triplex Forming Oligonucleotide in Physiological Conditions.

    Science.gov (United States)

    Saleh, Amer F; Fellows, Mick D; Ying, Liming; Gooderham, Nigel J; Priestley, Catherine C

    2017-01-01

    Triplex forming oligonucleotides (TFOs) bind in the major groove of DNA duplex in a sequence-specific manner imparted by Hoogsteen hydrogen bonds. There have been several reports demonstrating the ability of guanine-rich TFOs to induce targeted mutagenesis on an exogenous plasmid or an endogenous chromosomal locus. In particular, a 30mer guanine-rich triplex forming oligonucleotide, AG30, optimally designed to target the supFG1 reporter gene was reported to be mutagenic in the absence of DNA reactive agents in cultured cells and in vivo Here, we investigated the mutagenic potential of AG30 using the supFG1 shuttle vector forward mutation assay under physiological conditions. We also assessed the triplex binding potential of AG30 alongside cytotoxic and mutagenic assessment. In a cell free condition, AG30 was able to bind its polypurine target site in the supFG1 gene in the absence of potassium chloride and also aligned with a 5-fold increase in the mutant frequency when AG30 was pre-incubated with the supFG1 plasmid in the absence of potassium prior to transfection into COS-7 cells. However, when we analyzed triplex formation of AG30 and the supFG1 target duplex at physiological potassium levels, triplex formation was inhibited due to the formation of competing secondary structures. Subsequent assessment of mutant frequency under physiological conditions, by pre-transfecting COS-7 cells with the supFG1 plasmid prior to AG30 treatment led to a very small increase (1.4-fold) in the mutant frequency. Transfection of cells with even higher concentrations of AG30 did result in an elevated mutagenic response but this was also seen with a scrambled sequence, and was therefore considered unlikely to be biologically relevant as an associated increase in cytotoxicity was also apparent. Our findings also provide further assurance on the low potential of triplex-mediated mutation as a consequence of unintentional genomic DNA binding by therapeutic antisense oligonucleotides.

  15. Insulin binding to individual rat skeletal muscles

    International Nuclear Information System (INIS)

    Koerker, D.J.; Sweet, I.R.; Baskin, D.G.

    1990-01-01

    Studies of insulin binding to skeletal muscle, performed using sarcolemmal membrane preparations or whole muscle incubations of mixed muscle or typical red (soleus, psoas) or white [extensor digitorum longus (EDL), gastrocnemius] muscle, have suggested that red muscle binds more insulin than white muscle. We have evaluated this hypothesis using cryostat sections of unfixed tissue to measure insulin binding in a broad range of skeletal muscles; many were of similar fiber-type profiles. Insulin binding per square millimeter of skeletal muscle slice was measured by autoradiography and computer-assisted densitometry. We found a 4.5-fold range in specific insulin tracer binding, with heart and predominantly slow-twitch oxidative muscles (SO) at the high end and the predominantly fast-twitch glycolytic (FG) muscles at the low end of the range. This pattern reflects insulin sensitivity. Evaluation of displacement curves for insulin binding yielded linear Scatchard plots. The dissociation constants varied over a ninefold range (0.26-2.06 nM). Binding capacity varied from 12.2 to 82.7 fmol/mm2. Neither binding parameter was correlated with fiber type or insulin sensitivity; e.g., among three muscles of similar fiber-type profile, the EDL had high numbers of low-affinity binding sites, whereas the quadriceps had low numbers of high-affinity sites. In summary, considerable heterogeneity in insulin binding was found among hindlimb muscles of the rat, which can be attributed to heterogeneity in binding affinities and the numbers of binding sites. It can be concluded that a given fiber type is not uniquely associated with a set of insulin binding parameters that result in high or low binding

  16. Insulin binding to individual rat skeletal muscles

    Energy Technology Data Exchange (ETDEWEB)

    Koerker, D.J.; Sweet, I.R.; Baskin, D.G. (Univ. of Washington, Seattle (USA))

    1990-10-01

    Studies of insulin binding to skeletal muscle, performed using sarcolemmal membrane preparations or whole muscle incubations of mixed muscle or typical red (soleus, psoas) or white (extensor digitorum longus (EDL), gastrocnemius) muscle, have suggested that red muscle binds more insulin than white muscle. We have evaluated this hypothesis using cryostat sections of unfixed tissue to measure insulin binding in a broad range of skeletal muscles; many were of similar fiber-type profiles. Insulin binding per square millimeter of skeletal muscle slice was measured by autoradiography and computer-assisted densitometry. We found a 4.5-fold range in specific insulin tracer binding, with heart and predominantly slow-twitch oxidative muscles (SO) at the high end and the predominantly fast-twitch glycolytic (FG) muscles at the low end of the range. This pattern reflects insulin sensitivity. Evaluation of displacement curves for insulin binding yielded linear Scatchard plots. The dissociation constants varied over a ninefold range (0.26-2.06 nM). Binding capacity varied from 12.2 to 82.7 fmol/mm2. Neither binding parameter was correlated with fiber type or insulin sensitivity; e.g., among three muscles of similar fiber-type profile, the EDL had high numbers of low-affinity binding sites, whereas the quadriceps had low numbers of high-affinity sites. In summary, considerable heterogeneity in insulin binding was found among hindlimb muscles of the rat, which can be attributed to heterogeneity in binding affinities and the numbers of binding sites. It can be concluded that a given fiber type is not uniquely associated with a set of insulin binding parameters that result in high or low binding.

  17. The Origin and Evolution of Rich Clusters

    Science.gov (United States)

    Hora, Joseph

    Massive stars have an important role in many aspects of astrophysics, influencing the dynamics and composition of the ISM and shaping the structure of galaxies, and affect the formation of low mass stars and planets that form in their vicinity. However, the process of massive star formation is not as well understood as the formation of low-mass stars, and their study is made difficult because of their rarity and therefore large distances, and the high dust extinction present in the environment in which high mass stars form. Building on our successful Spitzer Legacy survey of the massive star formation region Cygnus-X, we propose to use Spitzer, Herschel, and WISE archival data, as well as other publicly available ancillary datasets, to extend our study of massive star forming regions to the richest clusters known outside of the Galactic center. With the data now available from these space missions, we now for the first time will be able to survey these regions to find and characterize the population of young stars in formation, locate the clusters and determine their relative ages, and explore the effects of feedback and triggering of new star formation by the massive stars in these regions. The star formation complexes we propose to study, which are at different evolutionary stages, will provide us with a view of massive star formation ranging from the early formation of the stars (protostars and protoclusters) to a revealed rich cluster. Moreover, we expect to significantly increase our statistics of the very rare high-mass protostars by identifying objects in the most active star-forming regions of the Galaxy. The existing data include several regions in the 5 kpc molecular ring, which is the most active region of star formation in our Galaxy. Star formation may be different in this region due to a higher overall density of massive molecular clouds and star formation, higher radiation fields and supernova rates, and a higher metallicity. Thus, the proposed

  18. Human plasminogen binding protein tetranectin

    DEFF Research Database (Denmark)

    Kastrup, J S; Rasmussen, H; Nielsen, B B

    1997-01-01

    The recombinant human plasminogen binding protein tetranectin (TN) and the C-type lectin CRD of this protein (TN3) have been crystallized. TN3 crystallizes in the tetragonal space group P4(2)2(1)2 with cell dimensions a = b = 64.0, c = 75.7 A and with one molecule per asymmetric unit. The crystals...... to at least 2.5 A. A full data set has been collected to 3.0 A. The asymmetric unit contains one monomer of TN. Molecular replacement solutions for TN3 and TN have been obtained using the structure of the C-type lectin CRD of rat mannose-binding protein as search model. The rhombohedral space group indicates...... diffract X-rays to at least 2.0 A resolution. A complete diffraction data set has been collected to 2.7 A resolution. The crystals of TN, obtained by the vapour-diffusion reverse salting-in method at 280 K, are rhombohedral, space group R3, with the hexagonal axes a = b = 89.1, c = 75.8 A, and diffract...

  19. Triphenyl borate as a bi-functional additive to improve surface stability of Ni-rich cathode material

    Science.gov (United States)

    Yim, Taeeun; Jang, Seol Heui; Han, Young-Kyu

    2017-12-01

    Nickel-rich cathode material has received marked attention as an advanced cathode material, however, its inferior surface property limits the achievement of high performance in lithium-ion batteries. We propose the use of a bi-functional additive of triphenyl borate (TPB) for improvement of the safety and electrochemical performance of Ni-rich cathode materials. First, TPB removes residual lithium species from the Ni-rich cathode surface via chemical binding with anion part of residual lithium species, and effectively reduces swelling behavior of the cell. Second, TPB creates effective cathode-electrolyte interphase (CEI) layers on the electrode surface by an electrochemical reaction, and greatly enhances the surface stability of the nickel-rich cathode. This work demonstrate that a cell cycled with the TPB additive exhibits a remarkable retention of 88.6% at 60 °C after 100 cycles for an NCM721 cathode material. We suggest a working mechanism for TPB based on systematic analyses, including in-situ and ex-situ experiments.

  20. Skipper Richness (Hesperiidae) Along Elevational Gradients in Brazilian Atlantic Forest.

    Science.gov (United States)

    Carneiro, E; Mielke, O H H; Casagrande, M M; Fiedler, K

    2014-02-01

    Hesperiidae are claimed to be a group of elusive butterflies that need major effort for sampling, thus being frequently omitted from tropical butterfly surveys. As no studies have associated species richness patterns of butterflies with environmental gradients of high altitudes in Brazil, we surveyed Hesperiidae ensembles in Serra do Mar along elevational transects (900-1,800 m above sea level) on three mountains. Transects were sampled 11-12 times on each mountain to evaluate how local species richness is influenced by mountain region, vegetation type, and elevational zones. Patterns were also analyzed for the subfamilies, and after disregarding species that exhibit hilltopping behavior. Species richness was evaluated by the observed richness, Jacknife2 estimator and Chao 1 estimator standardized by sample coverage. Overall, 155 species were collected, but extrapolation algorithms suggest a regional richness of about 220 species. Species richness was far higher in forest than in early successional vegetation or grassland. Richness decreased with elevation, and was higher on Anhangava mountain compared with the two others. Patterns were similar between observed and extrapolated Jacknife2 richness, but vegetation type and mountain richness became altered using sample coverage standardization. Hilltopping species were more easily detected than species that do not show this behavior; however, their inclusion did neither affect estimated richness nor modify the shape of the species accumulation curve. This is the first contribution to systematically study highland butterflies in southern Brazil where all records above 1,200 m are altitudinal extensions of the known geographical ranges of skipper species in the region.

  1. The Plant Leucine-Rich Repeat Receptor-Like Kinase PSY1R from Head to Toe

    DEFF Research Database (Denmark)

    Oehlenschlæger, Christian Berg

    PSY1R belongs to the family of plant leucine-rich repeat receptor-like kinases that play important roles in processes such as growth regulation and plant immunity response. PSY1R was proposed to be the receptor of the plant peptide hormone PSY1 which promotes cell expansion. PSY1R was furthermore...... are conserved among related plant leucine-rich repeat receptor-like kinases whereas Ser951 is unique for PSY1R which suggests that it may serve a specialized function in regulation of PSY1R kinase activity....... shown to phosphorylate and regulate the activity of the plasma membrane localized H+-ATPase, AHA2. While the mechanism of PSY1R-mediated AHA2 phosphorylation has previously been studied in detail, little is known about how PSY1R binds PSY1 peptide ligand and how the intracellular PSY1R kinase domain...

  2. Revascularization of Immature Necrotic Teeth: Platelet rich Fibrin an Edge over Platelet rich Plasma

    Directory of Open Access Journals (Sweden)

    Neelam Mittal

    2012-03-01

    Full Text Available Introduction: Revascularization is one such entity that has found its clinical application in the field of endodontics for the manage-ment of immature permanent necrotic teeth. The protocols for revascularization of such teeth focus especially on delivery of stem cells and scaffolds in a nonsurgical manner rather than concentrated growth micro molecules.The hypothesis: This article proposes the role of platelet concentrates such as platelet rich fibrin (PRF and platelet rich plasma (PRP in accelerating the regenerative process in such teeth. PRF unlike PRP is associated with slow, continuous and substantial re-lease of morphogens. It is hypothesized further if PRF instead of PRP when placed through immature apices in an orthograde manner can open newer gates for fast and controlled growth in young, ne-crotic, non-infected teeth.Evaluation of the hypothesis: Enhancement of the healing kinetics can be evaluated by change in size of periapical radiolucency, thickness of the dentinal walls, root elongation and apical closure compared between preoperative and postoperative standardized two dimensional/three dimensional radiographs taken on regular follow ups.

  3. Antimicrobial effect of platelet-rich plasma and platelet-rich fibrin.

    Science.gov (United States)

    Badade, Pallavi S; Mahale, Swapna A; Panjwani, Alisha A; Vaidya, Prutha D; Warang, Ayushya D

    2016-01-01

    Platelet concentrates have been extensively used in a variety of medical fields to promote soft- and hard-tissue regeneration. The significance behind their use lies in the abundance of growth factors (GFs) in platelets α-granules that promote wound healing. Other than releasing a pool of GFs upon activation, platelets also have many features that indicate their role in the anti-infective host defense. The aim of this study is to evaluate the antimicrobial activities of platelet-rich plasma (PRP) and platelet-rich fibrin (PRF) against periodontal disease-associated bacteria. Blood samples were obtained from ten adult male patients. PRP and PRF were procured using centrifugation. The antimicrobial activity of PRP and PRF was evaluated by microbial culturing using bacterial strains of Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans. P. gingivalis and A. actinomycetemcomitans were inhibited by PRP but not by PRF. PRP is a potentially useful substance in the fight against periodontal pathogens. This might represent a valuable property in adjunct to the enhancement of tissue regeneration.

  4. Platelet-rich plasma stimulates osteoblastic differentiation in the presence of BMPs

    International Nuclear Information System (INIS)

    Tomoyasu, Akihiro; Higashio, Kanji; Kanomata, Kazuhiro; Goto, Masaaki; Kodaira, Kunihiko; Serizawa, Hiroko; Suda, Tatsuo; Nakamura, Atsushi; Nojima, Junya; Fukuda, Toru; Katagiri, Takenobu

    2007-01-01

    Platelet-rich plasma (PRP) is clinically used as an autologous blood product to stimulate bone formation in vivo. In the present study, we examined the effects of PRP on proliferation and osteoblast differentiation in vitro in the presence of bone morphogenetic proteins (BMPs). PRP and its soluble fraction stimulated osteoblastic differentiation of myoblasts and osteoblastic cells in the presence of BMP-2, BMP-4, BMP-6 or BMP-7. The soluble PRP fraction stimulated osteoblastic differentiation in 3D cultures using scaffolds made of collagen or hydroxyapatite. Moreover, heparin-binding fractions obtained from serum also stimulated osteoblastic differentiation in the presence of BMP-4. These results suggested that platelets contain not only growth factors for proliferation but also novel potentiator(s) for BMP-dependent osteoblastic differentiation

  5. Capture ELISA for IgM antibodies against Plasmodium falciparum glutamate rich protein

    DEFF Research Database (Denmark)

    Dziegiel, Morten Hanefeld; Borre, M B; Petersen, E

    1992-01-01

    This report describes a novel mu chain capture ELISA for the detection of IgM antibodies against a Plasmodium falciparum antigen. A fragment of the 220 kDa P. falciparum glutamate rich protein containing amino acid residues 489-1271 was expressed in E. coli as a recombinant chimeric beta......-galactosidase fusion protein and used as antigen after purification and biotinylation. Specific IgM antibodies were found in 51% (39/77) of sera from adult Liberians immune to malaria. The binding of IgM antibodies was specific for the malaria portion of the fusion protein and no cross-reactivity was found in sera...... from patients with IgM antibodies due to other diseases. Inhibition studies with a fusion protein containing amino acid residues 816-1134 (GLURP816-1134) representing the carboxy-terminal repeat region suggested a different use of epitopes for IgM antibodies in different individuals....

  6. Susceptibility to Dental Caries and the Salivary Proline-Rich Proteins

    Directory of Open Access Journals (Sweden)

    Martin Levine

    2011-01-01

    Full Text Available Early childhood caries affects 28% of children aged 2–6 in the US and is not decreasing. There is a well-recognized need to identify susceptible children at birth. Caries-free adults neutralize bacterial acids in dental biofilms better than adults with severe caries. Saliva contains acidic and basic proline-rich proteins (PRPs which attach to oral streptococci. The PRPs are encoded within a small region of chromosome 12. An acidic PRP allele (Db protects Caucasian children from caries but is more common in African Americans. Some basic PRP allelic phenotypes have a three-fold greater frequency in caries-free adults than in those with severe caries. Early childhood caries may associate with an absence of certain basic PRP alleles which bind oral streptococci, neutralize biofilm acids, and are in linkage disequilibrium with Db in Caucasians. The encoding of basic PRP alleles is updated and a new technology for genotyping them is described.

  7. Anesthesia increases in vivo N-([{sup 18}F]fluoroethyl)piperidinyl benzilate binding to the muscarinic cholinergic receptor

    Energy Technology Data Exchange (ETDEWEB)

    Kilbourn, Michael R. [Division of Nuclear Medicine, Department of Radiology, University of Michigan Medical School, Ann Arbor, MI 48109-0552 (United States)]. E-mail: mkilbour@umich.edu; Ma Bing [Division of Nuclear Medicine, Department of Radiology, University of Michigan Medical School, Ann Arbor, MI 48109-0552 (United States); Butch, Elizabeth R. [Division of Nuclear Medicine, Department of Radiology, University of Michigan Medical School, Ann Arbor, MI 48109-0552 (United States); Quesada, Carole [Division of Nuclear Medicine, Department of Radiology, University of Michigan Medical School, Ann Arbor, MI 48109-0552 (United States); Sherman, Phillip S. [Division of Nuclear Medicine, Department of Radiology, University of Michigan Medical School, Ann Arbor, MI 48109-0552 (United States)

    2007-07-15

    The in vivo binding of N-[{sup 18}F]fluoroethyl-piperidinyl benzilate ([{sup 18}F]FEPB) to the muscarinic cholinergic receptor was measured in awake and anesthetized rats. Studies were done using an equilibrium infusion technique to provide estimates of specific binding as distribution volume ratios. Anesthesia with either isoflurane or sodium pentobarbital produced a significant (65-90%) increase of radiotracer binding in receptor-rich brain regions (striatum, cortex, hippocampus) relative to awake controls. Pretreatment of anesthetized animals with the acetylcholinesterase inhibitor phenserine produced no further increases in radioligand binding, in contrast to the large (>70%) increases previously observed in awake animals following drug treatment. These studies demonstrate that anesthesia can produce significant changes in baseline biochemical measures that can obscure even very large effects of pharmacological challenges.

  8. Radioautographic identification of lactogen binding sites in rat median eminence using 125I-human growth hormone

    International Nuclear Information System (INIS)

    Van Houten, M.; Posner, B.I.; Walsh, R.J.

    1980-01-01

    The binding characteristics of human growth hormone were exploited to identify radioautographically lactogen binding sites in the rat median eminence following systemic injection 125 I-human growth hormone bound preferentially to the lateral palisade zone, a region of median eminence rich in dopamine and LHRH. Coinjection of 125 I-human growth hormone with an excess of unlabeled human growth hormone or ovine prolactin, but not bovine growth hormone, competitively blocked 125 I-human growth hormone binding to the external median eminence. These observations provide direct evidence of recognition sites for lactogenic hormones in a discrete region of the median eminence associated with hypothalamic regulation of hypophyseal prolactin and luteinizing hormone secretion. Median eminence lactogen binding sites may mediate presumed direct effects of lactogenic hormones on the reproductive functions of the hypophysiotropic hypothalamus. (orig.) [de

  9. Binding characteristics of swine erythrocyte insulin receptors

    Energy Technology Data Exchange (ETDEWEB)

    Dieberg, G.; Bryan, G.S.; Sartin, J.L.; Williams, J.C.; Prince, T.J.; Kemppainen, R.J.

    1985-09-01

    Crossbred gilts had 8.8 +/- 1.1% maximum binding of ( SVI)insulin to insulin receptors on erythrocytes. The number of insulin-binding sites per cell was 137 +/- 19, with a binding affinity ranging from 7.4 X 10(7)M-1 to 11.2 X 10(7)M-1 and mean of 8.8 X 10(7)M-1. Pregnant sows had a significant increase in maximum binding due to an increase in number of receptor sites per cell. Lactating sows fed a high-fiber diet and a low-fiber diet did not develop a significant difference in maximum binding of insulin. Sows fed the low-fiber diet had a significantly higher number of binding sites and a significantly lower binding affinity than did sows fed a high-fiber diet. Receptor-binding affinity was lower in the low-fiber diet group than in cycling gilts, whereas data from sows fed the high-fiber diet did not differ from data for cycling gilts. Data from this study indicated that insulin receptors of swine erythrocytes have binding characteristics similar to those in other species. Pregnancy and diet will alter insulin receptor binding in swine.

  10. Hydrogen-Deuterium Exchange Mass Spectrometry Reveals Calcium Binding Properties and Allosteric Regulation of Downstream Regulatory Element Antagonist Modulator (DREAM).

    Science.gov (United States)

    Zhang, Jun; Li, Jing; Craig, Theodore A; Kumar, Rajiv; Gross, Michael L

    2017-07-18

    Downstream regulatory element antagonist modulator (DREAM) is an EF-hand Ca 2+ -binding protein that also binds to a specific DNA sequence, downstream regulatory elements (DRE), and thereby regulates transcription in a calcium-dependent fashion. DREAM binds to DRE in the absence of Ca 2+ but detaches from DRE under Ca 2+ stimulation, allowing gene expression. The Ca 2+ binding properties of DREAM and the consequences of the binding on protein structure are key to understanding the function of DREAM. Here we describe the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) and site-directed mutagenesis to investigate the Ca 2+ binding properties and the subsequent conformational changes of full-length DREAM. We demonstrate that all EF-hands undergo large conformation changes upon calcium binding even though the EF-1 hand is not capable of binding to Ca 2+ . Moreover, EF-2 is a lower-affinity site compared to EF-3 and -4 hands. Comparison of HDX profiles between wild-type DREAM and two EF-1 mutated constructs illustrates that the conformational changes in the EF-1 hand are induced by long-range structural interactions. HDX analyses also reveal a conformational change in an N-terminal leucine-charged residue-rich domain (LCD) remote from Ca 2+ -binding EF-hands. This LCD domain is responsible for the direct interaction between DREAM and cAMP response element-binding protein (CREB) and regulates the recruitment of the co-activator, CREB-binding protein. These long-range interactions strongly suggest how conformational changes transmit the Ca 2+ signal to CREB-mediated gene transcription.

  11. MHC-peptide binding: dimers of cysteine-containing nonapeptides bind with high affinity to HLA-A2.1 class I molecules.

    Science.gov (United States)

    Di Modugno, F; Mammi, C; Rosanò, L; Rubiu, O; Nisticò, P; Chersi, A

    1997-11-01

    Small peptides, 8-10 amino acids long, derived from degradation of cytoplasmic proteins by a proteasome-proteinase complex, are usually presented and recognized by CD8+ cytolytic T lymphocytes (CTLs) associated with major histocompatibility complex (MHC) class I molecules. Recently synthetic peptides were used for the in vitro induction of tumor-specific CTLs, offering another strategy in the study of the immune-response repertoire and providing a new tool in cancer vaccination and immunotherapy. Peptides derived from otherwise normal proteins, overexpressed in many tumors as products of the protooncogene, may represent a target for an immune response. This is the case of HER-2/neu gene (also known as ErbB-2), encoding a cysteine-rich glycoprotein transmembrane receptor with tyrosine kinase activity (gp185neu). Recent data, demonstrating that HLA-A2.1-related peptides are able to stimulate in vitro CD8+ lymphocytes, Prompted us to study the binding to HLA-A2.1 molecules of several gp185 synthetic peptides containing a cystein residue and to define the relevance of this amino acid residue in the reduced or oxidated form of the sulfhydryl group. We found that monomers and their homodimers, linked by a disulfide bridge, bind to HLA-A2.1 molecules with overlapping affinity. These results suggest that additional amino acids of the nonapeptide do not prevent the binding and the HLA refolding through chemical or sterical interactions. This might be of particular relevance for the in vivo processing of cysteine-rich proteins. Because ErbB-2 molecules, as tumor-differentiation antigens in melanoma, are cysteine-rich molecules, it may be relevant to evaluate the possible role of the cystine residues interacting with the T-cell receptor. The recognition of these heterodimers by CD8+ lymphocytes will require functional in vivo studies.

  12. Actin binding proteins and spermiogenesis

    Science.gov (United States)

    Mruk, Dolores D

    2011-01-01

    Drebrin E, an actin-binding protein lacking intrinsic activity in the regulation of actin dynamics (e.g., polymerization, capping, nucleation, branching, cross-linking, bundling and severing), is known to recruit actin regulatory proteins to a specific cellular site. Herein, we critically evaluate recent findings in the field which illustrate that drebrin E works together with two other actin-binding proteins, namely Arp3 (actin-related protein 3, a component of the Arp2/3 complex that simultaneously controls actin nucleation for polymerization and branching of actin filaments) and Eps8 (epidermal growth factor receptor pathway substrate 8 that controls capping of the barbed ends of actin filaments, as well as actin filament bundling) to regulate the homeostasis of F-actin filament bundles at the ectoplasmic specialization (ES), a testis-specific atypical adherens junction (AJ) in the seminiferous epithelium. This is mediated by the strict temporal and spatial expression of these three actin-binding proteins at the apical and basal ES at the Sertoli cell-spermatid (step 8–19) and Sertoli-Sertoli cell interface, respectively, during the seminiferous epithelial cycle of spermatogenesis. In this Commentary, we put forth a possible model by which drebrin E may be acting as a platform upon which proteins (e.g., Arp3) that are needed to alter the conformation of actin filament bundles at the ES can be recruited to the site, thus facilitating changes in cell shape and cell position in the epithelium during spermiogenesis and spermiation. In short, drebrin E may be acting as a “logistic” distribution center to manage different regulatory proteins at the apical ES, thereby regulating the dynamics of actin filament bundles and modulating the plasticity of the apical ES. This would allow adhesion to be altered continuously throughout the epithelial cycle to accommodate spermatid movement in the seminiferous epithelium during spermiogenesis and spermiation. We also

  13. The p53 target Wig-1 regulates p53 mRNA stability through an AU-rich element

    DEFF Research Database (Denmark)

    Vilborg, Anna; Glahder, Jacob-Andreas Harald; Wilhelm, Margareta T

    2009-01-01

    The p53 target gene Wig-1 encodes a double-stranded-RNA-binding zinc finger protein. We show here that Wig-1 binds to p53 mRNA and stabilizes it through an AU-rich element (ARE) in the 3' UTR of the p53 mRNA. This effect is mirrored by enhanced p53 protein levels in both unstressed cells and cells...... exposed to p53-activating stress agents. Thus, the p53 target Wig-1 is a previously undescribed ARE-regulating protein that acts as a positive feedback regulator of p53, with implications both for the steady-state levels of p53 and for the p53 stress response. Our data reveal a previously undescribed link...... between the tumor suppressor p53 and posttranscriptional gene regulation via AREs in mRNA....

  14. Investigation of the Copper Binding Site And the Role of Histidine As a Ligand in Riboflavin Binding Protein

    Energy Technology Data Exchange (ETDEWEB)

    Smith, S.R.; Bencze, K.Z.; Russ, K.A.; Wasiukanis, K.; Benore-Parsons, M.; Stemmler, T.L.

    2009-05-26

    Riboflavin Binding Protein (RBP) binds copper in a 1:1 molar ratio, forming a distinct well-ordered type II site. The nature of this site has been examined using X-ray absorption and pulsed electron paramagnetic resonance (EPR) spectroscopies, revealing a four coordinate oxygen/nitrogen rich environment. On the basis of analysis of the Cambridge Structural Database, the average protein bound copper-ligand bond length of 1.96 {angstrom}, obtained by extended x-ray absorption fine structure (EXAFS), is consistent with four coordinate Cu(I) and Cu(II) models that utilize mixed oxygen and nitrogen ligand distributions. These data suggest a Cu-O{sub 3}N coordination state for copper bound to RBP. While pulsed EPR studies including hyperfine sublevel correlation spectroscopy and electron nuclear double resonance show clear spectroscopic evidence for a histidine bound to the copper, inclusion of a histidine in the EXAFS simulation did not lead to any significant improvement in the fit.

  15. Disturbance alters local-regional richness relationships in appalachian forests

    Science.gov (United States)

    Belote, R.T.; Sanders, N.J.; Jones, R.H.

    2009-01-01

    Whether biological diversity within communities is limited by local interactions or regional species pools remains an important question in ecology. In this paper, we investigate how an experimentally applied tree-harvesting disturbance gradient influenced local-regional richness relationships. Plant species richness was measured at three spatial scales (2 ha = regional; 576 m2 and 1 m2 = local) on three occasions (one year pre-disturbance, one year post-disturbance, and 10 years post-disturbance) across five disturbance treatments (uncut control through clearcut) replicated throughout the southern Appalachian Mountains, USA. We investigated whether species richness in 576-m2 plots and 1-m2 subplots depended on species richness in 2-ha experimental units and whether this relationship changed through time before and after canopy disturbance. We found that, before disturbance, the relationship between local and regional richness was weak or nonexistent. One year after disturbance local richness was a positive function of regional richness, because local sites were colonized from the regional species pool. Ten years after disturbance, the positive relationship persisted, but the slope had decreased by half. These results suggest that disturbance can set the stage for strong influences of regional species pools on local community assembly in temperate forests. However, as time since disturbance increases, local controls on community assembly decouple the relationships between regional and local diversity. ?? 2009 by the Ecological Society of America.

  16. Synthetic LPS-Binding Polymer Nanoparticles

    Science.gov (United States)

    Jiang, Tian

    Lipopolysaccharide (LPS), one of the principal components of most gram-negative bacteria's outer membrane, is a type of contaminant that can be frequently found in recombinant DNA products. Because of its strong and even lethal biological effects, selective LPS removal from bioproducts solution is of particular importance in the pharmaceutical and health care industries. In this thesis, for the first time, a proof-of-concept study on preparing LPS-binding hydrogel-like NPs through facile one-step free-radical polymerization was presented. With the incorporation of various hydrophobic (TBAm), cationic (APM, GUA) monomers and cross-linkers (BIS, PEG), a small library of NPs was constructed. Their FITC-LPS binding behaviors were investigated and compared with those of commercially available LPS-binding products. Moreover, the LPS binding selectivity of the NPs was also explored by studying the NPs-BSA interactions. The results showed that all NPs obtained generally presented higher FITC-LPS binding capacity in lower ionic strength buffer than higher ionic strength. However, unlike commercial poly-lysine cellulose and polymyxin B agarose beads' nearly linear increase of FITC-LPS binding with particle concentration, NPs exhibited serious aggregation and the binding quickly saturated or even decreased at high particle concentration. Among various types of NPs, higher FITC-LPS binding capacity was observed for those containing more hydrophobic monomers (TBAm). However, surprisingly, more cationic NPs with higher content of APM exhibited decreased FITC-LPS binding in high ionic strength conditions. Additionally, when new cationic monomer and cross-linker, GUA and PEG, were applied to replace APM and BIS, the obtained NPs showed improved FITC-LPS binding capacity at low NP concentration. But compared with APM- and BIS-containing NPs, the FITC-LPS binding capacity of GUA- and PEG-containing NPs saturated earlier. To investigate the NPs' binding to proteins, we tested the NPs

  17. Sex hormone binding globulin phenotypes

    DEFF Research Database (Denmark)

    Cornelisse, M M; Bennett, Patrick; Christiansen, M

    1994-01-01

    Human sex hormone binding globulin (SHBG) is encoded by a normal and a variant allele. The resulting SHBG phenotypes (the homozygous normal SHBG, the heterozygous SHBG and the homozygous variant SHBG phenotype) can be distinguished by their electrophoretic patterns. We developed a novel detection....... This method of detection was used to determine the distribution of SHBG phenotypes in healthy controls of both sexes and in five different pathological conditions characterized by changes in the SHBG level or endocrine disturbances (malignant and benign ovarian neoplasms, hirsutism, liver cirrhosis...... on the experimental values. Differences in SHBG phenotypes do not appear to have any clinical significance and no sex difference was found in the SHBG phenotype distribution....

  18. Quantitative analysis and prediction of curvature in leucine-rich repeat proteins.

    Science.gov (United States)

    Hindle, K Lauren; Bella, Jordi; Lovell, Simon C

    2009-11-01

    Leucine-rich repeat (LRR) proteins form a large and diverse family. They have a wide range of functions most of which involve the formation of protein-protein interactions. All known LRR structures form curved solenoids, although there is large variation in their curvature. It is this curvature that determines the shape and dimensions of the inner space available for ligand binding. Unfortunately, large-scale parameters such as the overall curvature of a protein domain are extremely difficult to predict. Here, we present a quantitative analysis of determinants of curvature of this family. Individual repeats typically range in length between 20 and 30 residues and have a variety of secondary structures on their convex side. The observed curvature of the LRR domains correlates poorly with the lengths of their individual repeats. We have, therefore, developed a scoring function based on the secondary structure of the convex side of the protein that allows prediction of the overall curvature with a high degree of accuracy. We also demonstrate the effectiveness of this method in selecting a suitable template for comparative modeling. We have developed an automated, quantitative protocol that can be used to predict accurately the curvature of leucine-rich repeat proteins of unknown structure from sequence alone. This protocol is available as an online resource at http://www.bioinf.manchester.ac.uk/curlrr/.

  19. Proline-rich antimicrobial peptides: potential therapeutics against antibiotic-resistant bacteria.

    Science.gov (United States)

    Li, Wenyi; Tailhades, Julien; O'Brien-Simpson, Neil M; Separovic, Frances; Otvos, Laszlo; Hossain, M Akhter; Wade, John D

    2014-10-01

    The increasing resistance of pathogens to antibiotics causes a huge clinical burden that places great demands on academic researchers and the pharmaceutical industry for resolution. Antimicrobial peptides, part of native host defense, have emerged as novel potential antibiotic alternatives. Among the different classes of antimicrobial peptides, proline-rich antimicrobial peptides, predominantly sourced from insects, have been extensively investigated to study their specific modes of action. In this review, we focus on recent developments in these peptides. They show a variety of modes of actions, including mechanism shift at high concentration, non-lytic mechanisms, as well as possessing different intracellular targets and lipopolysaccharide binding activity. Furthermore, proline-rich antimicrobial peptides display the ability to not only modulate the immune system via cytokine activity or angiogenesis but also possess properties of penetrating cell membranes and crossing the blood brain barrier suggesting a role as potential novel carriers. Ongoing studies of these peptides will likely lead to the development of more potent antimicrobial peptides that may serve as important additions to the armoury of agents against bacterial infection and drug delivery.

  20. Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.

    Science.gov (United States)

    Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo; Schroeder, Susan J

    2017-05-01

    Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. © 2017 Phan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  1. Natural Proline-Rich Cyclopolypeptides from Marine Organisms: Chemistry, Synthetic Methodologies and Biological Status.

    Science.gov (United States)

    Fang, Wan-Yin; Dahiya, Rajiv; Qin, Hua-Li; Mourya, Rita; Maharaj, Sandeep

    2016-10-26

    Peptides have gained increased interest as therapeutics during recent years. More than 60 peptide drugs have reached the market for the benefit of patients and several hundreds of novel therapeutic peptides are in preclinical and clinical development. The key contributor to this success is the potent and specific, yet safe, mode of action of peptides. Among the wide range of biologically-active peptides, naturally-occurring marine-derived cyclopolypeptides exhibit a broad range of unusual and potent pharmacological activities. Because of their size and complexity, proline-rich cyclic peptides (PRCPs) occupy a crucial chemical space in drug discovery that may provide useful scaffolds for modulating more challenging biological targets, such as protein-protein interactions and allosteric binding sites. Diverse pharmacological activities of natural cyclic peptides from marine sponges, tunicates and cyanobacteria have encouraged efforts to develop cyclic peptides with well-known synthetic methods, including solid-phase and solution-phase techniques of peptide synthesis. The present review highlights the natural resources, unique structural features and the most relevant biological properties of proline-rich peptides of marine-origin, focusing on the potential therapeutic role that the PRCPs may play as a promising source of new peptide-based novel drugs.

  2. Recognition of Human Erythrocyte Receptors by the Tryptophan-Rich Antigens of Monkey Malaria Parasite Plasmodium knowlesi.

    Directory of Open Access Journals (Sweden)

    Kriti Tyagi

    Full Text Available The monkey malaria parasite Plasmodium knowlesi also infect humans. There is a lack of information on the molecular mechanisms that take place between this simian parasite and its heterologous human host erythrocytes leading to this zoonotic disease. Therefore, we investigated here the binding ability of P. knowlesi tryptophan-rich antigens (PkTRAgs to the human erythrocytes and sharing of the erythrocyte receptors between them as well as with other commonly occurring human malaria parasites.Six PkTRAgs were cloned and expressed in E.coli as well as in mammalian CHO-K1 cell to determine their human erythrocyte binding activity by cell-ELISA, and in-vitro rosetting assay, respectively.Three of six PkTRAgs (PkTRAg38.3, PkTRAg40.1, and PkTRAg67.1 showed binding to human erythrocytes. Two of them (PkTRAg40.1 and PkTRAg38.3 showed cross-competition with each other as well as with the previously described P.vivax tryptophan-rich antigens (PvTRAgs for human erythrocyte receptors. However, the third protein (PkTRAg67.1 utilized the additional but different human erythrocyte receptor(s as it did not cross-compete for erythrocyte binding with either of these two PkTRAgs as well as with any of the PvTRAgs. These three PkTRAgs also inhibited the P.falciparum parasite growth in in-vitro culture, further indicating the sharing of human erythrocyte receptors by these parasite species and the biological significance of this receptor-ligand interaction between heterologous host and simian parasite.Recognition and sharing of human erythrocyte receptor(s by PkTRAgs with human parasite ligands could be part of the strategy adopted by the monkey malaria parasite to establish inside the heterologous human host.

  3. Binding thermodynamics of a glutamate transporter homologue

    Science.gov (United States)

    Reyes, Nicolas; Oh, SeCheol; Boudker, Olga

    2013-01-01

    Glutamate transporters catalyze concentrative uptake of the neurotransmitter into glial cells and neurons. Their transport cycle involves binding and release of the substrate on the extra- and intracellular sides of the plasma membranes, and translocation of the substrate-binding site across the lipid bilayers. The energy of the ionic gradients, mainly sodium, fuels the cycle. Here, we used a cross-linking approach to trap a glutamate transporter homologue from Pyrococcus horikoshii in key conformational states with substrate-binding site facing either the extracellular or intracellular sides of the membrane to study their binding thermodynamics. We show that the chemical potential of sodium ions in solution is exclusively coupled to substrate binding and release, and not to substrate translocation. Despite the structural symmetry, the binding mechanisms are distinct on the opposite sides of the membrane and more complex than the current models suggest. PMID:23563139

  4. The rice transcription factor IDEF1 directly binds to iron and other divalent metals for sensing cellular iron status.

    Science.gov (United States)

    Kobayashi, Takanori; Itai, Reiko Nakanishi; Aung, May Sann; Senoura, Takeshi; Nakanishi, Hiromi; Nishizawa, Naoko K

    2012-01-01

    Iron is essential for most living organisms and its availability often determines survival and proliferation. The Oryza sativa (rice) transcription factor IDEF1 plays a crucial role in regulating iron deficiency-induced genes involved in iron homeostasis. In the present report, we found characteristic histidine-asparagine repeat and proline-rich regions in IDEF1 and its homolog in Hordeum vulgare (barley), HvIDEF1. An immobilized metal ion affinity chromatography assay revealed that IDEF1 and HvIDEF1 bind to various divalent metals, including Fe(2+) and Ni(2+) . Recombinant IDEF1 protein expressed in Escherichia coli contained mainly Fe and Zn. This metal-binding activity of IDEF1 was almost abolished by deletion of the histidine-asparagine and proline-rich regions, but DNA-binding and trans-activation functions were not impaired by the deletion. Transgenic rice plants constitutively overexpressing IDEF1 without these metal-binding domains failed to cause pleiotropic effects conferred by overexpression of full-length IDEF1, including a low germination rate, impaired seedling growth, tolerance to iron deficiency in hydroponic culture, and enhanced expression of various iron deficiency-inducible genes. Impairment of the transcriptional regulation of IDEF1 by deletion of the metal-binding domains occurred primarily at an early stage of iron deficiency. These results suggest that the histidine-asparagine and proline-rich regions in rice IDEF1 directly bind to divalent metals and sense the cellular metal ion balance caused by changes in iron availability. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

  5. Signatures of historical demography and pathogen richness on MHC class I genes.

    Science.gov (United States)

    Qutob, Nouar; Balloux, Francois; Raj, Towfique; Liu, Hua; Marion de Procé, Sophie; Trowsdale, John; Manica, Andrea

    2012-03-01

    The extreme polymorphism of MHC class I has been argued to be driven by balancing selection from pathogens, with the prediction that populations exposed to a wider variety of diseases should have higher diversity. We assembled a global database of allotype frequencies for MHC class I genes and investigated possible drivers of genetic diversity, measured in different ways. We first looked for a decline in diversity with distance from Africa (a consequence of drift during human expansions) and then investigated the link with pathogen richness once the effect of drift had been corrected for. Using heterozygosity, we recovered a clear decline in diversity from Africa and confirmed the positive relationship between genetic diversity and pathogen richness for all three classical MHC class I genes. However, when we considered a sequence-based measure of genetic diversity, the correlation with geographic distance from Africa vanished for HLA-C, and the correlations with pathogen richness for the three MHC class I genes were much weaker. HLA-C is known to consist of two functional classes of allotypes (classified with respect to the 80th residue), which interact with different KIR receptors. While this separation provided some improvement in the fit between genetic diversity and distance from Africa for one class, much clearer and consistent patterns were recovered when we used the 90th residue to separate HLA-C allotypes into two new classes. This suggests that this residue, which is also involved in the binding of KIR, might have had an important evolutionary role that has been overlooked.

  6. Binding of curcumin and its long chain derivatives to the activator binding domain of novel protein kinase C.

    Science.gov (United States)

    Majhi, Anjoy; Rahman, Ghazi M; Panchal, Shyam; Das, Joydip

    2010-02-15

    Protein kinase C (PKC) is a family of serine/threonine kinases that play a central role in cellular signal transduction. The second messenger diacylglycerol having two long carbon chains acts as the endogenous ligand for the PKCs. Polyphenol curcumin, the active constituent of Curcuma longa is an anti-cancer agent and modulates PKC activity. To develop curcumin derivatives as effective PKC activators, we synthesized several long chain derivatives of curcumin, characterized their absorption and fluorescence properties and studied their interaction with the activator binding second cysteine-rich C1B subdomain of PKCdelta, PKCepsilon and PKCtheta. Curcumin (1) and its C16 long chain analog (4) quenched the intrinsic fluorescence of PKCdeltaC1B, PKCepsilonC1B and PKCthetaC1B in a manner similar to that of PKC activator 12-O-tetradecanoylphorbol 13-acetate (TPA). The EC(50)s of the curcumin derivatives for fluorescence quenching varied in the range of 4-11 microM, whereas, EC(50)s for TPA varied in the range of 3-6 microM. Fluorescence emission maxima of 1 and 4 were blue shifted and the fluorescence anisotropy values were increased in the presence of the C1B domains in a manner similar to that shown by the fluorescent analog of TPA, sapintoxin-D, confirming that they were bound to the proteins. Molecular docking of 1 and 4 with novel PKC C1B revealed that both the molecules form hydrogen bonds with the protein residues. The present result shows that curcumin and its long chain derivatives bind to the C1B subdomain of novel PKCs and can be further modified structurally to improve its binding and activity. Copyright 2010 Elsevier Ltd. All rights reserved.

  7. Characterization of feline serum-cobalt binding.

    Science.gov (United States)

    Schnelle, Amy N; Barger, Anne M; MacNeill, Amy L; Mitchell, Mark M; Solter, Philip

    2015-06-01

    Oxidative stress inhibits albumin's ability to complex with cobalt. Feline serum-cobalt binding has not been described. The objective was to develop a cobalt binding test for use with feline serum, and correlate the results with other biochemical and cellular constituents in blood, and with clinical diseases of cats. A colorimetric test of cobalt binding, based on the oxidation-reduction reaction of Co(+2) and dithiothreitol, was developed using feline serum. The test was used to measure cobalt binding in stored serum from 176 cats presented to the University of Illinois Veterinary Teaching Hospital for a variety of disease conditions. Time-matched hematology and biochemical data, and clinical information, were obtained from the medical record of each cat and correlated with the serum-cobalt binding results. Serial dilution of feline serum with phosphate-buffered saline resulted in a highly linear decrease in serum-cobalt binding (r(2)  = .9984). Serum-cobalt binding of the clinical samples also correlated with albumin concentrations in a stepwise linear regression model (r(2)  = .425), and both cobalt binding and albumin were significantly decreased in cases of inflammation. Albumin and cobalt binding also shared significant correlations with several erythron variables, and serum concentration of total calcium and bilirubin. The correlation of cobalt binding measured by a colorimetric test with albumin concentration in the clinical samples and with serum dilution is consistent with feline albumin-cobalt complex formation. Hypoalbuminemia is the likely cause of reduced serum-cobalt binding in inflammation and the correlations observed between cobalt binding and other variables. © 2015 American Society for Veterinary Clinical Pathology.

  8. Binding energy of the barbell exciton

    Science.gov (United States)

    Peeters, F. M.; Golub, J. E.

    1991-02-01

    The exciton binding energy in asymmetric coupled double quantum wells is calculated. As the system is electrically tuned from type I to type II, the exciton binding energy decreases from that of a two-dimensional exciton to the binding energy of a spatially separated electron-hole pair, i.e., the barbell exciton.$-- We compare our theoretical results with a recent experiment and find good agreement.

  9. CAP binding proteins associated with the nucleus.

    OpenAIRE

    Patzelt, E; Blaas, D; Kuechler, E

    1983-01-01

    Cap binding proteins of HeLa cells were identified by photo-affinity labelling using the cap analogue gamma-[32P]-[4-(benzoyl-phenyl)methylamido]-7-methylguanosine-5'- triphosphate. Photoreaction with whole cell homogenates resulted in specific labelling of five major polypeptides. The small molecular weight polypeptide appeared to be identical to the 24 000 to 26 000 dalton cap binding protein previously identified in initiation factors. A cap binding protein of 37 000 dalton was found in in...

  10. Mutated Leguminous Lectin Containing a Heparin-Binding like Motif in a Carbohydrate-Binding Loop Specifically Binds to Heparin.

    Directory of Open Access Journals (Sweden)

    Hirohito Abo

    Full Text Available We previously introduced random mutations in the sugar-binding loops of a leguminous lectin and screened the resulting mutated lectins for novel specificities using cell surface display. Screening of a mutated peanut agglutinin (PNA, revealed a mutated PNA with a distinct preference for heparin. Glycan microarray analyses using the mutated lectin fused to the Fc region of human immunoglobulin, revealed that a particular sulfated glycosaminoglycan (GAG, heparin, had the highest binding affinity for mutated PNA among 97 glycans tested, although wild-type PNA showed affinity towards Galβ1-3GalNAc and similar galactosylated glycans. Further analyses of binding specificity using an enzyme-linked immunoadsorbent assay demonstrated that the mutated PNA specifically binds to heparin, and weakly to de-2-O-sulfated heparin, but not to other GAG chains including de-6-O-sulfated and de-N-sulfated heparins. The mutated PNA had six amino acid substitutions within the eight amino acid-long sugar-binding loop. In this loop, the heparin-binding like motif comprised three arginine residues at positions 124, 128, and 129, and a histidine at position 125 was present. Substitution of each arginine or histidine residue to alanine reduced heparin-binding ability, indicating that all of these basic amino acid residues contributed to heparin binding. Inhibition assay demonstrated that heparin and dextran sulfate strongly inhibited mutated PNA binding to heparin in dose-dependent manner. The mutated PNA could distinguish between CHO cells and proteoglycan-deficient mutant cells. This is the first report establishing a novel leguminous lectin that preferentially binds to highly sulfated heparin and may provide novel GAG-binding probes to distinguish between heterogeneous GAG repeating units.

  11. Mutated Leguminous Lectin Containing a Heparin-Binding like Motif in a Carbohydrate-Binding Loop Specifically Binds to Heparin.

    Science.gov (United States)

    Abo, Hirohito; Soga, Keisuke; Tanaka, Atsuhiro; Tateno, Hiroaki; Hirabayashi, Jun; Yamamoto, Kazuo

    2015-01-01

    We previously introduced random mutations in the sugar-binding loops of a leguminous lectin and screened the resulting mutated lectins for novel specificities using cell surface display. Screening of a mutated peanut agglutinin (PNA), revealed a mutated PNA with a distinct preference for heparin. Glycan microarray analyses using the mutated lectin fused to the Fc region of human immunoglobulin, revealed that a particular sulfated glycosaminoglycan (GAG), heparin, had the highest binding affinity for mutated PNA among 97 glycans tested, although wild-type PNA showed affinity towards Galβ1-3GalNAc and similar galactosylated glycans. Further analyses of binding specificity using an enzyme-linked immunoadsorbent assay demonstrated that the mutated PNA specifically binds to heparin, and weakly to de-2-O-sulfated heparin, but not to other GAG chains including de-6-O-sulfated and de-N-sulfated heparins. The mutated PNA had six amino acid substitutions within the eight amino acid-long sugar-binding loop. In this loop, the heparin-binding like motif comprised three arginine residues at positions 124, 128, and 129, and a histidine at position 125 was present. Substitution of each arginine or histidine residue to alanine reduced heparin-binding ability, indicating that all of these basic amino acid residues contributed to heparin binding. Inhibition assay demonstrated that heparin and dextran sulfate strongly inhibited mutated PNA binding to heparin in dose-dependent manner. The mutated PNA could distinguish between CHO cells and proteoglycan-deficient mutant cells. This is the first report establishing a novel leguminous lectin that preferentially binds to highly sulfated heparin and may provide novel GAG-binding probes to distinguish between heterogeneous GAG repeating units.

  12. Platelet-collagen adhesion enhances platelet aggregation induced by binding of VWF to platelets

    International Nuclear Information System (INIS)

    Laduca, F.M.; Bell, W.R.; Bettigole, R.E.

    1987-01-01

    Ristocetin-induced platelet aggregation (RIPA) was evaluated in the presence of platelet-collagen adhesion. RIPA of normal donor platelet-rich plasma (PRP) demonstrated a primary wave of aggregation mediated by the binding of von Willebrand factor (VWF) to platelets and a secondary aggregation wave, due to a platelet-release reaction, initiated by VWF-platelet binding and inhibitable by acetylsalicylic acid (ASA). An enhanced RIPA was observed in PRP samples to which collagen had been previously added. These subthreshold concentrations of collagen, which by themselves were insufficient to induce aggregation, caused measurable platelet-collagen adhesion. Subthreshold collagen did not cause microplatelet aggregation, platelet release of [ 3 H]serotonin, or alter the dose-responsive binding of 125 I-labeled VWF to platelets, which occurred with increasing ristocetin concentrations. However, ASA inhibition of the platelet release reaction prevented collagen-enhanced RIPA. These results demonstrate that platelet-collagen adhesion altered the platelet-release reaction induced by the binding of VWF to platelets causing a platelet-release reaction at a level of VWF-platelet binding not normally initiating a secondary aggregation. These findings suggest that platelet-collagen adhesion enhances platelet function mediated by VWF

  13. Characterization of two heparan sulphate-binding sites in the mycobacterial adhesin Hlp

    Directory of Open Access Journals (Sweden)

    Previato Jose O

    2008-05-01

    Full Text Available Abstract Background The histone-like Hlp protein is emerging as a key component in mycobacterial pathogenesis, being involved in the initial events of host colonization by interacting with laminin and glycosaminoglycans (GAGs. In the present study, nuclear magnetic resonance (NMR was used to map the binding site(s of Hlp to heparan sulfate and identify the nature of the amino acid residues directly involved in this interaction. Results The capacity of a panel of 30 mer synthetic peptides covering the full length of Hlp to bind to heparin/heparan sulfate was analyzed by solid phase assays, NMR, and affinity chromatography. An additional active region between the residues Gly46 and Ala60 was defined at the N-terminal domain of Hlp, expanding the previously defined heparin-binding site between Thr31 and Phe50. Additionally, the C-terminus, rich in Lys residues, was confirmed as another heparan sulfate binding region. The amino acids in Hlp identified as mediators in the interaction with heparan sulfate were Arg, Val, Ile, Lys, Phe, and Thr. Conclusion Our data indicate that Hlp interacts with heparan sulfate through two distinct regions of the protein. Both heparan sulfate-binding regions here defined are preserved in all mycobacterial Hlp homologues that have been sequenced, suggesting important but possibly divergent roles for this surface-exposed protein in both pathogenic and saprophic species.

  14. Drug binding properties of neonatal albumin

    DEFF Research Database (Denmark)

    Brodersen, R; Honoré, B

    1989-01-01

    Neonatal and adult albumin was isolated by gel chromatography on Sephacryl S-300, from adult and umbilical cord serum, respectively. Binding of monoacetyl-diamino-diphenyl sulfone, warfarin, sulfamethizole, and diazepam was studied by means of equilibrium dialysis and the binding data were analyzed...... by the method of several acceptable fitted curves. It was found that the binding affinity to neonatal albumin is less than to adult albumin for monoacetyl-diamino-diphenyl sulfone and warfarin. Sulfamethizole binding to the neonatal protein is similarly reduced when more than one molecule of the drug is bound...

  15. Bitopic Ligands and Metastable Binding Sites

    DEFF Research Database (Denmark)

    Fronik, Philipp; Gaiser, Birgit I; Sejer Pedersen, Daniel

    2017-01-01

    of orthosteric binding sites. Bitopic ligands have been employed to address the selectivity problem by combining (linking) an orthosteric ligand with an allosteric modulator, theoretically leading to high-affinity subtype selective ligands. However, it remains a challenge to identify suitable allosteric binding...... that have been reported to date, this type of bitopic ligands would be composed of two identical pharmacophores. Herein, we outline the concept of bitopic ligands, review metastable binding sites, and discuss their potential as a new source of allosteric binding sites....

  16. Parathyroid hormone binding to cultured avian osteoclasts

    Energy Technology Data Exchange (ETDEWEB)

    Teti, A.; Rizzoli, R.; Zambonin Zallone, A. (Univ. of Bari (Italy))

    1991-02-14

    Parathyroid hormone (PTH) increases serum calcium concentration via a controversial cellular mechanism. We investigated whether PTH binds avian osteoclasts. Isolated hypocalcaemic hen osteoclasts were incubated with ({sup 125}I)--bovine PTH (1-84). Specific binding of the hormone to the cells, which reached the equilibrium within 60 min, was observed. Half maximal binding was reached by 10 min. Binding was competitively inhibited by increasing doses of unlabeled PTH, and was about 55% displaced by adding, at the equilibrium, 10(-6) M unlabeled PTH. Autoradiography demonstrated specific label on the osteoclast. The cellular mechanism activated by the hormone remains to be elucidated.

  17. Expressed sequence tag analysis of vanadocytes in a vanadium-rich ascidian, Ascidia sydneiensis samea.

    Science.gov (United States)

    Yamaguchi, Nobuo; Kamino, Kei; Ueki, Tatsuya; Michibata, Hitoshi

    2004-01-01

    Some species in the family Ascidiidae accumulate vanadium at concentrations in excess of 350 mM, which corresponds to about 10(7) times higher than that in seawater. In these species signet ring cells, with a single huge vacuole in which vanadium ion is contained, function as vanadium-accumulating cells, vanadocytes. To investigate the mechanism underlying this phenomenon, we performed an expressed sequence tag (EST) analysis of a complementary DNA library from vanadocytes of a vanadium-rich ascidian, Ascidia sydneiensis samea. We determined the nucleotide sequences of 1000 ESTs and performed a BLAST analysis against the SwissProt database. We found 93 clones of metal-related gene homologues, including the ferritin heavy subunit, hemocyanin, and metallothionein. Two ESTs, in particular, exhibited significant similarity to vanabins that have been extracted from A. sydneiensis samea blood cells as low molecular weight vanadium-binding proteins. We have named the genes encoding these ESTs vanabin3 and vanabin4. Immobilized metal ion affinity chromatography revealed that these novel vanabin homologues bind vanadium(IV) ions.

  18. Disruption of Angiogenesis by Anthocyanin-Rich Extracts of Hibiscus sabdariffa

    Science.gov (United States)

    Joshua, Madu; Okere, Christiana; Sylvester, O’Donnell; Yahaya, Muhammad; Precious, Omale; Dluya, Thagriki; Um, Ji-Yeon; Neksumi, Musa; Boyd, Jessica; Vincent-Tyndall, Jennifer; Choo, Dong-Won; Gutsaeva, Diana R.; Jahng, Wan Jin

    2017-01-01

    Abnormal vessel formations contribute to the progression of specific angiogenic diseases including age-related macular degeneration. Adequate vessel growth and maintenance represent the coordinated process of endothelial cell proliferation, matrix remodeling, and differentiation. However, the molecular mechanism of the proper balance between angiogenic activators and inhibitors remains elusive. In addition, quantitative analysis of vessel formation has been challenging due to complex angiogenic morphology. We hypothesized that conjugated double bond containing-natural products, including anthocyanin extracts from Hibiscus sabdariffa, may control the proper angiogenesis. The current study was designed to determine whether natural molecules from African plant library modulate angiogenesis. Further, we questioned how the proper balance of anti- or pro-angiogenic signaling can be obtained in the vascular microenvironment by treating anthocyanin or fatty acids using chick chorioallantoic membrane angiogenesis model in ovo. The angiogenic morphology was analyzed systematically by measuring twenty one angiogenic indexes using Angiogenic Analyzer software. Chick chorioallantoic model demonstrated that anthocyanin-rich extracts inhibited angiogenesis in time- and concentration-dependent manner. Molecular modeling analysis proposed that hibiscetin as a component in Hibiscus may bind to the active site of vascular endothelial growth factor receptor 2 (VEGFR2) with ΔG= −8.42 kcal/mol of binding energy. Our results provided the evidence that anthocyanin is an angiogenic modulator that can be used to treat uncontrolled neovascular-related diseases, including age-related macular degeneration. PMID:28459020

  19. Disruption of Angiogenesis by Anthocyanin-Rich Extracts of Hibiscus sabdariffa.

    Science.gov (United States)

    Joshua, Madu; Okere, Christiana; Sylvester, O'Donnell; Yahaya, Muhammad; Precious, Omale; Dluya, Thagriki; Um, Ji-Yeon; Neksumi, Musa; Boyd, Jessica; Vincent-Tyndall, Jennifer; Choo, Dong-Won; Gutsaeva, Diana R; Jahng, Wan Jin

    2017-02-01

    Abnormal vessel formations contribute to the progression of specific angiogenic diseases including age-related macular degeneration. Adequate vessel growth and maintenance represent the coordinated process of endothelial cell proliferation, matrix remodeling, and differentiation. However, the molecular mechanism of the proper balance between angiogenic activators and inhibitors remains elusive. In addition, quantitative analysis of vessel formation has been challenging due to complex angiogenic morphology. We hypothesized that conjugated double bond containing-natural products, including anthocyanin extracts from Hibiscus sabdariffa , may control the proper angiogenesis. The current study was designed to determine whether natural molecules from African plant library modulate angiogenesis. Further, we questioned how the proper balance of anti- or pro-angiogenic signaling can be obtained in the vascular microenvironment by treating anthocyanin or fatty acids using chick chorioallantoic membrane angiogenesis model in ovo. The angiogenic morphology was analyzed systematically by measuring twenty one angiogenic indexes using Angiogenic Analyzer software. Chick chorioallantoic model demonstrated that anthocyanin-rich extracts inhibited angiogenesis in time- and concentration-dependent manner. Molecular modeling analysis proposed that hibiscetin as a component in Hibiscus may bind to the active site of vascular endothelial growth factor receptor 2 (VEGFR2) with ΔG= -8.42 kcal/mol of binding energy. Our results provided the evidence that anthocyanin is an angiogenic modulator that can be used to treat uncontrolled neovascular-related diseases, including age-related macular degeneration.

  20. Structural and functional insights into small, glutamine-rich, tetratricopeptide repeat protein alpha

    Directory of Open Access Journals (Sweden)

    Joanna D Roberts

    2015-12-01

    Full Text Available SGTA is a co-chaperone that interacts with molecular chaperones and steroid receptor complexes and plays an important role in various cellular pathways. It consists of three structural domains with individual functions, an N-terminal dimerisation domain (SGTA_NT that assists protein sorting pathways, a central tetratricopeptide repeat (TPR domain that interacts with heat-shock proteins and a C-terminal glutamine rich region that binds hydrophobic substrates. A range of biophysical techniques has been employed to characterize its structure and to investigate its interactions with binding partners. SGTA interacts with the androgen receptor and other steroid receptor complexes and has been shown to be linked to hormonally induced disease states. Therefore, a full structure of SGTA and further investigation of its function as a molecular co-chaperone could provide us with useful insights into the mechanisms of related pathologies. This review describes how some structural features of SGTA have been elucidated, and what this has uncovered about its function as a co-chaperone. A brief background on the structure and function of SGTA is given, highlighting its importance to biomedicine and related fields. The current level of knowledge and what remains to be understood about the structure and function of SGTA is summarised, discussing the potential direction of future research.

  1. Characterization of an aphid-specific, cysteine-rich protein enriched in salivary glands.

    Science.gov (United States)

    Guo, Kun; Wang, Wei; Luo, Lan; Chen, Jun; Guo, Ya; Cui, Feng

    2014-05-01

    Aphids secrete saliva into the phloem during their infestation of plants. Previous studies have identified numerous saliva proteins, but little is known about the characteristics (physical and chemical) and functions of these proteins in aphid-plant interactions. This study characterized an unknown protein (ACYPI39568) that was predicted to be enriched in the salivary glands of pea aphid. This protein belongs to an aphid-specific, cysteine-rich protein family that contains 14 conserved cysteines. ACYPI39568 is a monomeric globular protein with a high beta strand extent. The binding stoichiometric ratios for Zn(2+) and ACYPI39568 were approximately 3:1 and 1:1 at two binding sites. ACYPI39568 was predominantly expressed in the first instar stage and in the salivary glands. Aphids required more ACYPI39568 when feeding on plants than when feeding on an artificial diet. However, the interference of ACYPI39568 expression did not affect the survival rate of aphids on plants. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Retinoid-binding proteins: similar protein architectures bind similar ligands via completely different ways.

    Directory of Open Access Journals (Sweden)

    Yu-Ru Zhang

    Full Text Available BACKGROUND: Retinoids are a class of compounds that are chemically related to vitamin A, which is an essential nutrient that plays a key role in vision, cell growth and differentiation. In vivo, retinoids must bind with specific proteins to perform their necessary functions. Plasma retinol-binding protein (RBP and epididymal retinoic acid binding protein (ERABP carry retinoids in bodily fluids, while cellular retinol-binding proteins (CRBPs and cellular retinoic acid-binding proteins (CRABPs carry retinoids within cells. Interestingly, although all of these transport proteins possess similar structures, the modes of binding for the different retinoid ligands with their carrier proteins are different. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we analyzed the various retinoid transport mechanisms using structure and sequence comparisons, binding site analyses and molecular dynamics simulations. Our results show that in the same family of proteins and subcellular location, the orientation of a retinoid molecule within a binding protein is same, whereas when different families of proteins are considered, the orientation of the bound retinoid is completely different. In addition, none of the amino acid residues involved in ligand binding is conserved between the transport proteins. However, for each specific binding protein, the amino acids involved in the ligand binding are conserved. The results of this study allow us to propose a possible transport model for retinoids. CONCLUSIONS/SIGNIFICANCE: Our results reveal the differences in the binding modes between the different retinoid-binding proteins.

  3. RNA-binding domain in the nucleocapsid protein of gill-associated nidovirus of penaeid shrimp.

    Directory of Open Access Journals (Sweden)

    Chumporn Soowannayan

    Full Text Available Gill-associated virus (GAV infects Penaeus monodon shrimp and is the type species okavirus in the Roniviridae, the only invertebrate nidoviruses known currently. Electrophoretic mobility shift assays (EMSAs using His(6-tagged full-length and truncated proteins were employed to examine the nucleic acid binding properties of the GAV nucleocapsid (N protein in vitro. The EMSAs showed full-length N protein to bind to all synthetic single-stranded (ssRNAs tested independent of their sequence. The ssRNAs included (+ and (- sense regions of the GAV genome as well as a (+ sense region of the M RNA segment of Mourilyan virus, a crustacean bunya-like virus. GAV N protein also bound to double-stranded (dsRNAs prepared to GAV ORF1b gene regions and to bacteriophage M13 genomic ssDNA. EMSAs using the five N protein constructs with variable-length N-terminal and/or C-terminal truncations localized the RNA binding domain to a 50 amino acid (aa N-terminal sequence spanning Met(11 to Arg(60. Similarly to other RNA binding proteins, the first 16 aa portion of this sequence was proline/arginine rich. To examine this domain in more detail, the 18 aa peptide (M(11PVRRPLPPQPPRNARLI(29 encompassing this sequence was synthesized and found to bind nucleic acids similarly to the full-length N protein in EMSAs. The data indicate a fundamental role for the GAV N protein proline/arginine-rich domain in nucleating genomic ssRNA to form nucleocapsids. Moreover, as the synthetic peptide formed higher-order complexes in the presence of RNA, the domain might also play some role in protein/protein interactions stabilizing the helical structure of GAV nucleocapsids.

  4. Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1

    Directory of Open Access Journals (Sweden)

    Wang Xin

    2011-12-01

    Full Text Available Abstract Background RNA-binding proteins (RBPs play diverse roles in eukaryotic RNA processing. Despite their pervasive functions in coding and noncoding RNA biogenesis and regulation, elucidating the sequence specificities that define protein-RNA interactions remains a major challenge. Recently, CLIP-seq (Cross-linking immunoprecipitation followed by high-throughput sequencing has been successfully implemented to study the transcriptome-wide binding patterns of SRSF1, PTBP1, NOVA and fox2 proteins. These studies either adopted traditional methods like Multiple EM for Motif Elicitation (MEME to discover the sequence consensus of RBP's binding sites or used Z-score statistics to search for the overrepresented nucleotides of a certain size. We argue that most of these methods are not well-suited for RNA motif identification, as they are unable to incorporate the RNA structural context of protein-RNA interactions, which may affect to binding specificity. Here, we describe a novel model-based approach--RNAMotifModeler to identify the consensus of protein-RNA binding regions by integrating sequence features and RNA secondary structures. Results As an example, we implemented RNAMotifModeler on SRSF1 (SF2/ASF CLIP-seq data. The sequence-structural consensus we identified is a purine-rich octamer 'AGAAGAAG' in a highly single-stranded RNA context. The unpaired probabilities, the probabilities of not forming pairs, are significantly higher than negative controls and the flanking sequence surrounding the binding site, indicating that SRSF1 proteins tend to bind on single-stranded RNA. Further statistical evaluations revealed that the second and fifth bases of SRSF1octamer motif have much stronger sequence specificities, but weaker single-strandedness, while the third, fourth, sixth and seventh bases are far more likely to be single-stranded, but have more degenerate sequence specificities. Therefore, we hypothesize that nucleotide specificity and

  5. Structure of proton-rich nuclei of astrophysical interest

    Energy Technology Data Exchange (ETDEWEB)

    Roeckl, E. [Gesellschaft fuer Schwerionenforschung (GSI), Darmstadt (Germany)

    1998-06-01

    Recent experimental data concerning proton-rich nuclei between A=20 and A=100 are presented and discussed with respect to their relevance to the astrophysical rp process and to the calibration of solar neutrino detectors. (orig.)

  6. Antioxidative and Hepatoprotective Activities of Deinoxanthin-Rich ...

    African Journals Online (AJOL)

    Antioxidative and Hepatoprotective Activities of Deinoxanthin-Rich Extract from Deinococcus radiodurans R1 against Carbon Tetrachloride-Induced Liver Injury in Mice. J Cheng, Z Zhang, Z Zheng, G Lv, L Wang, B Tian, Y Hua ...

  7. Gridded Species Distribution, Version 1: Global Amphibians Family Richness Grids

    Data.gov (United States)

    National Aeronautics and Space Administration — Global Amphibians Family Richness Grids of the Gridded Species Distribution, Version 1 are aggregations of the presence grids data at the family level. They are...

  8. ELeaRNT: Evolutionary Learning of Rich Neural Network Topologies

    National Research Council Canada - National Science Library

    Matteucci, Matteo

    2006-01-01

    In this paper we present ELeaRNT an evolutionary strategy which evolves rich neural network topologies in order to find an optimal domain specific non linear function approximator with a good generalization performance...

  9. Ginkgotides: Proline-Rich Hevein-Like Peptides from GymnospermGinkgo biloba.

    Science.gov (United States)

    Wong, Ka H; Tan, Wei Liang; Serra, Aida; Xiao, Tianshu; Sze, Siu Kwan; Yang, Daiwen; Tam, James P

    2016-01-01

    Hevein and hevein-like peptides belong to the family of chitin-binding cysteine-rich peptides. They are classified into three subfamilies, the prototypic 8C- and the 6C- and 10C-hevein-like peptides. Thus far, only five 8C-hevein-like peptides have been characterized from three angiosperms and none from gymnosperm. To determine their occurrence and distribution in the gymnosperm, Ginkgo biloba leaves were examined. Here, we report the discovery and characterization of 11 novel 8C-hevein-like peptides, namely ginkgotides gB1-gB11. Proteomic analysis showed that the ginkgotides contain 41-44 amino acids (aa), a chitin-binding domain and are Pro-rich, a distinguishing feature that differs from other hevein-like peptides. Solution NMR structure determination revealed that gB5 contains a three β-stranded structure shaped by a cystine knot with an additional disulfide bond at the C-terminus. Transcriptomic analysis showed that the ginkgotide precursors contain a three-domain architecture, comprised of a C-terminal tail (20 aa) that is significantly shorter than those of other 8C- and 10C-hevein-like peptides, which generally contain a protein cargo such as a Barwin-like protein (126 aa) or class I chitinase (254 aa). Transcriptomic data mining found an additional 48 ginkgotide homologs in 39 different gymnosperms. Phylogenetic analysis revealed that ginkgotides and their homologs belong to a new class of 8C-hevein-like peptides. Stability studies showed that ginkgotides are highly resistant to thermal, acidic and endopeptidase degradation. Ginkgotides flanked at both the N- and C-terminal ends by Pro were resistant to exopeptidase degradation by carboxypeptidase A and aminopeptidase. Antifungal assays showed that ginkgotides inhibit the hyphal growth of phyto-pathogenic fungi. Taken together, ginkgotides represent the first suite of hevein-like peptides isolated and characterized from gymnosperms. As a group, they represent a novel class of 8C-hevein-like peptides that

  10. Ginkgotides: Proline-Rich Hevein-Like Peptides from Gymnosperm Ginkgo biloba

    Science.gov (United States)

    Wong, Ka H.; Tan, Wei Liang; Serra, Aida; Xiao, Tianshu; Sze, Siu Kwan; Yang, Daiwen; Tam, James P.

    2016-01-01

    Hevein and hevein-like peptides belong to the family of chitin-binding cysteine-rich peptides. They are classified into three subfamilies, the prototypic 8C- and the 6C- and 10C-hevein-like peptides. Thus far, only five 8C-hevein-like peptides have been characterized from three angiosperms and none from gymnosperm. To determine their occurrence and distribution in the gymnosperm, Ginkgo biloba leaves were examined. Here, we report the discovery and characterization of 11 novel 8C-hevein-like peptides, namely ginkgotides gB1–gB11. Proteomic analysis showed that the ginkgotides contain 41–44 amino acids (aa), a chitin-binding domain and are Pro-rich, a distinguishing feature that differs from other hevein-like peptides. Solution NMR structure determination revealed that gB5 contains a three β-stranded structure shaped by a cystine knot with an additional disulfide bond at the C-terminus. Transcriptomic analysis showed that the ginkgotide precursors contain a three-domain architecture, comprised of a C-terminal tail (20 aa) that is significantly shorter than those of other 8C- and 10C-hevein-like peptides, which generally contain a protein cargo such as a Barwin-like protein (126 aa) or class I chitinase (254 aa). Transcriptomic data mining found an additional 48 ginkgotide homologs in 39 different gymnosperms. Phylogenetic analysis revealed that ginkgotides and their homologs belong to a new class of 8C-hevein-like peptides. Stability studies showed that ginkgotides are highly resistant to thermal, acidic and endopeptidase degradation. Ginkgotides flanked at both the N- and C-terminal ends by Pro were resistant to exopeptidase degradation by carboxypeptidase A and aminopeptidase. Antifungal assays showed that ginkgotides inhibit the hyphal growth of phyto-pathogenic fungi. Taken together, ginkgotides represent the first suite of hevein-like peptides isolated and characterized from gymnosperms. As a group, they represent a novel class of 8C-hevein-like peptides

  11. Ginkgotides: Proline-rich Hevein-like Peptides from Gymnosperm Ginkgo biloba

    Directory of Open Access Journals (Sweden)

    Ka Ho Wong

    2016-11-01

    Full Text Available Hevein and hevein-like peptides belong to the family of chitin-binding cysteine-rich peptides. They are classified into three subfamilies, the prototypic 8C- and the 6C- and 10C-hevein-like peptides. Thus far, only five 8C-hevein-like peptides have been characterized from three angiosperms and none from gymnosperm. To determine their occurrence and distribution in the gymnosperm, Ginkgo biloba leaves were examined. Here, we report the discovery and characterization of eleven novel 8C-hevein-like peptides, namely ginkgotides gB1–gB11. Proteomic analysis showed that the ginkgotides contain 41–44 amino acids (aa, a chitin-binding domain and are Pro-rich, a distinguishing feature that differs from other hevein-like peptides. Solution 1H-NMR structure determination revealed that gB5 contains a three β-stranded structure shaped by a cystine knot with an additional disulfide bond at the C-terminus. Transcriptomic analysis showed that the ginkgotide precursors contain a three-domain architecture, comprised of a C-terminal tail (20 aa that is significantly shorter than those of other 8C- and 10C-hevein-like peptides, which generally contain a protein cargo such as a Barwin-like protein (126 aa or class I chitinase (254 aa. Transcriptomic data mining found an additional 48 ginkgotide homologs in 39 different gymnosperms. Phylogenetic analysis revealed that ginkgotides and their homologs belong to a new class of 8C-hevein-like peptides. Stability studies showed that ginkgotides are highly resistant to thermal, acidic and endopeptidase degradation. Ginkgotides flanked at both the N- and C-terminal ends by Pro were resistant to exopeptidase degradation by carboxypeptidase A and aminopeptidase. Antifungal assays showed that ginkgotides inhibit the hyphal growth of phyto-pathogenic fungi. Taken together, ginkgotides represent the first suite of hevein-like peptides isolated and characterized from gymnosperms. As a group, they represent a novel class of 8C

  12. Platelet Rich Plasma- mechanism of action and clinical applications

    OpenAIRE

    Cristina N. Cozma; Laura Raducu; Cristian R. Jecan

    2016-01-01

    Platelet-rich plasma (PRP) is a blood-derived fraction containing high level of platelets, a high concentration of leukocytes and growth factors. PRP therapy has been growing as a viable treatment alternative for a number of clinical applications and has a potential benefit for use in wound healing. Nowadays platelet rich plasma is used in stimulating wound healing in skin and soft tissue ulcerations, accelerating wound healing in diabetic patients and facilitating bone proliferation in ortho...

  13. Platelet-rich fibrin matrix for facial plastic surgery.

    Science.gov (United States)

    Sclafani, Anthony P; Saman, Masoud

    2012-05-01

    Platelets are known primarily for their role in hemostasis, but there is increasing interest in the effect of platelets on wound healing. Platelet isolates such as platelet-rich plasma have been advocated to enhance and accelerate wound healing. This article describes the use of a novel preparation, platelet-rich fibrin matrix (PRFM), for facial plastic surgery applications such as volume augmentation, fat transfer supplementation, and as an adjunct to open surgical procedures. Copyright © 2012 Elsevier Inc. All rights reserved.

  14. Geographic range size and determinants of avian species richness

    DEFF Research Database (Denmark)

    Jetz, Walter; Rahbek, Carsten

    2002-01-01

    species richness. Using both conventional and spatial regression models, we show that for sub-Saharan African birds, the apparent role of productivity diminishes with decreasing range size, whereas the significance of topographic heterogeneity increases. The relative importance of geometric constraints...... from the continental edge is moderate. Our findings highlight the failure of traditional species richness models to account for narrow-ranging species that frequently are also threatened....

  15. Monitoring of absolute mirror alignment at COMPASS RICH-1 detector

    Czech Academy of Sciences Publication Activity Database

    Alexeev, M.; Birsa, R.; Bradamante, F.; Bressan, A.; Chiosso, M.; Ciliberti, P.; Dalla Torre, S.; Denisov, O.; Duic, V.; Ferrero, A.; Finger, M.; Finger jr., M.; Gayde, J.Ch.; Giorgi, M.; Gobbo, B.; Levorato, S.; Maggiora, A.; Martin, A.; Menon, G.; Panzieri, D.; Pesaro, G.; Polák, Jaroslav; Rocco, E.; Sbrizzai, G.; Schiavon, P.; Slunečka, M.; Sozzi, F.; Steiger, Lukáš; Šulc, Miroslav; Takekawa, S.; Tessarotto, F.

    2014-01-01

    Roč. 766, December (2014), s. 208-211 ISSN 0168-9002. [International Workshop on Ring Imaging Cherenkov Detectors (RICH 2013)/8./. Hayama, Kanagawa, 02.12.2013-06.12.2013] Institutional support: RVO:61389021 Keywords : RICH * Cherenkov radiation * Mirror alignment * Photogrammetry Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.216, year: 2014 http://www.sciencedirect.com/science/article/pii/S0168900214008134#

  16. Partitioning sources of variation in vertebrate species richness

    Science.gov (United States)

    Boone, R.B.; Krohn, W.B.

    2000-01-01

    Aim: To explore biogeographic patterns of terrestrial vertebrates in Maine, USA using techniques that would describe local and spatial correlations with the environment. Location: Maine, USA. Methods: We delineated the ranges within Maine (86,156 km2) of 275 species using literature and expert review. Ranges were combined into species richness maps, and compared to geomorphology, climate, and woody plant distributions. Methods were adapted that compared richness of all vertebrate classes to each environmental correlate, rather than assessing a single explanatory theory. We partitioned variation in species richness into components using tree and multiple linear regression. Methods were used that allowed for useful comparisons between tree and linear regression results. For both methods we partitioned variation into broad-scale (spatially autocorrelated) and fine-scale (spatially uncorrelated) explained and unexplained components. By partitioning variance, and using both tree and linear regression in analyses, we explored the degree of variation in species richness for each vertebrate group that Could be explained by the relative contribution of each environmental variable. Results: In tree regression, climate variation explained richness better (92% of mean deviance explained for all species) than woody plant variation (87%) and geomorphology (86%). Reptiles were highly correlated with environmental variation (93%), followed by mammals, amphibians, and birds (each with 84-82% deviance explained). In multiple linear regression, climate was most closely associated with total vertebrate richness (78%), followed by woody plants (67%) and geomorphology (56%). Again, reptiles were closely correlated with the environment (95%), followed by mammals (73%), amphibians (63%) and birds (57%). Main conclusions: Comparing variation explained using tree and multiple linear regression quantified the importance of nonlinear relationships and local interactions between species

  17. High-resolution X-ray and NMR structures of the SMN Tudor domain : conformational variation in the binding site for symmetrically dimethylated arginine residues

    NARCIS (Netherlands)

    Sprangers, Remco; Groves, Matthew R; Sinning, Irmgard; Sattler, Michael

    2003-01-01

    The SMN protein, which is linked to spinal muscular atrophy (SMA), plays an important role in the assembly of the spliceosomal small nuclear ribonucleoprotein complexes. This function requires binding of SMN to the arginine-glycine (RG) rich C-terminal tails of the Sm proteins, which contain

  18. Tissue specificity of endothelin binding sites

    Energy Technology Data Exchange (ETDEWEB)

    Bolger, G.T.; Liard, F.; Krogsrud, R.; Thibeault, D.; Jaramillo, J. (BioMega, Inc., Laval, Quebec (Canada))

    1990-09-01

    A measurement was made of the binding of 125I-labeled endothelin (125I-ET) to crude membrane fractions prepared from rat aorta, atrium, ventricle, portal vein, trachea, lung parenchyma, vas deferens, ileum, bladder, and guinea-pig taenia coli and lung parenchyma. Scatchard analysis of 125I-ET binding in all tissues indicated binding to a single class of saturable sites. The affinity and density of 125I-ET binding sites varied between tissues. The Kd of 125I-ET binding was approximately 0.5 nM for rat aorta, trachea, lung parenchyma, ventricle, bladder, and vas deferens, and guinea-pig taenia coli and lung parenchyma, 1.8 nM for rat portal vein and atrium, and 3.3 nM for ileum. The Bmax of 125I-ET binding had the following rank order of density in rat tissues: trachea greater than lung parenchyma = vas deferens much greater than aorta = portal vein = atrium greater than bladder greater than ventricle = ileum. The properties of 125I-ET endothelin binding were characterized in rat ventricular membranes. 125I-ET binding was time dependent, reaching a maximum within 45-60 min at 25 degrees C. The calculated microassociation constant was 9.67 x 10(5) s-1 M-1. Only 15-20% of 125I-ET dissociated from its binding site even when dissociation was studied as long as 3 h. Preincubation of ventricular membranes with ET prevented binding of 125I-ET. 125I-ET binding was destroyed by boiling of ventricular membranes and was temperature, pH, and cation (Ca2+, Mg2+, and Na+) dependent.

  19. New DNA-binding radioprotectors

    Science.gov (United States)

    Martin, Roger

    The normal tissue damage associated with cancer radiotherapy has motivated the development at Peter Mac of a new class of DNA-binding radioprotecting drugs that could be applied top-ically to normal tissues at risk. Methylproamine (MP), the lead compound, reduces radiation induced cell kill at low concentrations. For example, experiments comparing the clonogenic survival of transformed human keratinocytes treated with 30 micromolar MP before and dur-ing various doses of ionising radiation, with the radiation dose response for untreated cells, indicate a dose reduction factor (DRF) of 2. Similar survival curve experiments using various concentrations of MP, with parallel measurements of uptake of MP into cell nuclei, have en-abled the relationship between drug uptake and extent of radioprotection to be established. Radioprotection has also been demonstrated after systemic administration to mice, for three different endpoints, namely lung, jejunum and bone marrow (survival at 30 days post-TBI). The results of pulse radiolysis studies indicated that the drugs act by reduction of transient radiation-induced oxidative species on DNA. This hypothesis was substantiated by the results of experiments in which MP radioprotection of radiation-induced DNA double-strand breaks, assessed as -H2AX foci, in the human keratinocyte cell line. For both endpoints, the extent of radioprotection increased with MP concentration up to a maximal value. These results are consistent with the hypothesis that radioprotection by MP is mediated by attenuation of the extent of initial DNA damage. However, although MP is a potent radioprotector, it becomes cytotoxic at higher concentrations. This limitation has been addressed in an extensive program of lead optimisation and some promising analogues have emerged from which the next lead will be selected. Given the clinical potential of topical radioprotection, the new analogues are being assessed in terms of delivery to mouse oral mucosa. This is

  20. Evaluation of nitrogen-rich macrocyclic ligands for the chelation of therapeutic bismuth radioisotopes.

    Science.gov (United States)

    Wilson, Justin J; Ferrier, Maryline; Radchenko, Valery; Maassen, Joel R; Engle, Jonathan W; Batista, Enrique R; Martin, Richard L; Nortier, Francois M; Fassbender, Michael E; John, Kevin D; Birnbaum, Eva R

    2015-05-01

    The use of α-emitting isotopes for radionuclide therapy is a promising treatment strategy for small micro-metastatic disease. The radioisotope (213)Bi is a nuclide that has found substantial use for targeted α-therapy (TAT). The relatively unexplored aqueous chemistry of Bi(3+), however, hinders the development of bifunctional chelating agents that can successfully deliver these Bi radioisotopes to the tumor cells. Here, a novel series of nitrogen-rich macrocyclic ligands is explored for their potential use as Bi-selective chelating agents. The ligands, 1,4,7,10-tetrakis(pyridin-2-ylmethyl)-1,4,7,10-tetraazacyclododecane (L(py)), 1,4,7,10-tetrakis(3-pyridazylmethyl)-1,4,7,10-tetraazacyclododecane (L(pyd)), 1,4,7,10-tetrakis(4-pyrimidylmethyl)-1,4,7,10-tetraazacyclododecane (L(pyr)), and 1,4,7,10-tetrakis(2-pyrazinylmethyl)-1,4,7,10-tetraazacyclododecane (L(pz)), were prepared by a previously reported method and investigated here for their abilities to bind Bi radioisotopes. The commercially available and commonly used ligands 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) and N-[(R)-2-amino-3-(p-isothiocyanato-phenyl)propyl]-trans-(S,S)- cyclohexane-1,2-diamine-N,N,N',N",N"-pentaacetic acid (CHX-A''-DTPA) were also explored for comparative purposes. Radio-thin-layer chromatography (TLC) was used to measure the binding kinetics and stabilities of the complexes formed. The long-lived isotope, (207)Bi (t(1/2)=32 years), was used for these studies. Density functional theory (DFT) calculations were also employed to probe the ligand interactions with Bi(3+) and the generator parent ion Ac(3+). In contrast to DOTA and CHX-A''-DTPA, these nitrogen-rich macrocycles selectively chelate Bi(3+) in the presence of the parent isotope Ac(3+). Among the four tested, L(py) was found to exhibit optimal Bi(3+)-binding kinetics and complex stability. L(py) complexes Bi(3+) more rapidly than DOTA, yet the resulting complexes are of similar stability. DFT calculations

  1. Geomorphic controls on elevational gradients of species richness.

    Science.gov (United States)

    Bertuzzo, Enrico; Carrara, Francesco; Mari, Lorenzo; Altermatt, Florian; Rodriguez-Iturbe, Ignacio; Rinaldo, Andrea

    2016-02-16

    Elevational gradients of biodiversity have been widely investigated, and yet a clear interpretation of the biotic and abiotic factors that determine how species richness varies with elevation is still elusive. In mountainous landscapes, habitats at different elevations are characterized by different areal extent and connectivity properties, key drivers of biodiversity, as predicted by metacommunity theory. However, most previous studies directly correlated species richness to elevational gradients of potential drivers, thus neglecting the interplay between such gradients and the environmental matrix. Here, we investigate the role of geomorphology in shaping patterns of species richness. We develop a spatially explicit zero-sum metacommunity model where species have an elevation-dependent fitness and otherwise neutral traits. Results show that ecological dynamics over complex terrains lead to the null expectation of a hump-shaped elevational gradient of species richness, a pattern widely observed empirically. Local species richness is found to be related to the landscape elevational connectivity, as quantified by a newly proposed metric that applies tools of complex network theory to measure the closeness of a site to others with similar habitat. Our theoretical results suggest clear geomorphic controls on elevational gradients of species richness and support the use of the landscape elevational connectivity as a null model for the analysis of the distribution of biodiversity.

  2. The Global Distribution and Drivers of Alien Bird Species Richness

    Science.gov (United States)

    Dyer, Ellie E.; Cassey, Phillip; Redding, David W.; Collen, Ben; Franks, Victoria; Gaston, Kevin J.; Jones, Kate E.; Kark, Salit; Orme, C. David L.; Blackburn, Tim M.

    2017-01-01

    Alien species are a major component of human-induced environmental change. Variation in the numbers of alien species found in different areas is likely to depend on a combination of anthropogenic and environmental factors, with anthropogenic factors affecting the number of species introduced to new locations, and when, and environmental factors influencing how many species are able to persist there. However, global spatial and temporal variation in the drivers of alien introduction and species richness remain poorly understood. Here, we analyse an extensive new database of alien birds to explore what determines the global distribution of alien species richness for an entire taxonomic class. We demonstrate that the locations of origin and introduction of alien birds, and their identities, were initially driven largely by European (mainly British) colonialism. However, recent introductions are a wider phenomenon, involving more species and countries, and driven in part by increasing economic activity. We find that, globally, alien bird species richness is currently highest at midlatitudes and is strongly determined by anthropogenic effects, most notably the number of species introduced (i.e., “colonisation pressure”). Nevertheless, environmental drivers are also important, with native and alien species richness being strongly and consistently positively associated. Our results demonstrate that colonisation pressure is key to understanding alien species richness, show that areas of high native species richness are not resistant to colonisation by alien species at the global scale, and emphasise the likely ongoing threats to global environments from introductions of species. PMID:28081142

  3. Environmental heterogeneity–species richness relationships from a global perspective

    Directory of Open Access Journals (Sweden)

    Anke Stein

    2016-01-01

    Full Text Available Spatial environmental heterogeneity (EH is considered one of the most important factors promoting species richness, but no general consent about the EH–richness relationship exists so far. This is because research methods and study settings vary widely, and because non-significant and negative associations have also been reported. My thesis provides a comprehensive review of the different measurements and terminologies of EH used in the literature, and presents strong quantitative evidence of a generally positive relationship between biotic and abiotic EH and species richness of terrestrial plants and animals from landscape to global extents. In a meta-analysis and a subsequent case study comparing multiple EH measures and their association with mammal species richness worldwide, I furthermore reveal that the outcome of EH–richness studies depends strongly on study design, including both the EH measure chosen and spatial scale. My research contributes to a better understanding of the EH–richness relationship, while identifying future research needs.

  4. Binding of (/sup 3/H)imipramine to human platelet membranes with compensation for saturable binding to filters and its implication for binding studies with brain membranes

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, O.M.; Wood, K.M.; Williams, D.C.

    1984-08-01

    Apparent specific binding of (/sup 3/H)imipramine to human platelet membranes at high concentrations of imipramine showed deviation from that expected of a single binding site, a result consistent with a low-affinity binding site. The deviation was due to displaceable, saturable binding to the glass fibre filters used in the assays. Imipramine, chloripramine, desipramine, and fluoxetine inhibited binding to filters whereas 5-hydroxytryptamine and ethanol were ineffective. Experimental conditions were developed that eliminated filter binding, allowing assay of high- and low-affinity binding to membranes. Failure to correct for filter binding may lead to overestimation of binding parameters, Bmax and KD for high-affinity binding to membranes, and may also be misinterpreted as indicating a low-affinity binding component in both platelet and brain membranes. Low-affinity binding (KD less than 2 microM) of imipramine to human platelet membranes was demonstrated and its significance discussed.

  5. Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

    KAUST Repository

    Evoli, Stefania

    2016-11-10

    Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S-isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. The most favorable binding modes correctly reproduce several experimentally identified binding locations, which include the two Sudlow\\'s drug sites (DS2 and DS1) and the fatty acid binding sites 6 and 2 (FA6 and FA2). Previously unknown details of the binding conformations were revealed for some of them, and formerly undetected binding modes were found in other protein sites. The calculated binding affinities exhibit trends which seem to agree with the available experimental data, and drastically degrade when the ligand is modeled in a protonated (neutral) state, indicating that ibuprofen associates with albumin preferentially in its charged form. These findings provide a detailed description of the binding of ibuprofen, help to explain a wide range of results reported in the literature in the last decades, and demonstrate the possibility of using simulation methods to predict ligand binding to albumin.

  6. Thermodynamics of Ligand Binding to Acyl-Coenzyme A Binding Protein Studied by Titration Calorimetry

    DEFF Research Database (Denmark)

    Færgeman, Nils Joakim; Sigurskjold, Bent Walther; Kragelund, Birthe B.

    1996-01-01

    Ligand binding to recombinant bovine acyl-CoA binding protein (ACBP) was examined using isothermal microcalorimetry. Microcalorimetric measurements confirm that the binding affinity of acyl-CoA esters for ACBP is strongly dependent on the length of the acyl chain with a clear preference for acyl-...

  7. Thermodynamics of ligand binding to acyl-coenzyme A binding protein studied by titration calorimetry

    DEFF Research Database (Denmark)

    Færgeman, Nils J.; Sigurskjold, B W; Kragelund, B B

    1996-01-01

    Ligand binding to recombinant bovine acyl-CoA binding protein (ACBP) was examined using isothermal microcalorimetry. Microcalorimetric measurements confirm that the binding affinity of acyl-CoA esters for ACBP is strongly dependent on the length of the acyl chain with a clear preference for acyl-...

  8. Intentional binding of visual effects.

    Science.gov (United States)

    Ruess, Miriam; Thomaschke, Roland; Kiesel, Andrea

    2018-04-01

    When an action produces an effect, the effect is perceived earlier in time compared to a stimulus without preceding action. This temporal bias is called intentional binding (IB) and serves as an implicit measure of sense of agency. Typically, IB is investigated by presenting a rotating clock hand while participants execute an action and perceive a resulting tone. Participants are asked to estimate the time point of tone onset by referring to the clock hand position. This time point estimate is compared to a time point estimate of a tone in a condition in which the tone occurs without preceding action. Studies employing this classic clock paradigm employed auditory action effects. We modified this paradigm to investigate potential IB of visual action effects, and, additionally, to investigate how IB differs for visual action effects (Experiment 1) in comparison to auditory action effects (Experiment 2). Our results show that, like the IB of an auditory effect, the time point of a visual action effect is shifted toward the causing action, and that the size of the IB depends on the delay duration of the effect. Comparable to auditory action effects, earlier action effects showed stronger IB compared to later action effects. Yet overall IB of the visual effects was weaker than IB of the auditory effects. As IB is seen as an indicator of sense of agency, this may have important implications for the design of human-machine interfaces.

  9. Localization-enhanced biexciton binding in semiconductors

    DEFF Research Database (Denmark)

    Langbein, Wolfgang Werner; Hvam, Jørn Märcher

    1999-01-01

    The influence of excitonic localization on the binding energy of biexcitons is investigated for quasi-three-dimensional and quasi-two-dimensional AlxGa1-xAs structures. An increase of the biexciton binding energy is observed for localization energies comparable to or larger than the free biexcito...

  10. Neurotransmitter Receptor Binding in Bovine Cerebral Microvessels

    Science.gov (United States)

    Peroutka, Stephen J.; Moskowitz, Michael A.; Reinhard, John F.; Synder, Solomon H.

    1980-05-01

    Purified preparations of microvessels from bovine cerebral cortex contain substantial levels of alpha-adrenergic, beta-adrenergic, and histamine 1 receptor binding sites but only negligible serotonin, muscarinic cholinergic, opiate, and benzodiazepine receptor binding. Norepinephrine and histamine may be endogenous regulators of the cerebral microcirculation at the observed receptors.

  11. Identification of Glossina morsitans morsitans odorant binding ...

    African Journals Online (AJOL)

    Tsetse flies are vectors of trypanosome parasites, causative agents of Trypanosomiasis in humans and animals. Odorant Binding Proteins (OBPs) are critical in insect olfaction as they bind volatile odours from the environment and transport them to receptors within olfactory receptor neurons for processing providing critical ...

  12. Binding of corroded ions to human saliva.

    Science.gov (United States)

    Mueller, H J

    1985-05-01

    Employing equilibrium dialysis, the binding abilities of Cu, Al, Co and Cr ions from corroded Cu-Al and Co-Cr dental casting alloys towards human saliva and two of its gel chromatographic fractions were determined. Results indicate that both Cu and Co bind to human saliva i.e. 0.045 and 0.027 mg/mg protein, respectively. Besides possessing the largest binding ability, Cu also possessed the largest binding capacity. The saturation of Cu binding was not reached up to the limit of 0.35 mg protein/ml employed in the tests, while Co reached full saturation at about 0.2 mg protein/ml. Chromium showed absolutely no binding to human saliva while Al ions did not pass through the dialysis membranes. Compared to the binding with solutions that were synthetically made up to contain added salivary-type proteins, it is shown that the binding to human saliva is about 1 order of magnitude larger, at least for Cu ions.

  13. Factor VIIa binding and internalization in hepatocytes

    DEFF Research Database (Denmark)

    Hjortoe, G; Sorensen, B B; Petersen, L C

    2005-01-01

    The liver is believed to be the primary clearance organ for coagulation proteases, including factor VIIa (FVIIa). However, at present, clearance mechanisms for FVIIa in liver are unknown. To obtain information on the FVIIa clearance mechanism, we investigated the binding and internalization...... no effect. HEPG2 cells internalized FVIIa with a rate of 10 fmol 10(-5) cells h(-1). In contrast to HEPG2 cells, FVIIa binding to primary rat hepatocytes was completely independent of TF, and excess unlabeled FVIIa partly reduced the binding of 125I-FVIIa to rat hepatocytes. Further, compared with HEPG2...... cells, three- to fourfold more FVIIa bound to rat primary hepatocytes, and the bound FVIIa was internalized at a faster rate. Similar FVIIa binding and internalization profiles were observed in primary human hepatocytes. Plasma inhibitors had no effect on FVIIa binding and internalization in hepatocytes...

  14. (TH) diazepam binding to human granulocytes

    Energy Technology Data Exchange (ETDEWEB)

    Bond, P.A.; Cundall, R.L.; Rolfe, B.

    1985-07-08

    (TH)-diazepam binds to sites on human granulocyte membranes, with little or no binding to platelets or lymphocytes. These (TH)-diazepam binding sites are of the peripheral type, being strongly inhibited by R05-4864 (Ki=6.23nM) but only weakly by clonazepam (Ki=14 M). Binding of (TH) diazepam at 0 is saturable, specific and stereoselective. Scatchard analysis indicates a single class of sites with Bmax of 109 +/- 17f moles per mg of protein and K/sub D/ of 3.07 +/- 0.53nM. Hill plots of saturation experiments gave straight lines with a mean Hill coefficient of 1.03 +/- 0.014. Binding is time dependent and reversible and it varies linearly with granulocyte protein concentration over the range 0.025-0.300 mg of protein. 11 references, 3 figures, 1 table.

  15. Ethylene binding site affinity in ripening apples

    Energy Technology Data Exchange (ETDEWEB)

    Blankenship, S.M. (North Carolina State Univ., Raleigh, NC (United States). Dept. of Horticultural Science); Sisler, E.C. (North Carolina State Univ., Raleigh, NC (United States))

    1993-09-01

    Scatchard plots for ethylene binding in apples (Malus domestica Borkh.), which were harvested weekly for 5 weeks to include the ethylene climacteric rise, showed C[sub 50] values (concentration of ethylene needed to occupy 50% of the ethylene binding sites) of 0.10, 0.11, 0.34, 0.40, and 0.57 [mu]l ethylene/liter[sup [minus]1], respectively, for each of the 5 weeks. Higher ethylene concentrations were required to saturate the binding sites during the climacteric rise than at other times. Diffusion of [sup 14]C-ethylene from the binding sites was curvilinear and did not show any indication of multiple binding sites. Ethylene was not metabolized by apple tissue.

  16. Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

    International Nuclear Information System (INIS)

    Gangi Setty, Thanuja; Cho, Christine; Govindappa, Sowmya; Apicella, Michael A.; Ramaswamy, S.

    2014-01-01

    Structure–function studies of sialic acid-binding proteins from F. nucleatum, P. multocida, V. cholerae and H. influenzae reveal a conserved network of hydrogen bonds involved in conformational change on ligand binding. Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states

  17. Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

    Energy Technology Data Exchange (ETDEWEB)

    Gangi Setty, Thanuja [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Cho, Christine [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Govindappa, Sowmya [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Apicella, Michael A. [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Ramaswamy, S., E-mail: ramas@instem.res.in [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India)

    2014-07-01

    Structure–function studies of sialic acid-binding proteins from F. nucleatum, P. multocida, V. cholerae and H. influenzae reveal a conserved network of hydrogen bonds involved in conformational change on ligand binding. Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.

  18. Specific insulin binding in bovine chromaffin cells; demonstration of preferential binding to adrenalin-storing cells

    International Nuclear Information System (INIS)

    Serck-Hanssen, G.; Soevik, O.

    1987-01-01

    Insulin binding was studied in subpopulations of bovine chromaffin cells enriched in adrenalin-producing cells (A-cells) or noradrenalin-producing cells (NA-cells). Binding of 125 I-insulin was carried out at 15 0 C for 3 hrs in the absence or presence of excess unlabeled hormone. Four fractions of cells were obtained by centrifugation on a stepwise bovine serum albumin gradient. The four fractions were all shown to bind insulin in a specific manner and the highest binding was measured in the cell layers of higher densities, containing mainly A-cells. The difference in binding of insulin to the four subpopulations of chromaffin cells seemed to be related to differences in numbers of receptors as opposed to receptor affinities. The authors conclude that bovine chromaffin cells possess high affinity binding sites for insulin and that these binding sites are mainly confined to A-cells. 24 references, 2 figures, 1 table

  19. Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain

    International Nuclear Information System (INIS)

    Suzuki, Nobuhiro; Yamazaki, Yasuo; Brown, R. Lane; Fujimoto, Zui; Morita, Takashi; Mizuno, Hiroshi

    2008-01-01

    The structures of pseudechetoxin and pseudecin suggest that both proteins bind to cyclic nucleotide-gated ion channels in a manner in which the concave surface occludes the pore entrance. Cyclic nucleotide-gated (CNG) ion channels play pivotal roles in sensory transduction by retinal photoreceptors and olfactory neurons. The elapid snake toxins pseudechetoxin (PsTx) and pseudecin (Pdc) are the only known protein blockers of CNG channels. These toxins belong to a cysteine-rich secretory protein (CRISP) family containing an N-terminal pathogenesis-related proteins of group 1 (PR-1) domain and a C-terminal cysteine-rich domain (CRD). PsTx and Pdc are highly homologous proteins, but their blocking affinities on CNG channels are different: PsTx blocks both the olfactory and retinal channels with ∼15–30-fold higher affinity than Pdc. To gain further insights into their structure and function, the crystal structures of PsTx, Pdc and Zn 2+ -bound Pdc were determined. The structures revealed that most of the amino-acid-residue differences between PsTx and Pdc are located around the concave surface formed between the PR-1 domain and the CRD, suggesting that the concave surface is functionally important for CNG-channel binding and inhibition. A structural comparison in the presence and absence of Zn 2+ ion demonstrated that the concave surface can open and close owing to movement of the CRD upon Zn 2+ binding. The data suggest that PsTx and Pdc occlude the pore entrance and that the dynamic motion of the concave surface facilitates interaction with the CNG channels

  20. Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Nobuhiro [Department of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572 (Japan); Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); Yamazaki, Yasuo [Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan); Brown, R. Lane [Neurological Science Institute, Oregon Health and Science University, Beaverton, Oregon 97006 (United States); Fujimoto, Zui [Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); Morita, Takashi, E-mail: tmorita@my-pharm.ac.jp [Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588 (Japan); Mizuno, Hiroshi, E-mail: tmorita@my-pharm.ac.jp [Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 (Japan); VALWAY Technology Center, NEC Soft Ltd, Koto-ku, Tokyo 136-8627 (Japan); Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Central 6, Tsukuba, Ibaraki 305-8566 (Japan); Department of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572 (Japan)

    2008-10-01

    The structures of pseudechetoxin and pseudecin suggest that both proteins bind to cyclic nucleotide-gated ion channels in a manner in which the concave surface occludes the pore entrance. Cyclic nucleotide-gated (CNG) ion channels play pivotal roles in sensory transduction by retinal photoreceptors and olfactory neurons. The elapid snake toxins pseudechetoxin (PsTx) and pseudecin (Pdc) are the only known protein blockers of CNG channels. These toxins belong to a cysteine-rich secretory protein (CRISP) family containing an N-terminal pathogenesis-related proteins of group 1 (PR-1) domain and a C-terminal cysteine-rich domain (CRD). PsTx and Pdc are highly homologous proteins, but their blocking affinities on CNG channels are different: PsTx blocks both the olfactory and retinal channels with ∼15–30-fold higher affinity than Pdc. To gain further insights into their structure and function, the crystal structures of PsTx, Pdc and Zn{sup 2+}-bound Pdc were determined. The structures revealed that most of the amino-acid-residue differences between PsTx and Pdc are located around the concave surface formed between the PR-1 domain and the CRD, suggesting that the concave surface is functionally important for CNG-channel binding and inhibition. A structural comparison in the presence and absence of Zn{sup 2+} ion demonstrated that the concave surface can open and close owing to movement of the CRD upon Zn{sup 2+} binding. The data suggest that PsTx and Pdc occlude the pore entrance and that the dynamic motion of the concave surface facilitates interaction with the CNG channels.

  1. Spatial heterogeneity influences native and nonnative plant species richness.

    Science.gov (United States)

    Kumar, Sunil; Stohlgren, Thomas J; Chong, Geneva W

    2006-12-01

    Spatial heterogeneity may have differential effects on the distribution of native and nonnative plant species richness. We examined the effects of spatial heterogeneity on native and nonnative plant species richness distributions in the central part of Rocky Mountain National Park, Colorado, USA. Spatial heterogeneity around vegetation plots was characterized using landscape metrics, environmental/topographic variables (slope, aspect, elevation, and distance from stream or river), and soil variables (nitrogen, clay, and sand). The landscape metrics represented five components of landscape heterogeneity and were measured at four spatial extents (within varying radii of 120, 240, 480, and 960 m) using the FRAGSTATS landscape pattern analysis program. Akaike's Information Criterion adjusted for small sample size (AICc) was used to select the best models from a set of multiple linear regression models developed for native and nonnative plant species richness at four spatial extents and three levels of ecological hierarchy (i.e., landscape, land cover, and community). Both native and nonnative plant species richness were positively correlated with edge density, Simpson's diversity index and interspersion/juxtaposition index, and were negatively correlated with mean patch size. The amount of variation explained at four spatial extents and three hierarchical levels ranged from 30% to 70%. At the landscape level, the best models explained 43% of the variation in native plant species richness and 70% of the variation in nonnative plant species richness (240-m extent). In general, the amount of variation explained was always higher for nonnative plant species richness, and the inclusion of landscape metrics always significantly improved the models. The best models explained 66% of the variation in nonnative plant species richness for both the conifer land cover type and lodgepole pine community. The relative influence of the components of spatial heterogeneity differed for

  2. Butterfly Species Richness in Selected West Albertine Rift Forests

    Directory of Open Access Journals (Sweden)

    Patrice Kasangaki

    2012-01-01

    Full Text Available The butterfly species richness of 17 forests located in the western arm of the Albertine Rift in Uganda was compared using cluster analysis and principal components analysis (PCA to assess similarities among the forests. The objective was to compare the butterfly species richness of the forests. A total of 630 butterfly species were collected in 5 main families. The different species fell into 7 ecological groupings with the closed forest group having the most species and the swamp/wetland group with the fewest number of species. Three clusters were obtained. The first cluster had forests characterized by relatively high altitude and low species richness despite the big area in the case of Rwenzori and being close to the supposed Pleistocene refugium. The second cluster had forests far away from the supposed refugium except Kisangi and moderate species richness with small areas, whereas the third cluster had those forests that were more disturbed, high species richness, and low altitudinal levels with big areas.

  3. The RICH detector of the NA62 experiment at CERN

    Energy Technology Data Exchange (ETDEWEB)

    Aisa, D.; Anzivino, G. [Dipartimento di Fisica e Geologia dell' Università di Perugia (Italy); INFN – Sezione di Perugia (Italy); Bizzetti, A. [Dipartimento di Fisica dell' Università di Modena e Reggio Emilia (Italy); INFN – Sezione di Firenze (Italy); Bucci, F. [INFN – Sezione di Firenze (Italy); Campeggi, C. [Dipartimento di Fisica e Geologia dell' Università di Perugia (Italy); INFN – Sezione di Perugia (Italy); Carassiti, V. [INFN – Sezione di Ferrara (Italy); Cassese, A. [INFN – Sezione di Firenze (Italy); Dipartimento di Fisica dell' Università di Firenze (Italy); Cenci, P. [INFN – Sezione di Perugia (Italy); Ciaranfi, R. [INFN – Sezione di Firenze (Italy); Duk, V.; Farnesini, L. [INFN – Sezione di Perugia (Italy); Fry, J.R. [University of Liverpool (Italy); CERN (Italy); Iacopini, E. [INFN – Sezione di Firenze (Italy); Dipartimento di Fisica dell' Università di Firenze (Italy); Lami, S. [INFN – Sezione di Pisa (Italy); Lenti, M.; Maletta, F. [INFN – Sezione di Firenze (Italy); Pepe, M. [INFN – Sezione di Perugia (Italy); Piandani, R. [INFN – Sezione di Pisa (Italy); Piccini, M. [INFN – Sezione di Perugia (Italy); Piluso, A. [Dipartimento di Fisica e Geologia dell' Università di Perugia (Italy); INFN – Sezione di Perugia (Italy); and others

    2014-12-01

    The NA62 experiment at CERN aims to measure the branching ratio of the ultra-rare charged kaon decay K{sup +}→π{sup +}νν{sup ¯} with a 10% accuracy and with a background contamination at the 10% level. Since the branching ratio of this decay is O(10{sup −10}), to fulfill such request one of the main backgrounds, the decay K{sup +}→μ{sup +}ν (BR∼63%), must be suppressed by a rejection factor of 4×10{sup −13} (assuming 10% signal acceptance). This can be partially accomplished using a combination of kinematical cuts (8×10{sup −6}) and the different power of penetration through matter of pions and muons (10{sup −5}). A further 5×10{sup −3} suppression factor will be provided by a RICH detector, in a momentum range between 15 and 35 GeV/c. The details of the RICH project as well as the results from test runs performed on a RICH prototype of the same length of the final detector will be presented. The current status of the construction and the description of the final readout and trigger electronics will also be reviewed. - Highlights: • The RICH of the NA62 experiment will separate pions from muons in kaon decays. • Crossing time of charged particles is measured with a resolution better than 100 ps. • RICH will also be fundamental for the low level trigger of the experiment.

  4. Multi-Messenger Observations of Neutron Rich Matter

    Energy Technology Data Exchange (ETDEWEB)

    Horowitz, C. J. [UTK/ORNL/Indiana University

    2012-01-01

    At very high densities, electrons react with protons to form neutron rich matter. This material is central to many fundamental questions in nuclear physics and astrophysics. Moreover, neutron rich matter is being studied with an extraordinary variety of new tools such as the Facility for Rare Isotope Beams (FRIB) and the Laser Interferometer Gravitational Wave Observatory (LIGO). We describe the Lead Radius Experiment (PREX) that uses parity violating electron scattering to measure the neutron radius in 208Pb. This has important implications for neutron stars and their crusts. We discuss X-ray observations of neutron star radii. These also have important implications for neutron rich matter. Gravitational waves (GW) open a new window on neutron rich matter. They come from sources such as neutron star mergers, rotating neutron star mountains, and collective r-mode oscillations. Using large scale molecular dynamics simulations, we find neutron star crust to be very strong. It can support mountains on rotating neutron stars large enough to generate detectable gravitational waves. We believe that combing astronomical observations using photons, GW, and neutrinos, with laboratory experiments on nuclei, heavy ion collisions, and radioactive beams will fundamentally advance our knowledge of compact objects in the heavens, the dense phases of QCD, the origin of the elements, and of neutron rich matter.

  5. Human population, grasshopper and plant species richness in European countries

    Science.gov (United States)

    Steck, Claude E.; Pautasso, Marco

    2008-11-01

    Surprisingly, several studies over large scales have reported a positive spatial correlation of people and biodiversity. This pattern has important implications for conservation and has been documented for well studied taxa such as plants, amphibians, reptiles, birds and mammals. However, it is unknown whether the pattern applies also to invertebrates other than butterflies and more work is needed to establish whether the species-people relationship is explained by both variables correlating with other environmental factors. We studied whether grasshopper species richness (Orthoptera, suborder Caelifera) is related to human population size in European countries. As expected, the number of Caelifera species increases significantly with increasing human population size. But this is not the case when controlling for country area, latitude and number of plant species. Variations in Caelifera species richness are primarily associated with variations in plant species richness. Caelifera species richness also increases with decreasing mean annual precipitation, Gross Domestic Product per capita (used as an indicator for economic development) and net fertility rate of the human population. Our analysis confirms the hypothesis that the broad-scale human population-biodiversity correlations can be explained by concurrent variations in factors other than human population size such as plant species richness, environmental productivity, or habitat heterogeneity. Nonetheless, more populated countries in Europe still have more Caelifera species than less populated countries and this poses a particular challenge for conservation.

  6. LHCB : The upgraded LHCb RICH detector: status and perspectives

    CERN Multimedia

    Cardinale, Roberta

    2015-01-01

    The LHCb experiment is designed to perform high-precision measurements of CP violation and search for New Physics using the enormous flux of beauty and charmed hadrons produced at the Large Hadron Collider (LHC). The two RICH detectors installed in LHCb have performed successfully during the 2010-2012 data taking period. The data from these detectors were essential to most of the physics results published by LHCb. In order to extend its potential for discovery and study of new phenomena it is planned to upgrade the LHCb experiment in 2018 with a 40MHz readout and a much more flexible software-based triggering system. This would increase the readout rate and occupancies for the RICH detectors. The RICH detector will require new photon detectors and modifications of the optics of the upstream RICH detector. Tests of the complete opto-electronic chain have been performed during testbeam sessions in autumn 2014. The status and perspectives of the RICH upgrade project will be presented.

  7. Mapping and predictive variations of soil bacterial richness across France.

    Directory of Open Access Journals (Sweden)

    Sébastien Terrat

    Full Text Available Although numerous studies have demonstrated the key role of bacterial diversity in soil functions and ecosystem services, little is known about the variations and determinants of such diversity on a nationwide scale. The overall objectives of this study were i to describe the bacterial taxonomic richness variations across France, ii to identify the ecological processes (i.e. selection by the environment and dispersal limitation influencing this distribution, and iii to develop a statistical predictive model of soil bacterial richness. We used the French Soil Quality Monitoring Network (RMQS, which covers all of France with 2,173 sites. The soil bacterial richness (i.e. OTU number was determined by pyrosequencing 16S rRNA genes and related to the soil characteristics, climatic conditions, geomorphology, land use and space. Mapping of bacterial richness revealed a heterogeneous spatial distribution, structured into patches of about 111km, where the main drivers were the soil physico-chemical properties (18% of explained variance, the spatial descriptors (5.25%, 1.89% and 1.02% for the fine, medium and coarse scales, respectively, and the land use (1.4%. Based on these drivers, a predictive model was developed, which allows a good prediction of the bacterial richness (R2adj of 0.56 and provides a reference value for a given pedoclimatic condition.

  8. Mapping and predictive variations of soil bacterial richness across France.

    Science.gov (United States)

    Terrat, Sébastien; Horrigue, Walid; Dequiedt, Samuel; Saby, Nicolas P A; Lelièvre, Mélanie; Nowak, Virginie; Tripied, Julie; Régnier, Tiffanie; Jolivet, Claudy; Arrouays, Dominique; Wincker, Patrick; Cruaud, Corinne; Karimi, Battle; Bispo, Antonio; Maron, Pierre Alain; Chemidlin Prévost-Bouré, Nicolas; Ranjard, Lionel

    2017-01-01

    Although numerous studies have demonstrated the key role of bacterial diversity in soil functions and ecosystem services, little is known about the variations and determinants of such diversity on a nationwide scale. The overall objectives of this study were i) to describe the bacterial taxonomic richness variations across France, ii) to identify the ecological processes (i.e. selection by the environment and dispersal limitation) influencing this distribution, and iii) to develop a statistical predictive model of soil bacterial richness. We used the French Soil Quality Monitoring Network (RMQS), which covers all of France with 2,173 sites. The soil bacterial richness (i.e. OTU number) was determined by pyrosequencing 16S rRNA genes and related to the soil characteristics, climatic conditions, geomorphology, land use and space. Mapping of bacterial richness revealed a heterogeneous spatial distribution, structured into patches of about 111km, where the main drivers were the soil physico-chemical properties (18% of explained variance), the spatial descriptors (5.25%, 1.89% and 1.02% for the fine, medium and coarse scales, respectively), and the land use (1.4%). Based on these drivers, a predictive model was developed, which allows a good prediction of the bacterial richness (R2adj of 0.56) and provides a reference value for a given pedoclimatic condition.

  9. Drivers of species richness in European Tenebrionidae (Coleoptera)

    Science.gov (United States)

    Fattorini, Simone; Ulrich, Werner

    2012-08-01

    The species-area relationship (SAR) and the latitudinal gradient in species richness are the most widespread and best-documented patterns in ecology, yet few studies have explored how the two patterns are interrelated. We used tenebrionid beetles as a species rich invertebrate group to investigate how area, habitat heterogeneity, climate, and ecological history act together in shaping species richness across Europe. We tested the effects of various climatic gradients on tenebrionid richness, with separate analyses for endemics and non-endemics. To take into account differences in area size among geographical units, we included species-area relationships using simultaneous autoregressive models. Although area had a significant effect on richness, the signal associated with temperature is so strong that it is still evident as a major driver. Also, the effect of area was only apparent when the effect of spatial coordinates had been accounted for, which has important implications for the use of SARs to locate diversity hotspots. The influence of latitude was mainly explained by a temperature gradient. Our findings support a postglacial European colonisation mainly from glacial southern refuges. Large Mediterranean islands were also important refugial areas.

  10. Current Understanding of Physicochemical Mechanisms for Cell Membrane Penetration of Arginine-rich Cell Penetrating Peptides: Role of Glycosaminoglycan Interactions.

    Science.gov (United States)

    Takechi-Haraya, Yuki; Saito, Hiroyuki

    2018-01-01

    Arginine-rich cell penetrating peptides (CPPs) are very promising drug carriers to deliver membrane-impermeable pharmaceuticals, such as siRNA, bioactive peptides and proteins. CPPs directly penetrate into cells across cell membranes via a spontaneous energy-independent process, in which CPPs appear to interact with acidic lipids in the outer leaflet of the cell membrane. However, acidic lipids represent only 10 to 20% of the total membrane lipid content and in mammalian cell membranes they are predominantly located in the inner leaflet. Alternatively, CPPs favorably bind in a charge density- dependent manner to negatively charged, sulfated glycosaminoglycans (GAGs), such as heparan sulfate and chondroitin sulfate, which are abundant on the cell surface and are involved in many biological functions. We have recently demonstrated that the interaction of CPPs with sulfated GAGs plays a critical role in their direct cell membrane penetration: the favorable enthalpy contribution drives the high-affinity binding of arginine-rich CPPs to sulfated GAGs, initiating an efficient cell membrane penetration. The favorable enthalpy gain is presumably mainly derived from a unique property of the guanidino group of arginine residues forming multidentate hydrogen bonding with sulfate and carboxylate groups in GAGs. Such interactions can be accompanied with charge neutralization of arginine-rich CPPs, promoting their partition into cell membranes. This review summarizes the current understanding of the physicochemical mechanism for lipid membrane penetration of CPPs, and discusses the role of the GAG interactions on the cell membrane penetration of CPPs. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  11. Thermodynamic binding constants for gallium transferrin

    Energy Technology Data Exchange (ETDEWEB)

    Harris, W.R.; Pecoraro, V.L.

    1983-01-18

    Gallium-67 is widely used as an imaging agent for tumors and inflammatory abscesses. It is well stablished that Ga/sup 3 +/ travels through the circulatory system bound to the serum iron transport protein transferrin and that this protein binding is an essential step in tumor localization. However, there have been conflicting reports on the magnitude of the gallium-transferrin binding constants. Therefore, thermodynamic binding constants for gallium complexation at the two specific metal binding sites of human serum transferrin at pH 7.4 and 5 mM NaHCO/sub 3/ have been determined by UV difference spectroscopy. The conditional constants calculated for 27 mM NaHCO/sub 3/ are log K/sub 1/* = 20.3 and log K/sub 2/* = 19.3. These results are discussed in relation to the thermodynamics of transferrin binding of Fe/sup 3 +/ and to previous reports on gallium binding. The strength of transferrin complexation is also compared to that of a series of low molecular weight ligands by using calculated pM values (pM = -log (Ga(H/sub 2/O)/sub 6/)) to express the effective binding strength at pH 7.4.

  12. Interactions among motility, fertilizing ability, and testosterone binding on spermatozoa of bonnet monkey (Macaca radiata).

    Science.gov (United States)

    Warikoo, P K; Majumdar, S S; Allag, I S; Das, R P; Roy, S

    1986-01-01

    Fresh ejaculates of bonnet monkeys were separated into fractions rich with highly motile and sluggishly motile spermatozoa. The motility, ability to fertilize zona-free hamster eggs, and distribution of testosterone-binding sites on spermatozoa were assessed to determine the relation between these sperm functions. Two parameters of objective assessment of motility--velocity and degree of flagellar bending--were significantly correlated with the ability to form pronuclei in zona-free hamster eggs. Only spermatozoa with good motility could form pronuclei, which might be important for assessment of the fertilizing ability. The motility was directly related to the distribution of testosterone-binding sites; the fraction having mostly motile spermatozoa was distributed over the sperm surface. The technique is simple and may be used to evaluate semen of nonhuman primates.

  13. Myeloperoxidase selectively binds and selectively kills microbes.

    Science.gov (United States)

    Allen, Robert C; Stephens, Jackson T

    2011-01-01

    Myeloperoxidase (MPO) is reported to selectively bind to bacteria. The present study provides direct evidence of MPO binding selectivity and tests the relationship of selective binding to selective killing. The microbicidal effectiveness of H(2)O(2) and of OCl(-) was compared to that of MPO plus H(2)O(2). Synergistic microbicidal action was investigated by combining Streptococcus sanguinis, a H(2)O(2)-producing microbe showing low MPO binding, with high-MPO-binding Escherichia coli, Staphylococcus aureus, or Pseudomonas aeruginosa without exogenous H(2)O(2), with and without MPO, and with and without erythrocytes (red blood cells [RBCs]). Selectivity of MPO microbicidal action was conventionally measured as the MPO MIC and minimal bactericidal concentration (MBC) for 82 bacteria including E. coli, P. aeruginosa, S. aureus, Enterococcus faecalis, Streptococcus pyogenes, Streptococcus agalactiae, and viridans streptococci. Both H(2)O(2) and OCl(-) destroyed RBCs at submicrobicidal concentrations. Nanomolar concentrations of MPO increased H(2)O(2) microbicidal action 1,000-fold. Streptococci plus MPO produced potent synergistic microbicidal action against all microbes tested, and RBCs caused only a small decrease in potency without erythrocyte damage. MPO directly killed H(2)O(2)-producing S. pyogenes but was ineffective against non-H(2)O(2)-producing E. faecalis. The MPO MICs and MBCs for E. coli, P. aeruginosa, and S. aureus were significantly lower than those for E. faecalis. The streptococcal studies showed much higher MIC/MBC results, but such testing required lysed horse blood-supplemented medium, thus preventing valid comparison of these results to those for the other microbes. E. faecalis MPO binding is reportedly weak compared to binding of E. coli, P. aeruginosa, and S. aureus but strong compared to binding of streptococci. Selective MPO binding results in selective killing.

  14. Identification of MDP (muramyl dipeptide)-binding key domains in NOD2 (nucleotide-binding and oligomerization domain-2) receptor of Labeo rohita.

    Science.gov (United States)

    Maharana, Jitendra; Swain, Banikalyan; Sahoo, Bikash R; Dikhit, Manas R; Basu, Madhubanti; Mahapatra, Abhijit S; Jayasankar, Pallipuram; Samanta, Mrinal

    2013-08-01

    In lower eukaryotes-like fish, innate immunity contributed by various pattern recognition receptor (PRR) plays an essential role in protection against diseases. Nucleotide-binding and oligomerization domain (NOD)-2 is a cytoplasmic PRR that recognizes MDP (muramyl dipeptide) of the Gram positive and Gram negative bacteria as ligand and activates signalling to induce innate immunity. Hypothesizing a similar NOD2 signalling pathway of higher eukaryotes, the peripheral blood leucocytes (PBLs) of rohu (Labeo rohita) was stimulated with MDP. The data of quantitative real-time PCR (qRT-PCR) revealed MDP-mediated inductive expression of NOD2 and its down-stream molecule RICK/RIP2 (receptor-interacting serine-threonine protein kinase-2). This observation suggested the existence of MDP-binding sites in rohu NOD2 (rNOD2). To investigate it, 3D model of ligand-binding leucine-rich repeat (LRR) region of rNOD2 (rNOD2-LRR) was constructed following ab initio and threading approaches in I-TASSER web server. Structural refinement of the model was performed by energy minimization, and MD (molecular dynamics) simulation was performed in GROMACS (Groningen Machine for Chemical Simulations). The refined model of rNOD2-LRR was validated through SAVES, ProSA, ProQ, WHAT IF and MolProbity servers, and molecular docking with MDP was carried out in GOLD 4.1. The result of docking identified LRR3-7 comprising Lys820, Phe821, Asn822, Arg847, Gly849, Trp877, Trp901 and Trp931 as MDP-binding critical amino acids in rNOD2. This is the first study in fish to provide an insight into the 3D structure of NOD2-LRR region and its important motifs that are expected to be engaged in MDP binding and innate immunity.

  15. Druggability of methyl-lysine binding sites

    Science.gov (United States)

    Santiago, C.; Nguyen, K.; Schapira, M.

    2011-12-01

    Structural modules that specifically recognize—or read—methylated or acetylated lysine residues on histone peptides are important components of chromatin-mediated signaling and epigenetic regulation of gene expression. Deregulation of epigenetic mechanisms is associated with disease conditions, and antagonists of acetyl-lysine binding bromodomains are efficacious in animal models of cancer and inflammation, but little is known regarding the druggability of methyl-lysine binding modules. We conducted a systematic structural analysis of readers of methyl marks and derived a predictive druggability landscape of methyl-lysine binding modules. We show that these target classes are generally less druggable than bromodomains, but that some proteins stand as notable exceptions.

  16. Measuring Binding Affinity of Protein-Ligand Interaction Using Spectrophotometry: Binding of Neutral Red to Riboflavin-Binding Protein

    Science.gov (United States)

    Chenprakhon, Pirom; Sucharitakul, Jeerus; Panijpan, Bhinyo; Chaiyen, Pimchai

    2010-01-01

    The dissociation constant, K[subscript d], of the binding of riboflavin-binding protein (RP) with neutral red (NR) can be determined by titrating RP to a fixed concentration of NR. Upon adding RP to the NR solution, the maximum absorption peak of NR shifts to 545 nm from 450 nm for the free NR. The change of the absorption can be used to determine…

  17. How rich is consciousness? The partial awareness hypothesis.

    Science.gov (United States)

    Kouider, Sid; de Gardelle, Vincent; Sackur, Jérôme; Dupoux, Emmanuel

    2010-07-01

    Current theories of consciousness posit a dissociation between 'phenomenal' consciousness (rich) and 'access' consciousness (limited). Here, we argue that the empirical evidence for phenomenal consciousness without access is equivocal, resulting either from a confusion between phenomenal and unconscious contents, or from an impression of phenomenally rich experiences arising from illusory contents. We propose a refined account of access that relies on a hierarchy of representational levels and on the notion of partial awareness, whereby lower and higher levels are accessed independently. Reframing of the issue of dissociable forms of consciousness into dissociable levels of access provides a more parsimonious account of the existing evidence. In addition, the rich phenomenology illusion can be studied and described in terms of testable cognitive mechanisms. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  18. Ilmenite-rich pyroclastic deposits - An ideal lunar resource

    Science.gov (United States)

    Hawke, B. R.; Clark, B.; Coombs, C. R.

    1990-01-01

    With a view of investigating possible economic benefits that a permanent lunar settlement might provide to the near-earth space infrastructures, consideration was given to the ilmenite-rich pyroclastic deposits as sources of oxygen (for use as a propellant) and He-3 (for nuclear fusion fuel). This paper demonstrates that ilmenite-rich pyroclastic deposits would be excellent sources of a wide variety of valuable elements besides O and He-3, including Fe, Ti, H2, N, C, S, Cu, Zn, Cd, Bi, and Pb. It is shown that several ilmenite-rich pyroclastic deposits of regional extent exist on the lunar surface. The suitability of regional pyroclastic deposits for lunar mining operations, construction activities, and the establishment of permanent lunar settlements is examined.

  19. Plant species richness and ecosystem multifunctionality in global drylands

    Science.gov (United States)

    Maestre, Fernando T.; Quero, Jose L.; Gotelli, Nicholas J.; Escudero, Adrian; Ochoa, Victoria; Delgado-Baquerizo, Manuel; Garcia-Gomez, Miguel; Bowker, Matthew A.; Soliveres, Santiago; Escolar, Cristina; Garcia-Palacios, Pablo; Berdugo, Miguel; Valencia, Enrique; Gozalo, Beatriz; Gallardo, Antonio; Aguilera, Lorgio; Arredondo, Tulio; Blones, Julio; Boeken, Bertrand; Bran, Donaldo; Conceicao, Abel A.; Cabrera, Omar; Chaieb, Mohamed; Derak, Mchich; Eldridge, David J.; Espinosa, Carlos I.; Florentino, Adriana; Gaitan, Juan; Gatica, M. Gabriel; Ghiloufi, Wahida; Gomez-Gonzalez, Susana; Gutie, Julio R.; Hernandez, Rosa M.; Huang, Xuewen; Huber-Sannwald, Elisabeth; Jankju, Mohammad; Miriti, Maria; Monerris, Jorge; Mau, Rebecca L.; Morici, Ernesto; Naseri, Kamal; Ospina, Abelardo; Polo, Vicente; Prina, Anibal; Pucheta, Eduardo; Ramirez-Collantes, David A.; Romao, Roberto; Tighe, Matthew; Torres-Diaz, Cristian; Val, James; Veiga, Jose P.; Wang, Deli; Zaady, Eli

    2012-01-01

    Experiments suggest that biodiversity enhances the ability of ecosystems to maintain multiple functions, such as carbon storage, productivity, and the buildup of nutrient pools (multifunctionality). However, the relationship between biodiversity and multifunctionality has never been assessed globally in natural ecosystems. We report here on a global empirical study relating plant species richness and abiotic factors to multifunctionality in drylands, which collectively cover 41% of Earth's land surface and support over 38% of the human population. Multifunctionality was positively and significantly related to species richness. The best-fitting models accounted for over 55% of the variation in multifunctionality and always included species richness as a predictor variable. Our results suggest that the preservation of plant biodiversity is crucial to buffer negative effects of climate change and desertification in drylands.

  20. Global variation in woodpecker species richness shaped by tree availability

    DEFF Research Database (Denmark)

    Ilsøe, Sigrid Kistrup; Kissling, W. Daniel; Fjeldså, Jon

    2017-01-01

    heterogeneity and biogeographical region. We further used structural equation models to test for direct and indirect effects of predictor variables. Results: There was a strong positive relationship between woodpecker species richness and current tree cover and annual precipitation, respectively. Precipitation...... a negative indirect effect on woodpecker species richness. Main conclusions: Global species richness of woodpeckers is primarily shaped by current tree cover and precipitation, reflecting a strong biotic association between woodpeckers and trees. Human influence can have a negative effect on woodpecker...... diversity when humans reduce tree availability. Hence, woodpeckers exemplify how broad-scale diversity patterns are predominantly shaped by a biotic factor, and how climate and human influence can have indirect effects on animal biodiversity via the effects on tree availability and forest cover....

  1. Characteristics of the brown hagfish Paramyxine atami transthyretin: Metal ion-dependent thyroid hormone binding.

    Science.gov (United States)

    Suzuki, Shunsuke; Kasai, Kentaro; Nishiyama, Norihito; Ishihara, Akinori; Yamauchi, Kiyoshi

    2017-08-01

    Transthyretin (TTR) is a vertebrate-specific protein involved in thyroid hormone distribution in plasma, and its gene is thought to have emerged by gene duplication from the gene for the ancient TTR-related protein, 5-hydroxyisourate hydrolase, at some early stage of chordate evolution. We investigated the molecular and hormone-binding properties of the brown hagfish Paramyxine atami TTR. The amino acid sequence deduced from the cloned hagfish TTR cDNA shared 33-50% identities with those of other vertebrate TTRs but less than 24% identities with those of vertebrate and deuterostome invertebrate 5-hydroxyisourate hydrolases. Hagfish TTR, as well as lamprey and little skate TTRs, had an N-terminal histidine-rich segment, allowing purification by metal-affinity chromatography. The affinity of hagfish TTR for 3,3',5-triiodo-L-thyronine (T3) was 190 times higher than that for L-thyroxine, with a dissociation constant of 1.5-3.9nM at 4°C. The high-affinity binding sites were strongly sensitive to metal ions. Zn 2+ and Cu 2+ decreased the dissociation constant to one-order of magnitude, whereas a chelator, o-phenanthroline, increased it four times. The number of metal ions (mainly Zn 2+ and Cu 2+ ) was approximately 12/TTR (mol/mol). TTR was also a major T3-binding protein in adult hagfish sera and its serum concentration was approximately 8μM. These results suggest that metal ions and the acquisition of N-terminal histidine-rich segment may cooperatively contribute to the evolution toward an ancient TTR with high T3 binding activity from either 5-hydroxyisourate hydrolase after gene duplication. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Resemblance of actin-binding protein/actin gels to covalently crosslinked networks

    Science.gov (United States)

    Janmey, Paul A.; Hvidt, Søren; Lamb, Jennifer; Stossel, Thomas P.

    1990-05-01

    THE maintainance of the shape of cells is often due to their surface elasticity, which arises mainly from an actin-rich cytoplasmic cortex1,2. On locomotion, phagocytosis or fission, however, these cells become partially fluid-like. The finding of proteins that can bind to actin and control the assembly of, or crosslink, actin filaments, and of intracellular messages that regulate the activities of some of these actin-binding proteins, indicates that such 'gel sol' transformations result from the rearrangement of cortical actin-rich networks3. Alternatively, on the basis of a study of the mechanical properties of mixtures of actin filaments and an Acanthamoeba actin-binding protein, α-actinin, it has been proposed that these transformations can be accounted for by rapid exchange of crosslinks between actin filaments4: the cortical network would be solid when the deformation rate is greater than the rate of crosslink exchange, but would deform or 'creep' when deformation is slow enough to permit crosslinker molecules to rearrange. Here we report, however, that mixtures of actin filaments and actin-binding protein (ABP), an actin crosslinking protein of many higher eukaryotes, form gels Theologically equivalent to covalently crosslinked networks. These gels do not creep in response to applied stress on a time scale compatible with most cell-surface movements. These findings support a more complex and controlled mechanism underlying the dynamic mechanical properties of cortical cytoplasm, and can explain why cells do not collapse under the constant shear forces that often exist in tissues.

  3. Functional richness: Overview of indices and underlying concepts

    Science.gov (United States)

    Legras, G.; Loiseau, N.; Gaertner, J.-C.

    2018-02-01

    Functional richness, currently defined as the amount of niche space occupied by the species within a community, is one of the three major components of functional diversity. Different indices have been developed in order to quantify this component. However, the range of indices available for assessing functional richness, often mathematically complex and based on different rationales, can cause confusion for field ecologists and lead to misinterpretation of the results obtained. In this context, we have provided the first study exclusively focused on the comparison of the definitions, advantages and drawbacks of a large set of functional richness indices. The first part of this work is focused on four indices (FDP&G, FRic, TOP and N-hypervolumes indices) that are currently the most commonly used for assessing functional richness. We have completed our study by including recently developed indices that enable us to take into account the intraspecific trait variability (i.e. FRim index and TDP framework), because there is currently a growing scientific consensus regarding the necessity of including this aspect in the assessment of the functional diversity of communities. We demonstrate that although authors have argued that their index describes the functional richness, each of them describes only part of it, and this part may strongly differ from one index to another. Rather than advocating the general use of a single index and/or systematically avoiding others, our study highlights the need for selecting indices in close relation with the context, the available data and the aims of each study. Such a strategy is an essential preliminary step for preventing misunderstanding and artefactual controversies. Along these lines, we propose some guidelines to help users in selecting the most appropriate indices according both to the facet of functional richness on which they wish to focus and to the characteristics of the available data.

  4. Genotypic richness predicts phenotypic variation in an endangered clonal plant

    Directory of Open Access Journals (Sweden)

    Suzanna M. Evans

    2016-02-01

    Full Text Available Declines in genetic diversity within a species can affect the stability and functioning of populations. The conservation of genetic diversity is thus a priority, especially for threatened or endangered species. The importance of genetic variation, however, is dependent on the degree to which it translates into phenotypic variation for traits that affect individual performance and ecological processes. This is especially important for predominantly clonal species, as no single clone is likely to maximise all aspects of performance. Here we show that intraspecific genotypic diversity as measured using microsatellites is a strong predictor of phenotypic variation in morphological traits and shoot productivity of the threatened, predominantly clonal seagrass Posidonia australis, on the east coast of Australia. Biomass and surface area variation was most strongly predicted by genotypic richness, while variation in leaf chemistry (phenolics and nitrogen was unrelated to genotypic richness. Genotypic richness did not predict tissue loss to herbivores or epiphyte load, however we did find that increased herbivore damage was positively correlated with allelic richness. Although there was no clear relationship between higher primary productivity and genotypic richness, variation in shoot productivity within a meadow was significantly greater in more genotypically diverse meadows. The proportion of phenotypic variation explained by environmental conditions varied among different genotypes, and there was generally no variation in phenotypic traits among genotypes present in the same meadows. Our results show that genotypic richness as measured through the use of presumably neutral DNA markers does covary with phenotypic variation in functionally relevant traits such as leaf morphology and shoot productivity. The remarkably long lifespan of individual Posidonia plants suggests that plasticity within genotypes has played an important role in the longevity of

  5. Cysteine-rich mini-proteins in human biology.

    Science.gov (United States)

    Lavergne, Vincent; Taft, Ryan J; Alewood, Paul F

    2012-01-01

    Understanding the relationship between structure and function underpins both biochemistry and chemical biology, and has enabled the discovery of numerous agricultural and therapeutic agents. Small cysteine-rich proteins, which form a unique set of protein frameworks and folds, are found in all living organisms and often play crucial roles as hormones, growth factors, ion channel modulators and enzyme inhibitors in various biological pathways. Here we review secreted human cysteine-rich mini-proteins, classify them into broad families and briefly describe their structure and function. To systematically investigate this protein sub-class we designed a step-wise high throughput algorithm that is able to isolate the mature and active forms of human secreted cysteine-rich proteins (up to 200 amino acids in length) and extract their cysteine scaffolds. We limited our search to frameworks that contain an even number of cysteine residues (cysteine-rich frameworks spread over 378 secreted cysteine-rich mini-proteins. Restricting our search to those that contain >5% cysteine residues led to the identification of 22 cysteine-rich frameworks representing 21 protein families. Analysis of their molecular targets showed that these mini-proteins are frequently ligands for G protein- and enzyme-coupled receptors, transporters, extracellular enzyme inhibitors, and antimicrobial peptides. It is clear that these human secreted mini-proteins possess a wide diversity of frameworks and folds, some of which are conserved across the phylogenetic spectrum. Further study of these proteins will undoubtedly lead to insights into unresolved questions of basic biology, and the development of system-specific human therapeutics.

  6. Coupling the Torpedo microplate-receptor binding assay with mass spectrometry to detect cyclic imine neurotoxins.

    Science.gov (United States)

    Aráoz, Rómulo; Ramos, Suzanne; Pelissier, Franck; Guérineau, Vincent; Benoit, Evelyne; Vilariño, Natalia; Botana, Luis M; Zakarian, Armen; Molgó, Jordi

    2012-12-04

    Cyclic imine neurotoxins constitute an emergent family of neurotoxins of dinoflagellate origin that are potent antagonists of nicotinic acetylcholine receptors. We developed a target-directed functional method based on the mechanism of action of competitive agonists/antagonists of nicotinic acetylcholine receptors for the detection of marine cyclic imine neurotoxins. The key step for method development was the immobilization of Torpedo electrocyte membranes rich in nicotinic acetylcholine receptors on the surface of microplate wells and the use of biotinylated-α-bungarotoxin as tracer. Cyclic imine neurotoxins competitively inhibit biotinylated-α-bungarotoxin binding to Torpedo-nicotinic acetylcholine receptors in a concentration-dependent manner. The microplate-receptor binding assay allowed rapid detection of nanomolar concentrations of cyclic imine neurotoxins directly in shellfish samples. Although highly sensitive and specific for the detection of neurotoxins targeting nicotinic acetylcholine receptors as a class, the receptor binding assay cannot identify a given analyte. To address the low selectivity of the microplate-receptor binding assay, the cyclic imine neurotoxins tightly bound to the coated Torpedo nicotinic receptor were eluted with methanol, and the chemical nature of the eluted ligands was identified by mass spectrometry. The immobilization of Torpedo electrocyte membranes on the surface of microplate wells proved to be a high-throughput format for the survey of neurotoxins targeting nicotinic acetylcholine receptors directly in shellfish matrixes with high sensitivity and reproducibility.

  7. Modulation of [3H]-glutamate binding by serotonin in the rat hippocampus: An autoradiographic study

    International Nuclear Information System (INIS)

    Mennini, T.; Miari, A.

    1991-01-01

    Serotonin (5-HT) added in vitro increased [ 3 H]-glutamate specific binding in the rat hippocampus, reaching statistical significance in layers rich in N-Methyl-D-Aspartate sensitive glutamate receptors. This effect was explained by a significant increase in the apparent affinity of [ 3 H]-glutamate when 5-HT is added in vitro. Two days after lesion of serotonergic afferents to the hippocampus with 5,7- Dihydroxytryptamine [ 3 H]-glutamate binding was significantly decreased in the CA3 region and stratum lacunosum moleculare of the hippocampus, this reduction being reversed by in vitro addition of 10 μM 5-HT. The decrease observed is due to a significant reduction of quisqualate-insensitive (radiatum CA3) and kainate receptors (strata oriens, radiatum, pyramidal of CA3). Five days after lesion [ 3 H]-glutamate binding increased significantly in the CA3 region of the hippocampus but was not different from sham animals in the other hippocampal layers. Two weeks after lesion [ 3 H]-glutamate binding to quisqualate-insensitive receptors was increased in all the hippocampal layers, while kainate and quisqualate-sensitive receptors were not affected. These data are consistent with the possibility that 5-HT is a direct positive modulator of glutamate receptor subtypes

  8. Structural Basis for Sialoglycan Binding by the Streptococcus sanguinis SrpA Adhesin.

    Science.gov (United States)

    Bensing, Barbara A; Loukachevitch, Lioudmila V; McCulloch, Kathryn M; Yu, Hai; Vann, Kendra R; Wawrzak, Zdzislaw; Anderson, Spencer; Chen, Xi; Sullam, Paul M; Iverson, T M

    2016-04-01

    Streptococcus sanguinisis a leading cause of infective endocarditis, a life-threatening infection of the cardiovascular system. An important interaction in the pathogenesis of infective endocarditis is attachment of the organisms to host platelets.S. sanguinisexpresses a serine-rich repeat adhesin, SrpA, similar in sequence to platelet-binding adhesins associated with increased virulence in this disease. In this study, we determined the first crystal structure of the putative binding region of SrpA (SrpABR) both unliganded and in complex with a synthetic disaccharide ligand at 1.8 and 2.0 Å resolution, respectively. We identified a conserved Thr-Arg motif that orients the sialic acid moiety and is required for binding to platelet monolayers. Furthermore, we propose that sequence insertions in closely related family members contribute to the modulation of structural and functional properties, including the quaternary structure, the tertiary structure, and the ligand-binding site. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. SATB1 regulates SPARC expression in K562 cell line through binding to a specific sequence in the third intron

    International Nuclear Information System (INIS)

    Li, K.; Cai, R.; Dai, B.B.; Zhang, X.Q.; Wang, H.J.; Ge, S.F.; Xu, W.R.; Lu, J.

    2007-01-01

    Special AT-rich binding protein 1 (SATB1), a cell type-specific nuclear matrix attachment region (MAR) DNA-binding protein, tethers to a specific DNA sequence and regulates gene expression through chromatin remodeling and HDAC (histone deacetylase complex) recruitment. In this study, a SATB1 eukaryotic expression plasmid was transfected into the human erythroleukemia K562 cell line and individual clones that stably over-expressed the SATB1 protein were isolated. Microarray analysis revealed that hundreds of genes were either up- or down-regulated in the SATB1 over-expressing K562 cell lines. One of these was the extra-cellular matrix glycoprotein, SPARC (human secreted protein acidic and rich in cysteine). siRNA knock-down of SATB1 also reduced SPARC expression, which was consistent with elevated SPARC levels in the SATB1 over-expressing cell line. Bioinformatics software Mat-inspector showed that a 17 bp DNA sequence in the third intron of SPARC possessed a high potential for SATB1 binding; a finding confirmed by Chromatin immunoprecipitation (ChIP) with anti-SATB1 antibody. Our results show for the first time that forced-expression of SATB1 in K562 cells triggers SPARC up-regulation by binding to a 17 bp DNA sequence in the third intron

  10. Solution structure of the human BTK SH3 domain complexed with a proline-rich peptide from p120cbl

    Energy Technology Data Exchange (ETDEWEB)

    Tzeng, S.-R.; Lou, Y.-C.; Pai, M.-T.; Jain, Moti L.; Cheng, J.-W. [National Tsing Hua University, Division of Structural Biology and Biomedical Science, Department of Life Science (China)

    2000-04-15

    X-linked agammaglobulinemia (XLA), an inherited disease, is caused by mutations in the Bruton's tyrosine kinase (BTK). The absence of functional BTK leads to failure of B cell differentiation which incapacitates antibody production in XLA patients leading to, sometimes lethal, bacterial infections. Point mutation in the BTK gene that leads to deletion of C-terminal 14 aa residues of BTK SH3 domain was found in one patient family. To understand the role of BTK in B cell development, we have determined the solution structure of BTK SH3 domain complexed with a proline-rich peptide from the protein product of c-cbl protooncogene (p120{sup cbl}). Like other SH3 domains, BTK SH3 domain consists of five {beta}-strands packed in two {beta}-sheets forming a {beta}-barrel-like structure. The rmsd calculated from the averaged coordinates for the BTK SH3 domain residues 218-271 and the p120{sup cbl} peptide residues 6-12 of the complex was 0.87 A ({+-}0.16 A) for the backbone heavy atoms (N, C, and C{sub {alpha}}) and 1.64 A ({+-}0.16 A) for all heavy atoms. Based on chemical shift changes and inter-molecular NOEs, we have found that the residues located in the RT loop, n-Src loop and helix-like loop between {beta}4 and {beta}5 of BTK SH3 domain are involved in ligand binding. We have also determined that the proline-rich peptide from p120{sup cbl} binds to BTK SH3 domain in a class I orientation. These results correlate well with our earlier observation that the truncated BTK SH3 domain (deletion of {beta}4, {beta}5 and the helix-like loop) exhibits weaker affinity for the p120{sup cbl} peptide. It is likely that the truncated SH3 domain fails to present to the ligand the crucial residues in the correct context and hence the weaker binding. These results delineate the importance of the C-terminus in the binding of SH3 domains and also indicate that improper folding and the altered binding behavior of mutant BTK SH3 domain likely lead to XLA.

  11. Calculation of the radii of neutron rich light exotic nuclei

    International Nuclear Information System (INIS)

    Charagi, S.K.; Gupta, S.K.

    1991-01-01

    The interaction cross section of a few unstable neutron rich nuclei have been measured using exotic isotope beams produced through the projectile fragmentation process in high energy heavy-ion collisions. Interaction cross section of He, Li, Be and B isotope projectiles with Be, C and Al targets have thus been measured at 790 MeV/nucleon. We have made a comprehensive analysis of the data on the interaction cross section, to extract the radii of these neutron rich light nuclei. 7 refs., 1 fig., 3 tabs

  12. SOI MESFETs on high-resistivity, trap-rich substrates

    Science.gov (United States)

    Mehr, Payam; Zhang, Xiong; Lepkowski, William; Li, Chaojiang; Thornton, Trevor J.

    2018-04-01

    The DC and RF characteristics of metal-semiconductor field-effect-transistors (MESFETs) on conventional CMOS silicon-on-insulator (SOI) substrates are compared to nominally identical devices on high-resistivity, trap-rich SOI substrates. While the DC transfer characteristics are statistically identical on either substrate, the maximum available gain at GHz frequencies is enhanced by ∼2 dB when using the trap-rich substrates, with maximum operating frequencies, fmax, that are approximately 5-10% higher. The increased fmax is explained by the reduced substrate conduction at GHz frequencies using a lumped-element, small-signal model.

  13. Neutron-rich isotopes of the lightest elements

    International Nuclear Information System (INIS)

    Oganesyan, Yu.Ts.; Penionzhkevich, Yu.Eh.; Kalpakchieva, R.

    1989-01-01

    A review is presented of the experimental investigations on the stability of very neutron-rich light nuclei carried out at the JINR Laboratory of Nuclear Reactions. Results on mass excess measurements are reported for 4 H, 5 H, 6 H, 7 H and for the superheavy helium isotope 9 He. Some results from the joint JINR-Ganil experiment on the search for and study of new neutron-rich light nuclei are also given. Analyzed are new possibilities for the investigation of multineutron decay of light nuclei. 14 refs.; 10 figs

  14. Properties of neutron-rich hafnium high-spin isomers

    CERN Multimedia

    Tungate, G; Walker, P M; Neyens, G; Billowes, J; Flanagan, K; Koester, U H; Litvinov, Y

    It is proposed to study highly-excited multi-quasiparticle isomers in neutron-rich hafnium (Z=72) isotopes. Long half-lives have already been measured for such isomers in the storage ring at GSI, ensuring their accessibility with ISOL production. The present proposal focuses on:\\\\ (i) an on-line experiment to measure isomer properties in $^{183}$Hf and $^{184}$Hf, and\\\\ (ii) an off-line molecular breakup test using REXTRAP, to provide Hf$^{+}$ beams for future laser spectroscopy and greater sensitivity for the future study of more neutron-rich isotopes.

  15. Antibodies to a recombinant glutamate-rich Plasmodium falciparum protein

    DEFF Research Database (Denmark)

    Hogh, B; Petersen, E; Dziegiel, Morten Hanefeld

    1992-01-01

    A Plasmodium falciparum antigen gene coding for a 220-kD glutamate-rich protein (GLURP) has been cloned, and the 783 C-terminal amino acids of this protein (GLURP489-1271) have been expressed as a beta-galactosidase fusion protein in Escherichia coli. The encoded 783 amino acid residues contain two...... areas of repeated amino acid sequences. Antibodies against recombinant GLURP489-1271, as well as against a synthetic peptide corresponding to GLURP899-916, and against a synthetic peptide representing the major glutamate rich repeat sequence from the P. falciparum ring erythrocyte surface antigen (Pf155...

  16. LHCb Upgraded RICH 2 Engineering Design Review Report

    CERN Document Server

    Garsed, Philip John; Cardinale, Roberta; Petrolini, Alessandro; Benettoni, Massimo; Simi, Gabriele; Zago, M; Easo, Sajan; D'Ambrosio, Carmelo; Frei, Christoph; He, Jibo; Piedigrossi, Didier

    2016-01-01

    During the Long Shutdown 2 of the LHC, the LHCb experiment and, specifically, its two Ring Imaging Cherenkov (RICH) detectors will undergo a major upgrade. RICH 2 will be refurbished with new photon detectors and their associated electronics, with the capability of up to 40 MHz sustained acquisition rate. A new support and cooling system has been developed for the two photodetector arrays, retaining the vessel, gas and optical systems unchanged. This document describes their new mechanical arrangement, its engineering design, installation and alignment. A summary of the project schedule and Institute responsibilities is provided.

  17. Proscene: A feature-rich framework for interactive environments

    Science.gov (United States)

    Charalambos, Jean Pierre

    We introduce Proscene, a feature-rich, open-source framework for interactive environments. The design of Proscene comprises a three-layered onion-like software architecture, promoting different possible development scenarios. The framework innermost layer decouples user gesture parsing from user-defined actions. The in-between layer implements a feature-rich set of widely-used motion actions allowing the selection and manipulation of objects, including the scene viewpoint. The outermost layer exposes those features as a Processing library. The results have shown the feasibility of our approach together with the simplicity and flexibility of the Proscene framework API.

  18. Proscene: A feature-rich framework for interactive environments

    Directory of Open Access Journals (Sweden)

    Jean Pierre Charalambos

    2017-01-01

    Full Text Available We introduce Proscene, a feature-rich, open-source framework for interactive environments. The design of Proscene comprises a three-layered onion-like software architecture, promoting different possible development scenarios. The framework innermost layer decouples user gesture parsing from user-defined actions. The in-between layer implements a feature-rich set of widely-used motion actions allowing the selection and manipulation of objects, including the scene viewpoint. The outermost layer exposes those features as a Processing library. The results have shown the feasibility of our approach together with the simplicity and flexibility of the Proscene framework API.

  19. Performance of the LHCb RICH detector at the LHC

    Energy Technology Data Exchange (ETDEWEB)

    Adinolfi, M.; Brook, N.H.; Coombes, M.; Hampson, T.; Rademacker, J.H.; Solomin, A.; Voong, D. [University of Bristol, H.H. Wills Physics Laboratory, Bristol (United Kingdom); Aglieri Rinella, G.; Albrecht, E.; D' Ambrosio, C.; Forty, R.; Frei, C.; Gys, T.; Kanaya, N.; Koblitz, S.; Mollen, A.; Morant, J.; Piedigrossi, D.; Storaci, B.; Ullaland, O.; Vervink, K.; Wyllie, K. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Bellunato, T.; Calvi, M.; Fanchini, E.; Giachero, A.; Gotti, C.; Kucharczyk, M.; Maino, M.; Matteuzzi, C.; Perego, D.L.; Pessina, G. [Sezione INFN di Milano Bicocca, Milano (Italy); Benson, S.; Eisenhardt, S.; Fitzpatrick, C.; Kim, Y.M.; Lambert, D.; Main, A.; Muheim, F.; Playfer, S.; Sparkes, A.; Young, R. [University of Edinburgh, School of Physics and Astronomy, Edinburgh (United Kingdom); Blake, T. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Imperial College London, London (United Kingdom); Blanks, C.; Cameron, B.; Carson, L.; Egede, U.; Owen, P.; Patel, M.; Plackett, R.; Savidge, T.; Sepp, I.; Soomro, F.; Websdale, D. [Imperial College London, London (United Kingdom); Brisbane, S.; Contu, A.; Gandini, P.; Gao, R.; Harnew, N.; Hill, D.; Hunt, P.; John, M.; Johnson, D.; Malde, S.; Muresan, R.; Powell, A.; Thomas, C.; Topp-Joergensen, S.; Torr, N.; Wilkinson, G.; Xing, F. [University of Oxford, Department of Physics, Oxford (United Kingdom); Cardinale, R.; Fontanelli, F.; Mini' , G.; Petrolini, A.; Sannino, M. [Sezione INFN di Genova, Genova (Italy); Easo, S. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); STFC Rutherford Appleton Laboratory, Didcot (United Kingdom); Garra Tico, J.; Gibson, V.; Gregson, S.; Haines, S.C.; Jones, C.R.; Katvars, S.; Kerzel, U.; Mangiafave, N.; Rogers, G.J.; Sigurdsson, S.; Wotton, S.A. [University of Cambridge, Cavendish Laboratory, Cambridge (United Kingdom); Mountain, R. [Syracuse University, Syracuse, NY (United States); Morris, J.V.; Nardulli, J.; Papanestis, A.; Patrick, G.N.; Ricciardi, S. [STFC Rutherford Appleton Laboratory, Didcot (United Kingdom); Sail, P.; Soler, F.J.P.; Spradlin, P. [University of Glasgow, School of Physics and Astronomy, Glasgow (United Kingdom); Collaboration: The LHCb RICH Collaboration

    2013-05-15

    The LHCb experiment has been taking data at the Large Hadron Collider (LHC) at CERN since the end of 2009. One of its key detector components is the Ring-Imaging Cherenkov (RICH) system. This provides charged particle identification over a wide momentum range, from 2-100 GeV/c. The operation and control, software, and online monitoring of the RICH system are described. The particle identification performance is presented, as measured using data from the LHC. Excellent separation of hadronic particle types ({pi}, K, p) is achieved. (orig.)

  20. Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding

    Energy Technology Data Exchange (ETDEWEB)

    Tewary, Sunil K.; Liang, Lingfei; Lin, Zihan; Lynn, Annie [Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 (United States); Cotmore, Susan F. [Departments of Laboratory Medicine, Yale University Medical School, New Haven, CT 06510 (United States); Tattersall, Peter [Departments of Laboratory Medicine, Yale University Medical School, New Haven, CT 06510 (United States); Departments of Genetics, Yale University Medical School, New Haven, CT 06510 (United States); Zhao, Haiyan, E-mail: zhaohy@ku.edu [Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 (United States); Tang, Liang, E-mail: tangl@ku.edu [Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 (United States)

    2015-02-15

    Members of the Parvoviridae family all encode a non-structural protein 1 (NS1) that directs replication of single-stranded viral DNA, packages viral DNA into capsid, and serves as a potent transcriptional activator. Here we report the X-ray structure of the minute virus of mice (MVM) NS1 N-terminal domain at 1.45 Å resolution, showing that sites for dsDNA binding, ssDNA binding and cleavage, nuclear localization, and other functions are integrated on a canonical fold of the histidine-hydrophobic-histidine superfamily of nucleases, including elements specific for this Protoparvovirus but distinct from its Bocaparvovirus or Dependoparvovirus orthologs. High resolution structural analysis reveals a nickase active site with an architecture that allows highly versatile metal ligand binding. The structures support a unified mechanism of replication origin recognition for homotelomeric and heterotelomeric parvoviruses, mediated by a basic-residue-rich hairpin and an adjacent helix in the initiator proteins and by tandem tetranucleotide motifs in the replication origins. - Highlights: • The structure of a parvovirus replication initiator protein has been determined; • The structure sheds light on mechanisms of ssDNA binding and cleavage; • The nickase active site is preconfigured for versatile metal ligand binding; • The binding site for the double-stranded replication origin DNA is identified; • A single domain integrates multiple functions in virus replication.

  1. Deleted in Malignant Brain Tumors-1 Protein (DMBT1: A Pattern Recognition Receptor with Multiple Binding Sites

    Directory of Open Access Journals (Sweden)

    Enno C. I. Veerman

    2010-12-01

    Full Text Available Deleted in Malignant Brain Tumors-1 protein (DMBT1, salivary agglutinin (DMBT1SAG, and lung glycoprotein-340 (DMBT1GP340 are three names for glycoproteins encoded by the same DMBT1 gene. All these proteins belong to the scavenger receptor cysteine-rich (SRCR superfamily of proteins: a superfamily of secreted or membrane-bound proteins with SRCR domains that are highly conserved down to sponges, the most ancient metazoa. In addition to SRCR domains, all DMBT1s contain two CUB domains and one zona pellucida domain. The SRCR domains play a role in the function of DMBT1s, which is the binding of a broad range of pathogens including cariogenic streptococci, Helicobacter pylori and HIV. Mucosal defense proteins like IgA, surfactant proteins and lactoferrin also bind to DMBT1s through their SRCR domains. The binding motif on the SRCR domains comprises an 11-mer peptide in which a few amino acids are essential for binding (GRVEVLYRGSW. Adjacent to each individual SRCR domain are glycosylation domains, where the attached carbohydrate chains play a role in the binding of influenza A virus and Helicobacter pylori. The composition of the carbohydrate chains is not only donor specific, but also varies between different organs. These data demonstrate a role for DMBT1s as pattern recognition molecules containing various peptide and carbohydrate binding motifs.

  2. The Drosophila hnRNP F/H Homolog Glorund Uses Two Distinct RNA-Binding Modes to Diversify Target Recognition

    Energy Technology Data Exchange (ETDEWEB)

    Tamayo, Joel V.; Teramoto, Takamasa; Chatterjee, Seema; Hall, Traci M. Tanaka; Gavis, Elizabeth R. (Princeton); (NIH)

    2017-04-01

    The Drosophila hnRNP F/H homolog, Glorund (Glo), regulates nanos mRNA translation by interacting with a structured UA-rich motif in the nanos 3' untranslated region. Glo regulates additional RNAs, however, and mammalian homologs bind G-tract sequences to regulate alternative splicing, suggesting that Glo also recognizes G-tract RNA. To gain insight into how Glo recognizes both structured UA-rich and G-tract RNAs, we used mutational analysis guided by crystal structures of Glo’s RNA-binding domains and identified two discrete RNA-binding surfaces that allow Glo to recognize both RNA motifs. By engineering Glo variants that favor a single RNA-binding mode, we show that a subset of Glo’s functions in vivo is mediated solely by the G-tract binding mode, whereas regulation of nanos requires both recognition modes. Our findings suggest a molecular mechanism for the evolution of dual RNA motif recognition in Glo that may be applied to understanding the functional diversity of other RNA-binding proteins.

  3. Display of disulfide-rich proteins by complementary DNA display and disulfide shuffling assisted by protein disulfide isomerase.

    Science.gov (United States)

    Naimuddin, Mohammed; Kubo, Tai

    2011-12-01

    We report an efficient system to produce and display properly folded disulfide-rich proteins facilitated by coupled complementary DNA (cDNA) display and protein disulfide isomerase-assisted folding. The results show that a neurotoxin protein containing four disulfide linkages can be displayed in the folded state. Furthermore, it can be refolded on a solid support that binds efficiently to its natural acetylcholine receptor. Probing the efficiency of the display proteins prepared by these methods provided up to 8-fold higher enrichment by the selective enrichment method compared with cDNA display alone, more than 10-fold higher binding to its receptor by the binding assays, and more than 10-fold higher affinities by affinity measurements. Cotranslational folding was found to have better efficiency than posttranslational refolding between the two investigated methods. We discuss the utilities of efficient display of such proteins in the preparation of superior quality proteins and protein libraries for directed evolution leading to ligand discovery. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. Crystal Structures of Multicopper Oxidase CueO Bound to Copper(I) and Silver(I): Functional Role of a Methonine-Rich Sequence

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Satish K.; Roberts, Sue A.; McDevitt, Sylvia F.; Weichsel, Andrzej; Wildner, Guenter F.; Grass, Gregor B.; Rensing, Christopher; Montfort, William R. (Skidmore); (Bundeswehr); (Ariz)

    2011-10-24

    The multicopper oxidase CueO oxidizes toxic Cu(I) and is required for copper homeostasis in Escherichia coli. Like many proteins involved in copper homeostasis, CueO has a methionine-rich segment that is thought to be critical for copper handling. How such segments function is poorly understood. Here, we report the crystal structure of CueO at 1.1 {angstrom} with the 45-residue methionine-rich segment fully resolved, revealing an N-terminal helical segment with methionine residues juxtaposed for Cu(I) ligation and a C-terminal highly mobile segment rich in methionine and histidine residues. We also report structures of CueO with a C500S mutation, which leads to loss of the T1 copper, and CueO with six methionines changed to serine. Soaking C500S CueO crystals with Cu(I), or wild-type CueO crystals with Ag(I), leads to occupancy of three sites, the previously identified substrate-binding site and two new sites along the methionine-rich helix, involving methionines 358, 362, 368, and 376. Mutation of these residues leads to a {approx}4-fold reduction in kcat for Cu(I) oxidation. Ag(I), which often appears with copper in nature, strongly inhibits CueO oxidase activities in vitro and compromises copper tolerance in vivo, particularly in the absence of the complementary copper efflux cus system. Together, these studies demonstrate a role for the methionine-rich insert of CueO in the binding and oxidation of Cu(I) and highlight the interplay among cue and cus systems in copper and silver homeostasis.

  5. Peptide binding specificity of the chaperone calreticulin

    DEFF Research Database (Denmark)

    Sandhu, N.; Duus, K.; Jorgensen, C.S.

    2007-01-01

    Calreticulin is a molecular chaperone with specificity for polypeptides and N-linked monoglucosylated glycans. In order to determine the specificity of polypeptide binding, the interaction of calreticulin with polypeptides was investigated using synthetic peptides of different length and composit...

  6. HEAVY QUARK POTENTIALS AND QUARKONIA BINDING.

    Energy Technology Data Exchange (ETDEWEB)

    PETRECZKY,P.

    2004-11-04

    The author reviews recent progress in studying in-medium modification of inter-quark forces at finite temperature in lattice QCD. Some applications to the problem of quarkonium binding in potential models is also discussed.

  7. Fatty Acid Binding Proteins in Prostate Cancer

    National Research Council Canada - National Science Library

    Jett, Marti

    2000-01-01

    We have shown that there is a distinct pattern of fatty acid binding protein (FAEP) expression in prostate cancer vs normal cells and that finding has be confirmed in patient samples of biopsy specimens...

  8. Adjustment of legally binding local plans

    DEFF Research Database (Denmark)

    Hvingel, Line Træholt; Aunsborg, Christian; Christensen, Finn Kjær

    2012-01-01

    Traditionally, and by law, new urban areas in Denmark are regulated and planned through legally binding local plans. Recently a tendency has occurred: The municipalities make the legally binding local plans quite open for future adjustment, and they are using a substantial amount of ‘empowerment......, which seem to be beyond the scope of the Danish Planning Act. This paper deals with this problem through case studies and a legal analysis of present law. If the combination of the legally binding local plan and subsequent added requirements is misused, it will weaken the legal rights of the citizens...... the considerations of legal rights, the extend of the legal use of empowerment provisions and the combination of the use of legal binding local plans and other legal instruments such as easements and sales agreements....

  9. Extended hormone binding site of the human thyroid stimulating hormone receptor: distinctive acidic residues in the hinge region are involved in bovine thyroid stimulating hormone binding and receptor activation.

    Science.gov (United States)

    Mueller, Sandra; Kleinau, Gunnar; Jaeschke, Holger; Paschke, Ralf; Krause, Gerd

    2008-06-27

    The human thyroid stimulating hormone receptor (hTSHR) belongs to the glycoprotein hormone receptors that bind the hormones at their large extracellular domain. The extracellular hinge region of the TSHR connects the N-terminal leucine-rich repeat domain with the membrane-spanning serpentine domain. From previous studies we reasoned that apart from hormone binding at the leucine-rich repeat domain, additional multiple hormone contacts might exist at the hinge region of the TSHR by complementary charge-charge recognition. Here we investigated highly conserved charged residues in the hinge region of the TSHR by site-directed mutagenesis to identify amino acids interacting with bovine TSH (bTSH). Indeed, the residues Glu-297, Glu-303, and Asp-382 in the TSHR hinge region are essential for bTSH binding and partially for signal transduction. Side chain substitutions showed that the negative charge of Glu-297 and Asp-382 is necessary for recognition of bTSH by the hTSHR. Multiple combinations of alanine mutants of the identified positions revealed an increased negative effect on hormone binding. An assembled model suggests that the deciphered acidic residues form negatively charged patches at the hinge region resulting in an extended binding mode for bTSH on the hTSHR. Our data indicate that certain positively charged residues of bTSH might be involved in interaction with the identified negatively charged amino acids of the hTSHR hinge region. We demonstrate that the hinge region represents an extracellular intermediate connector for both hormone binding and signal transduction of the hTSHR.

  10. Radioligand binding assays in the drug discovery process: potential pitfalls of high throughput screenings.

    Science.gov (United States)

    Noël, F; Mendonça-Silva, D L; Quintas, L E

    2001-02-01

    Radioligand binding assays evaluating directly the ability of a drug to interact with a defined molecular target is part of the drug discovery process. The need for a high throughput rate in screening drugs is actually leading to simplified experimental schemes that increase the probability of false negative results. Special concern involves voltage-gated ion channel drug discovery where a great care is required in designing assays because of frequent multiplicity of (interacting) binding sites. To clearly illustrate this situation, three different assays used in the academic drug discovery program of the authors were selected because they are rich of intrinsic artifacts: (I) (20 mmol/l caffeine almost duplicated [3H]ryanodine binding (89% higher than control) to rat heart microsomes at 0.3 mumol/l free calcium but did not exert any effect when using a high (107 mumol/l) free calcium, as mostly used in ryanodine binding assays; (II) An agonist for the ionotropic glutamate receptor of the kainate type can distinctly affect [3H]kainate binding to chicken cerebellum membranes depending on its concentration: unlabelled kainic acid per se either stimulated about 30% (at 50-100 nmol/l), had no effect (at 200 nmol/l) or even progressively decreased (at 0.3-2 mumol/l) the binding of 5 nmol/l [3H]kainate, emphasizing the risk of using a single concentration for screening a drug; (III) in a classical [3H]flunitrazepam binding assay, the stimulatory effect of a GABA (gamma-aminobutyric acid) agonist was only observed when using extensively washed rat brain synaptosomes (10 mumol/l GABA increased flunitrazepam binding by 90%). On the other hand, the inhibitory effect of a GABA antagonist was only observed when using crude synaptosomes (10 mumol/l bicuculine reduced [3H]flunitrazepam binding by 40%). It can be concluded that carefully designed radioligand assays which can be performed in an academic laboratory are appropriate for screening a small number of drugs, especially if

  11. Exciton Binding Energy of Monolayer WS2

    Science.gov (United States)

    Zhu, Bairen; Chen, Xi; Cui, Xiaodong

    2015-03-01

    The optical properties of monolayer transition metal dichalcogenides (TMDC) feature prominent excitonic natures. Here we report an experimental approach to measuring the exciton binding energy of monolayer WS2 with linear differential transmission spectroscopy and two-photon photoluminescence excitation spectroscopy (TP-PLE). TP-PLE measurements show the exciton binding energy of 0.71 +/- 0.01 eV around K valley in the Brillouin zone.

  12. Antimicrobial activities of heparin-binding peptides.

    OpenAIRE

    Andersson, Emma; Rydengård, Victoria; Sonesson, Andreas; Mörgelin, Matthias; Björck, Lars; Schmidtchen, Artur

    2004-01-01

    Antimicrobial peptides are effector molecules of the innate immune system. We recently showed that the human antimicrobial peptides alpha-defensin and LL-37 bind to glycosaminoglycans (heparin and dermatan sulphate). Here we demonstrate the obverse, i.e. structural motifs associated with heparin affinity (cationicity, amphipaticity, and consensus regions) may confer antimicrobial properties to a given peptide. Thus, heparin-binding peptides derived from laminin isoforms, von Willebrand factor...

  13. THE REACH AND RICHNESS OF WIKINOMICS: IS THE FREE WEB-BASED ENCYCLOPEDIA WIKIPEDIA ONLY FOR RICH COUNTRIES?

    DEFF Research Database (Denmark)

    Rask, Morten

    2007-01-01

    In this article, a model of the patterns of correlation in Wikipedia, reach and richness, lays the foundation for studying whether the free Web-based encyclopedia Wikipedia is only for developed countries. Based on data from 12 different Wikipedia language editions, the author finds that the cent......In this article, a model of the patterns of correlation in Wikipedia, reach and richness, lays the foundation for studying whether the free Web-based encyclopedia Wikipedia is only for developed countries. Based on data from 12 different Wikipedia language editions, the author finds...... that the central structural effect is on the level of human development in the current country. In other words, Wikipedia is in general more for rich countries than for less developed countries. It is suggested that policy makers make investments in increasing the general level of literacy, education, and standard...

  14. Electrostatically biased binding of kinesin to microtubules.

    Directory of Open Access Journals (Sweden)

    Barry J Grant

    2011-11-01

    Full Text Available The minimum motor domain of kinesin-1 is a single head. Recent evidence suggests that such minimal motor domains generate force by a biased binding mechanism, in which they preferentially select binding sites on the microtubule that lie ahead in the progress direction of the motor. A specific molecular mechanism for biased binding has, however, so far been lacking. Here we use atomistic Brownian dynamics simulations combined with experimental mutagenesis to show that incoming kinesin heads undergo electrostatically guided diffusion-to-capture by microtubules, and that this produces directionally biased binding. Kinesin-1 heads are initially rotated by the electrostatic field so that their tubulin-binding sites face inwards, and then steered towards a plus-endwards binding site. In tethered kinesin dimers, this bias is amplified. A 3-residue sequence (RAK in kinesin helix alpha-6 is predicted to be important for electrostatic guidance. Real-world mutagenesis of this sequence powerfully influences kinesin-driven microtubule sliding, with one mutant producing a 5-fold acceleration over wild type. We conclude that electrostatic interactions play an important role in the kinesin stepping mechanism, by biasing the diffusional association of kinesin with microtubules.

  15. DNA-Aptamers Binding Aminoglycoside Antibiotics

    Directory of Open Access Journals (Sweden)

    Nadia Nikolaus

    2014-02-01

    Full Text Available Aptamers are short, single stranded DNA or RNA oligonucleotides that are able to bind specifically and with high affinity to their non-nucleic acid target molecules. This binding reaction enables their application as biorecognition elements in biosensors and assays. As antibiotic residues pose a problem contributing to the emergence of antibiotic-resistant pathogens and thereby reducing the effectiveness of the drug to fight human infections, we selected aptamers targeted against the aminoglycoside antibiotic kanamycin A with the aim of constructing a robust and functional assay that can be used for water analysis. With this work we show that aptamers that were derived from a Capture-SELEX procedure targeting against kanamycin A also display binding to related aminoglycoside antibiotics. The binding patterns differ among all tested aptamers so that there are highly substance specific aptamers and more group specific aptamers binding to a different variety of aminoglycoside antibiotics. Also the region of the aminoglycoside antibiotics responsible for aptamer binding can be estimated. Affinities of the different aptamers for their target substance, kanamycin A, are measured with different approaches and are in the micromolar range. Finally, the proof of principle of an assay for detection of kanamycin A in a real water sample is given.

  16. Radiation damage to DNA-binding proteins

    International Nuclear Information System (INIS)

    Culard, G.; Eon, S.; DeVuyst, G.; Charlier, M.; Spotheim-Maurizot, M.

    2003-01-01

    The DNA-binding properties of proteins are strongly affected upon irradiation. The tetrameric lactose repressor (a dimer of dimers) losses its ability to bind operator DNA as soon as at least two damages per protomer of each dimer occur. The monomeric MC1 protein losses its ability to bind DNA in two steps : i) at low doses only the specific binding is abolished, whereas the non-specific one is still possible; ii) at high doses all binding vanishes. Moreover, the DNA bending induced by MC1 binding is less pronounced for a protein that underwent the low dose irradiation. When the entire DNA-protein complexes are irradiated, the observed disruption of the complexes is mainly due to the damage of the proteins and not to that of DNA. The doses necessary for complex disruption are higher than those inactivating the free protein. This difference, larger for MC1 than for lactose repressor, is due to the protection of the protein by the bound DNA. The oxidation of the protein side chains that are accessible to the radiation-induced hydroxyl radicals seems to represent the inactivating damage

  17. Identification of pseudomurein cell wall binding domains.

    Science.gov (United States)

    Steenbakkers, Peter J M; Geerts, Wim J; Ayman-Oz, Nilgün A; Keltjens, Jan T

    2006-12-01

    Methanothermobacter thermautotrophicus is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. Currently, no information is available on extracellular pseudomurein biology and so far only two prophage pseudomurein autolysins, PeiW and PeiP, have been reported. In this paper we show that PeiW and PeiP contain two different N-terminal pseudomurein cell wall binding domains. This finding was used to identify a novel domain, PB007923, on the M. thermautotrophicus genome present in 10 predicted open reading frames. Three homologues were identified in the Methanosphaera stadtmanae genome. Binding studies of fusion constructs of three separate PB007923 domains to green fluorescent protein revealed that it also constituted a cell wall binding domain. Both prophage domains and the PB007923 domain bound to the cell walls of Methanothermobacter species and fluorescence microscopy showed a preference for the septal region. Domain specificities were revealed by binding studies with other pseudomurein-containing archaea. Localized binding was observed for M. stadtmanae and Methanobrevibacter species, while others stained evenly. The identification of the first pseudomurein cell wall binding domains reveals the dynamics of the pseudomurein cell wall and provides marker proteins to study the extracellular pseudomurein biology of M. thermautotrophicus and of other pseudomurein-containing archaea.

  18. The readiness potential reflects intentional binding

    Directory of Open Access Journals (Sweden)

    Han-Gue eJo

    2014-06-01

    Full Text Available When a voluntary action is causally linked with a sensory outcome, the action and its consequent effect are perceived as being closer together in time. This effect is called intentional binding. Although many experiments were conducted on this phenomenon, the underlying neural mechanisms are not well understood. While intentional binding is specific to voluntary action, we presumed that preconscious brain activity (the readiness potential, RP, which occurs before an action is made, might play an important role in this binding effect. In this study, the brain dynamics were recorded with electroencephalography (EEG and analyzed in single-trials in order to estimate whether intentional binding is correlated with the early neural processes. Moreover, we were interested in different behavioral performance between meditators and non-meditators since meditators are expected to be able to keep attention more consistently on a task. Thus, we performed the intentional binding paradigm with twenty mindfulness meditators and compared them to matched controls. Although, we did not observe a group effect on either behavioral data or EEG recordings, we found that self-initiated movements following ongoing negative deflections of slow cortical potentials (SCPs result in a stronger binding effect compared to positive potentials, especially regarding the perceived time of the consequent effect. Our results provide the first direct evidence that the early neural activity within the range of SCPs affects perceived time of a sensory outcome that is caused by intentional action.

  19. LIBRA: LIgand Binding site Recognition Application.

    Science.gov (United States)

    Hung, Le Viet; Caprari, Silvia; Bizai, Massimiliano; Toti, Daniele; Polticelli, Fabio

    2015-12-15

    In recent years, structural genomics and ab initio molecular modeling activities are leading to the availability of a large number of structural models of proteins whose biochemical function is not known. The aim of this study was the development of a novel software tool that, given a protein's structural model, predicts the presence and identity of active sites and/or ligand binding sites. The algorithm implemented by ligand binding site recognition application (LIBRA) is based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites. The algorithm makes use of two predefined databases for active sites and ligand binding sites, respectively, derived from the Catalytic Site Atlas and the Protein Data Bank. Tests indicate that LIBRA is able to identify the correct binding/active site in 90% of the cases analyzed, 90% of which feature the identified site as ranking first. As far as ligand binding site recognition is concerned, LIBRA outperforms other structure-based ligand binding sites detection tools with which it has been compared. The application, developed in Java SE 7 with a Swing GUI embedding a JMol applet, can be run on any OS equipped with a suitable Java Virtual Machine (JVM), and is available at the following URL: http://www.computationalbiology.it/software/LIBRAv1.zip. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  20. Zinc Binding by Lactic Acid Bacteria

    Directory of Open Access Journals (Sweden)

    Jasna Mrvčić

    2009-01-01

    Full Text Available Zinc is an essential trace element in all organisms. A common method for the prevention of zinc deficiency is pharmacological supplementation, especially in a highly available form of a metalloprotein complex. The potential of different microbes to bind essential and toxic heavy metals has recently been recognized. In this work, biosorption of zinc by lactic acid bacteria (LAB has been investigated. Specific LAB were assessed for their ability to bind zinc from a water solution. Significant amount of zinc ions was bound, and this binding was found to be LAB species-specific. Differences among the species in binding performance at a concentration range between 10–90 mg/L were evaluated with Langmuir model for biosorption. Binding of zinc was a fast process, strongly influenced by ionic strength, pH, biomass concentration, and temperature. The most effective metal-binding LAB species was Leuconostoc mesenteroides (27.10 mg of Zn2+ per gram of dry mass bound at pH=5 and 32 °C, during 24 h. FT-IR spectroscopy analysis and electron microscopy demonstrated that passive adsorption and active uptake of the zinc ions were involved.

  1. Immobilized purified folate-binding protein: binding characteristics and use for quantifying folate in erythrocytes

    International Nuclear Information System (INIS)

    Hansen, S.I.; Holm, J.; Nexo, E.

    1987-01-01

    Purified folate-binding protein from cow's milk was immobilized on monodisperse polymer particles (Dynospheres) activated by rho-toluenesulfonyl chloride. Leakage from the spheres was less than 0.1%, and the binding properties were similar to those of the soluble protein with regard to dissociation, pH optimum for binding pteroylglutamic acid, and specificity for binding various folate derivatives. We used the immobilized folate-binding protein as binding protein in an isotope-dilution assay for quantifying folate in erythrocytes. The detection limit was 50 nmol/L and the CV over a six-month period was 2.3% (means = 1.25 mumol/L, n = 15). The reference interval, for folate measured in erythrocytes of 43 blood donors, was 0.4-1.5 mumol/L

  2. To Bind or not to Bind: It’s in the Contract

    DEFF Research Database (Denmark)

    Tvarnø, Christina D.

    2015-01-01

    This article discusses the formalization of collaboration through partnering contracts in the construction industry in the USA, Great Britain and Denmark. The article compares the different types of collaborative partnering contracts in the three countries, and provides a conclusion on whether...... the collaborative partnering contract should be binding or non-binding, based on the three empirical contracts analyzed in this article. The partnering contracts in Great Britain and Denmark are legally binding, while in the USA the partnering agreements are non-binding charters or letters of intent. This article...... discusses, in a theoretical perspective, the legal reasoning behind the different partnering approaches, both from a historical and contract law perspective, and furthermore applies a game theoretical approach in evaluating binding versus non-binding partnering contracts. The analysis focuses on private...

  3. Ammonium transformation in a nitrogen-rich tidal freshwater marsh

    DEFF Research Database (Denmark)

    Gribsholt, B.; Andersson, M.; Boschker, H.T.S.

    2006-01-01

    The fate and transport of watershed-derived ammonium in a tidal freshwater marsh fringing the nutrient rich Scheldt River, Belgium, was quantified in a whole ecosystem 15N labeling experiment. In late summer (September) we added 15N-NH4+ to the flood water entering a 3477 m2 tidal freshwater marsh...

  4. Species richness and composition of bird community in Abalo ...

    African Journals Online (AJOL)

    This paper presents results of avifaunal survey made in Abalo-Gunacho forest, southern Ethiopia, in May 2014 to determine the species richness and to examine guild composition of bird community of the forest. Birds were surveyed using Timed-Species Count technique along eight randomly selected transects. Fifty-one ...

  5. The effect of intercropping Sclerocarya birrea (A. Rich.) Hochst ...

    African Journals Online (AJOL)

    Sclerocarya birrea (A. Rich.) Hochst. (marula) is native to Africa occurring in the semi-arid, deciduous savannas of much of sub-Saharan Africa. It has multiple uses, including the fruits, kernels, oil, bark, wood and leaves which make it a key species to support the development of rural enterprises. Enhancing positive ...

  6. Structure of light neutron-rich nuclei through Coulomb dissociation

    Indian Academy of Sciences (India)

    Home; Journals; Pramana – Journal of Physics; Volume 57; Issue 2-3. Structure of light neutron-rich nuclei through Coulomb dissociation. U Datta Pramanik T Aumann D Cortina H Emling H Geissel M Hellström R Holzmann N Iwasa Y Leifels G Münzenberg M Rejmund C Scheidenberger K Sümmerer A Leistenschneider ...

  7. The effects of forest destruction on the abundance, species richness ...

    African Journals Online (AJOL)

    SARAH

    2013-04-25

    Apr 25, 2013 ... The effects of forest destruction on the abundance, species richness and diversity of butterflies in the. Bosomkese Forest Reserve, Brong Ahafo Region,. Ghana. Addai, G. and Baidoo P. K*. Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology,. Kumasi ...

  8. GraphMeta: Managing HPC Rich Metadata in Graphs

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Dong; Chen, Yong; Carns, Philip; Jenkins, John; Zhang, Wei; Ross, Robert

    2016-01-01

    High-performance computing (HPC) systems face increasingly critical metadata management challenges, especially in the approaching exascale era. These challenges arise not only from exploding metadata volumes, but also from increasingly diverse metadata, which contains data provenance and arbitrary user-defined attributes in addition to traditional POSIX metadata. This ‘rich’ metadata is becoming critical to supporting advanced data management functionality such as data auditing and validation. In our prior work, we identified a graph-based model as a promising solution to uniformly manage HPC rich metadata due to its flexibility and generality. However, at the same time, graph-based HPC rich metadata anagement also introduces significant challenges to the underlying infrastructure. In this study, we first identify the challenges on the underlying infrastructure to support scalable, high-performance rich metadata management. Based on that, we introduce GraphMeta, a graphbased engine designed for this use case. It achieves performance scalability by introducing a new graph partitioning algorithm and a write-optimal storage engine. We evaluate GraphMeta under both synthetic and real HPC metadata workloads, compare it with other approaches, and demonstrate its advantages in terms of efficiency and usability for rich metadata management in HPC systems.

  9. Plant species richness regulates soil respiration through changes in productivity.

    NARCIS (Netherlands)

    Tavares Correa Dias, A.; van Ruijven, J.; Berendse, F.

    2010-01-01

    Soil respiration is an important pathway of the C cycle. However, it is still poorly understood how changes in plant community diversity can affect this ecosystem process. Here we used a long-term experiment consisting of a gradient of grassland plant species richness to test for effects of

  10. Plant species richness regulates soil respiration through changes in productivity

    NARCIS (Netherlands)

    Dias, A.A.; Ruijven, van J.; Berendse, F.

    2010-01-01

    Soil respiration is an important pathway of the C cycle. However, it is still poorly understood how changes in plant community diversity can affect this ecosystem process. Here we used a long-term experiment consisting of a gradient of grassland plant species richness to test for effects of

  11. Fission decay properties of ultra neutron-rich uranium isotopes

    Indian Academy of Sciences (India)

    Abstract. The fission decay of highly neutron-rich uranium isotopes is investigated which shows interesting new features in the barrier properties and neutron emission char- acteristics in the fission process. 233U and 235U are the nuclei in the actinide region in the beta stability valley which are thermally fissile and have ...

  12. Ant species richness of fynbos and forest ecosystems in the ...

    African Journals Online (AJOL)

    The ant fauna in fynbos and forest habitats in the southern Cape are compared. There is no significant difference in ant species richness between the two undisturbed habitat types, and the only two species common to both are Acantholepis capensis and Camponotus maculatus. The degree of Hakea sericea infestation in ...

  13. High-spin structure of neutron-rich Dy isotopes

    Indian Academy of Sciences (India)

    Abstract. In view of recent experimental progress on production and spectroscopy of neutron-rich isotopes of Dy with mass number A. 166 and 168, we have made theoretical investigations on the structure of high spin states of164 170Dy isotopes in the cranked Hartree–Fock–Bogoliubov (CHFB) theory employing a ...

  14. Species Richness and Diversity Reveal that Human-Modified ...

    African Journals Online (AJOL)

    Spider abundance differed significantly between habitat types and was influenced by the sampling methods used. Family diversity and richness showed no significant differences across the sites. The spider species consisted of primarily three functional groups: ground wanderers, web builders and plant wanderers, and ...

  15. A protocol for sampling vascular epiphyte richness and abundance

    NARCIS (Netherlands)

    Wolf, J.H.D.; Gradstein, S.R.; Nadkarni, N.M.

    2009-01-01

    The sampling of epiphytes is fraught with methodological difficulties. We present a protocol to sample and analyse vascular epiphyte richness and abundance in forests of different structure (SVERA). Epiphyte abundance is estimated as biomass by recording the number of plant components in a range of

  16. Structure of light neutron-rich nuclei through Coulomb dissociation

    Indian Academy of Sciences (India)

    O, the low-lying E1 strength amounts up to about 12% of the energy weighted dipole sum rule strength depending on neutron excess. The cluster sum rule limit with. ½. O as a core is almost exhausted for. ½,½. O, while for more neutron rich isotopes the strength with respect to that limit decreases. Keywords. Coulomb ...

  17. Algae of the Bohemian Forest. 1. Specieses richness

    Czech Academy of Sciences Publication Activity Database

    Lederer, F.; Lukavský, Jaromír

    2001-01-01

    Roč. 6, - (2001), s. 97-104 ISSN 1211-7420 R&D Projects: GA AV ČR IA60504; GA ČR GA206/99/1411 Institutional research plan: CEZ:AV0Z6005908 Keywords : Bohemian Forest * species richness * biodiversity * algae * cyanobacteria * lakes * brooks * rivers * bogs Subject RIV: EH - Ecology, Behaviour

  18. Patterns of species richness in sandy beaches of South America ...

    African Journals Online (AJOL)

    The middle shore is primarily occupied by cirolanids and bivalves, and hippid crabs, bivalves and amphipods dominate the lower beach. Generally, species richness increases from upper to lower beach levels. Studies carried out on exposed sandy beaches of south-central Chile (ca. 40°S) show that different beach states ...

  19. Patterns of species richness in sandy beaches of South America

    African Journals Online (AJOL)

    Instituto de Zoologia, Universidad Austral de Chile, Valdivia, Chile. Received 22 Occobcr 1993; accepted 19 Jan.uary 1994. Species richness of the intertidal macroinfauna of exposed sandy beaches around South America is reviewed in relation to geographic location. This macrolnfauna is dominated by drolanid isopods ...

  20. Transition metal chemistry of hydroxy(–OH)-rich molecules ...

    Indian Academy of Sciences (India)

    Administrator

    Transition metal chemistry of hydroxy(–OH)-rich molecules: Syntheses, crystal structures and solution reactivity studies. MISHTU DEY 1, P K SAARENKETO 2, E KOLEHMAINEN 2,. K RISSANEN 2 and CHEBROLU P RAO 1. 1Bioinorganic Laboratory, Department of Chemistry, Indian Institute of. Technology Bombay, Powai ...