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Sample records for selective allosteric potentiator

  1. Orthosteric and allosteric potentiation of heteromeric neuronal nicotinic acetylcholine receptors.

    Science.gov (United States)

    Wang, Jingyi; Lindstrom, Jon

    2018-06-01

    Heteromeric nicotinic ACh receptors (nAChRs) were thought to have two orthodox agonist-binding sites at two α/β subunit interfaces. Highly selective ligands are hard to develop by targeting orthodox agonist sites because of high sequence similarity of this binding pocket among different subunits. Recently, unorthodox ACh-binding sites have been discovered at some α/α and β/α subunit interfaces, such as α4/α4, α5/α4 and β3/α4. Targeting unorthodox sites may yield subtype-selective ligands, such as those for (α4β2) 2 α5, (α4β2) 2 β3 and (α6β2) 2 β3 nAChRs. The unorthodox sites have unique pharmacology. Agonist binding at one unorthodox site is not sufficient to activate nAChRs, but it increases activation from the orthodox sites. NS9283, a selective agonist for the unorthodox α4/α4 site, was initially thought to be a positive allosteric modulator (PAM). NS9283 activates nAChRs with three engineered α4/α4 sites. PAMs, on the other hand, act at allosteric sites where ACh cannot bind. Known PAM sites include the ACh-homologous non-canonical site (e.g. morantel at β/α), the C-terminus (e.g. Br-PBTC and 17β-estradiol), a transmembrane domain (e.g. LY2087101) or extracellular and transmembrane domain interfaces (e.g. NS206). Some of these PAMs, such as Br-PBTC and 17β-estradiol, require only one subunit to potentiate activation of nAChRs. In this review, we will discuss differences between activation from orthosteric and allosteric sites, their selective ligands and clinical implications. These studies have advanced understanding of the structure, assembly and pharmacology of heteromeric neuronal nAChRs. This article is part of a themed section on Nicotinic Acetylcholine Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.11/issuetoc. © 2017 The British Pharmacological Society.

  2. The therapeutic potential of allosteric ligands for free fatty acid sensitive GPCRs

    DEFF Research Database (Denmark)

    Hudson, Brian D; Ulven, Trond; Milligan, Graeme

    2013-01-01

    G protein coupled receptors (GPCRs) are the most historically successful therapeutic targets. Despite this success there are many important aspects of GPCR pharmacology and function that have yet to be exploited to their full therapeutic potential. One in particular that has been gaining attention...... safety, more physiologically appropriate responses, better target selectivity, and reduced likelihood of desensitisation and tachyphylaxis. Despite these advantages, the development of allosteric ligands is often difficult from a medicinal chemistry standpoint due to the more complex challenge...

  3. Selective Negative Allosteric Modulation Of Metabotropic Glutamate Receptors - A Structural Perspective of Ligands and Mutants

    DEFF Research Database (Denmark)

    Harpsøe, Kasper; Isberg, Vignir; Tehan, Benjamin G

    2015-01-01

    modulators. In this analysis, we make the first comprehensive structural comparison of all metabotropic glutamate receptors, placing selective negative allosteric modulators and critical mutants into the detailed context of the receptor binding sites. A better understanding of how the different m......Glu allosteric modulator binding modes relates to selective pharmacological actions will be very valuable for rational design of safer drugs....

  4. Are AMPA Receptor Positive Allosteric Modulators Potential Pharmacotherapeutics for Addiction?

    Directory of Open Access Journals (Sweden)

    Lucas R. Watterson

    2013-12-01

    Full Text Available Positive allosteric modulators (PAMs of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA receptors are a diverse class of compounds that increase fast excitatory transmission in the brain. AMPA PAMs have been shown to facilitate long-term potentiation, strengthen communication between various cortical and subcortical regions, and some of these compounds increase the production and release of brain-derived neurotrophic factor (BDNF in an activity-dependent manner. Through these mechanisms, AMPA PAMs have shown promise as broad spectrum pharmacotherapeutics in preclinical and clinical studies for various neurodegenerative and psychiatric disorders. In recent years, a small collection of preclinical animal studies has also shown that AMPA PAMs may have potential as pharmacotherapeutic adjuncts to extinction-based or cue-exposure therapies for the treatment of drug addiction. The present paper will review this preclinical literature, discuss novel data collected in our laboratory, and recommend future research directions for the possible development of AMPA PAMs as anti-addiction medications.

  5. Allosteric Inhibition of SHP2: Identification of a Potent, Selective, and Orally Efficacious Phosphatase Inhibitor

    Energy Technology Data Exchange (ETDEWEB)

    Fortanet, Jorge Garcia; Chen, Christine Hiu-Tung; Chen, Ying-Nan P.; Chen, Zhouliang; Deng, Zhan; Firestone, Brant; Fekkes, Peter; Fodor, Michelle; Fortin, Pascal D.; Fridrich, Cary; Grunenfelder, Denise; Ho, Samuel; Kang, Zhao B.; Karki, Rajesh; Kato, Mitsunori; Keen, Nick; LaBonte, Laura R.; Larrow, Jay; Lenoir, Francois; Liu, Gang; Liu, Shumei; Lombardo, Franco; Majumdar, Dyuti; Meyer, Matthew J.; Palermo, Mark; Perez, Lawrence; Pu, Minying; Ramsey, Timothy; Sellers, William R.; Shultz, Michael D.; Stams, Travis; Towler, Christopher; Wang, Ping; Williams, Sarah L.; Zhang, Ji-Hu; LaMarche, Matthew J. (Novartis)

    2016-09-08

    SHP2 is a nonreceptor protein tyrosine phosphatase (PTP) encoded by the PTPN11 gene involved in cell growth and differentiation via the MAPK signaling pathway. SHP2 also purportedly plays an important role in the programmed cell death pathway (PD-1/PD-L1). Because it is an oncoprotein associated with multiple cancer-related diseases, as well as a potential immunomodulator, controlling SHP2 activity is of significant therapeutic interest. Recently in our laboratories, a small molecule inhibitor of SHP2 was identified as an allosteric modulator that stabilizes the autoinhibited conformation of SHP2. A high throughput screen was performed to identify progressable chemical matter, and X-ray crystallography revealed the location of binding in a previously undisclosed allosteric binding pocket. Structure-based drug design was employed to optimize for SHP2 inhibition, and several new protein–ligand interactions were characterized. These studies culminated in the discovery of 6-(4-amino-4-methylpiperidin-1-yl)-3-(2,3-dichlorophenyl)pyrazin-2-amine (SHP099, 1), a potent, selective, orally bioavailable, and efficacious SHP2 inhibitor.

  6. Screening and identification of potential PTP1B allosteric inhibitors using in silico and in vitro approaches.

    Science.gov (United States)

    Shinde, Ranajit Nivrutti; Kumar, G Siva; Eqbal, Shahbaz; Sobhia, M Elizabeth

    2018-01-01

    Protein tyrosine phosphatase 1B (PTP1B) is a validated therapeutic target for Type 2 diabetes due to its specific role as a negative regulator of insulin signaling pathways. Discovery of active site directed PTP1B inhibitors is very challenging due to highly conserved nature of the active site and multiple charge requirements of the ligands, which makes them non-selective and non-permeable. Identification of the PTP1B allosteric site has opened up new avenues for discovering potent and selective ligands for therapeutic intervention. Interactions made by potent allosteric inhibitor in the presence of PTP1B were studied using Molecular Dynamics (MD). Computationally optimized models were used to build separate pharmacophore models of PTP1B and TCPTP, respectively. Based on the nature of interactions the target residues offered, a receptor based pharmacophore was developed. The pharmacophore considering conformational flexibility of the residues was used for the development of pharmacophore hypothesis to identify potentially active inhibitors by screening large compound databases. Two pharmacophore were successively used in the virtual screening protocol to identify potential selective and permeable inhibitors of PTP1B. Allosteric inhibition mechanism of these molecules was established using molecular docking and MD methods. The geometrical criteria values confirmed their ability to stabilize PTP1B in an open conformation. 23 molecules that were identified as potential inhibitors were screened for PTP1B inhibitory activity. After screening, 10 molecules which have good permeability values were identified as potential inhibitors of PTP1B. This study confirms that selective and permeable inhibitors can be identified by targeting allosteric site of PTP1B.

  7. Allosteric Mutant IDH1 Inhibitors Reveal Mechanisms for IDH1 Mutant and Isoform Selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Xiaoling; Baird, Daniel; Bowen, Kimberly; Capka, Vladimir; Chen, Jinyun; Chenail, Gregg; Cho, YoungShin; Dooley, Julia; Farsidjani, Ali; Fortin, Pascal; Kohls, Darcy; Kulathila, Raviraj; Lin, Fallon; McKay, Daniel; Rodrigues, Lindsey; Sage, David; Touré, B. Barry; van der Plas, Simon; Wright, Kirk; Xu, Ming; Yin, Hong; Levell, Julian; Pagliarini, Raymond A. (Novartis)

    2017-03-01

    Oncogenic IDH1 and IDH2 mutations contribute to cancer via production of R-2-hydroxyglutarate (2-HG). Here, we characterize two structurally distinct mutant- and isoform-selective IDH1 inhibitors that inhibit 2-HG production. Both bind to an allosteric pocket on IDH1, yet shape it differently, highlighting the plasticity of this site. Oncogenic IDH1R132H mutation destabilizes an IDH1 “regulatory segment,” which otherwise restricts compound access to the allosteric pocket. Regulatory segment destabilization in wild-type IDH1 promotes inhibitor binding, suggesting that destabilization is critical for mutant selectivity. We also report crystal structures of oncogenic IDH2 mutant isoforms, highlighting the fact that the analogous segment of IDH2 is not similarly destabilized. This intrinsic stability of IDH2 may contribute to observed inhibitor IDH1 isoform selectivity. Moreover, discrete residues in the IDH1 allosteric pocket that differ from IDH2 may also guide IDH1 isoform selectivity. These data provide a deeper understanding of how IDH1 inhibitors achieve mutant and isoform selectivity.

  8. Modulation in selectivity and allosteric properties of small-molecule ligands for CC-chemokine receptors

    DEFF Research Database (Denmark)

    Thiele, Stefanie; Malmgaard-Clausen, Mikkel; Engel-Andreasen, Jens

    2012-01-01

    Among 18 human chemokine receptors, CCR1, CCR4, CCR5, and CCR8 were activated by metal ion Zn(II) or Cu(II) in complex with 2,2'-bipyridine or 1,10-phenanthroline with similar potencies (EC(50) from 3.9 to 172 μM). Besides being agonists, they acted as selective allosteric enhancers of CCL3. Thes...

  9. Binding and Signaling Studies Disclose a Potential Allosteric Site for Cannabidiol in Cannabinoid CB2 Receptors

    Directory of Open Access Journals (Sweden)

    Eva Martínez-Pinilla

    2017-10-01

    Full Text Available The mechanism of action of cannabidiol (CBD, the main non-psychotropic component of Cannabis sativa L., is not completely understood. First assumed that the compound was acting via cannabinoid CB2 receptors (CB2Rs it is now suggested that it interacts with non-cannabinoid G-protein-coupled receptors (GPCRs; however, CBD does not bind with high affinity to the orthosteric site of any GPCR. To search for alternative explanations, we tested CBD as a potential allosteric ligand of CB2R. Radioligand and non-radioactive homogeneous binding, intracellular cAMP determination and ERK1/2 phosphorylation assays were undertaken in heterologous systems expressing the human version of CB2R. Using membrane preparations from CB2R-expressing HEK-293T (human embryonic kidney 293T cells, we confirmed that CBD does not bind with high affinity to the orthosteric site of the human CB2R where the synthetic cannabinoid, [3H]-WIN 55,212-2, binds. CBD was, however, able to produce minor but consistent reduction in the homogeneous binding assays in living cells using the fluorophore-conjugated CB2R-selective compound, CM-157. The effect on binding to CB2R-expressing living cells was different to that exerted by the orthosteric antagonist, SR144528, which decreased the maximum binding without changing the KD. CBD at nanomolar concentrations was also able to significantly reduce the effect of the selective CB2R agonist, JWH133, on forskolin-induced intracellular cAMP levels and on activation of the MAP kinase pathway. These results may help to understand CBD mode of action and may serve to revisit its therapeutic possibilities.

  10. Binding and Signaling Studies Disclose a Potential Allosteric Site for Cannabidiol in Cannabinoid CB2 Receptors.

    Science.gov (United States)

    Martínez-Pinilla, Eva; Varani, Katia; Reyes-Resina, Irene; Angelats, Edgar; Vincenzi, Fabrizio; Ferreiro-Vera, Carlos; Oyarzabal, Julen; Canela, Enric I; Lanciego, José L; Nadal, Xavier; Navarro, Gemma; Borea, Pier Andrea; Franco, Rafael

    2017-01-01

    The mechanism of action of cannabidiol (CBD), the main non-psychotropic component of Cannabis sativa L., is not completely understood. First assumed that the compound was acting via cannabinoid CB 2 receptors (CB 2 Rs) it is now suggested that it interacts with non-cannabinoid G-protein-coupled receptors (GPCRs); however, CBD does not bind with high affinity to the orthosteric site of any GPCR. To search for alternative explanations, we tested CBD as a potential allosteric ligand of CB 2 R. Radioligand and non-radioactive homogeneous binding, intracellular cAMP determination and ERK1/2 phosphorylation assays were undertaken in heterologous systems expressing the human version of CB 2 R. Using membrane preparations from CB 2 R-expressing HEK-293T (human embryonic kidney 293T) cells, we confirmed that CBD does not bind with high affinity to the orthosteric site of the human CB 2 R where the synthetic cannabinoid, [ 3 H]-WIN 55,212-2, binds. CBD was, however, able to produce minor but consistent reduction in the homogeneous binding assays in living cells using the fluorophore-conjugated CB 2 R-selective compound, CM-157. The effect on binding to CB 2 R-expressing living cells was different to that exerted by the orthosteric antagonist, SR144528, which decreased the maximum binding without changing the K D . CBD at nanomolar concentrations was also able to significantly reduce the effect of the selective CB 2 R agonist, JWH133, on forskolin-induced intracellular cAMP levels and on activation of the MAP kinase pathway. These results may help to understand CBD mode of action and may serve to revisit its therapeutic possibilities.

  11. Design and optimization of selective azaindole amide M1 positive allosteric modulators.

    Science.gov (United States)

    Davoren, Jennifer E; O'Neil, Steven V; Anderson, Dennis P; Brodney, Michael A; Chenard, Lois; Dlugolenski, Keith; Edgerton, Jeremy R; Green, Michael; Garnsey, Michelle; Grimwood, Sarah; Harris, Anthony R; Kauffman, Gregory W; LaChapelle, Erik; Lazzaro, John T; Lee, Che-Wah; Lotarski, Susan M; Nason, Deane M; Obach, R Scott; Reinhart, Veronica; Salomon-Ferrer, Romelia; Steyn, Stefanus J; Webb, Damien; Yan, Jiangli; Zhang, Lei

    2016-01-15

    Selective activation of the M1 receptor via a positive allosteric modulator (PAM) is a new approach for the treatment of the cognitive impairments associated with schizophrenia and Alzheimer's disease. A novel series of azaindole amides and their key pharmacophore elements are described. The nitrogen of the azaindole core is a key design element as it forms an intramolecular hydrogen bond with the amide N-H thus reinforcing the bioactive conformation predicted by published SAR and our homology model. Representative compound 25 is a potent and selective M1 PAM that has well aligned physicochemical properties, adequate brain penetration and pharmacokinetic (PK) properties, and is active in vivo. These favorable properties indicate that this series possesses suitable qualities for further development and studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Development of allosteric modulators of GPCRs for treatment of CNS disorders.

    Science.gov (United States)

    Nickols, Hilary Highfield; Conn, P Jeffrey

    2014-01-01

    The discovery of allosteric modulators of G protein-coupled receptors (GPCRs) provides a promising new strategy with potential for developing novel treatments for a variety of central nervous system (CNS) disorders. Traditional drug discovery efforts targeting GPCRs have focused on developing ligands for orthosteric sites which bind endogenous ligands. Allosteric modulators target a site separate from the orthosteric site to modulate receptor function. These allosteric agents can either potentiate (positive allosteric modulator, PAM) or inhibit (negative allosteric modulator, NAM) the receptor response and often provide much greater subtype selectivity than orthosteric ligands for the same receptors. Experimental evidence has revealed more nuanced pharmacological modes of action of allosteric modulators, with some PAMs showing allosteric agonism in combination with positive allosteric modulation in response to endogenous ligand (ago-potentiators) as well as "bitopic" ligands that interact with both the allosteric and orthosteric sites. Drugs targeting the allosteric site allow for increased drug selectivity and potentially decreased adverse side effects. Promising evidence has demonstrated potential utility of a number of allosteric modulators of GPCRs in multiple CNS disorders, including neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, as well as psychiatric or neurobehavioral diseases such as anxiety, schizophrenia, and addiction. © 2013.

  13. Allosteric Binding in the Serotonin Transporter - Pharmacology, Structure, Function and Potential Use as a Novel Drug Target

    DEFF Research Database (Denmark)

    Loland, Claus J.; Sanchez, Connie; Plenge, Per

    2017-01-01

    The serotonin transporter (SERT) is an important drug target and the majority of currently used antidepressants are potent inhibitors of SERT, binding primarily to the substrate binding site. However, even though the existence of an allosteric modulator site was realized more than 30 years ago......, the research into this mechanism is still in its early days. The current knowledge about the allosteric site with respect to pharmacology, structure and function, and pharmacological tool compounds, is reviewed and a perspective is given on its potential as a drug target....

  14. A novel strategy for selection of allosteric ribozymes yields RiboReporter™ sensors for caffeine and aspartame

    Science.gov (United States)

    Ferguson, Alicia; Boomer, Ryan M.; Kurz, Markus; Keene, Sara C.; Diener, John L.; Keefe, Anthony D.; Wilson, Charles; Cload, Sharon T.

    2004-01-01

    We have utilized in vitro selection technology to develop allosteric ribozyme sensors that are specific for the small molecule analytes caffeine or aspartame. Caffeine- or aspartame-responsive ribozymes were converted into fluorescence-based RiboReporter™ sensor systems that were able to detect caffeine or aspartame in solution over a concentration range from 0.5 to 5 mM. With read-times as short as 5 min, these caffeine- or aspartame-dependent ribozymes function as highly specific and facile molecular sensors. Interestingly, successful isolation of allosteric ribozymes for the analytes described here was enabled by a novel selection strategy that incorporated elements of both modular design and activity-based selection methods typically used for generation of catalytic nucleic acids. PMID:15026535

  15. Comparison of crystal and solution hemoglobin binding of selected antigelling agents and allosteric modifiers

    International Nuclear Information System (INIS)

    Mehanna, A.S.; Abraham, D.J.

    1990-01-01

    This paper details comprehensive binding studies (solution and X-ray) of human hemoglobin A with a group of halogenated carboxylic acids that were investigated as potential antisickling agents. It is, to our knowledge, the first study to compare solution and crystal binding for a series of compounds under similar high-salt conditions used for cocrystallization. The compounds include [(3,4-dichlorobenzyl)oxy]acetic acid, [(p-bromobenzyl)oxy]acetic acid, clofibric acid, and bezafibrate. The location and stereochemistry of binding sites have been established by X-ray crystallography, while the number of binding sites and affinity constants were measured by using equilibrium dialysis. The observed crystal structures are consistent with the binding observed in solution and that the number of binding sites is independent of salt concentration, while the binding constant increases with increasing salt concentration. The studies also reveal that relatively small changes in the chemical structure of a drug molecule can result in entirely different binding sites on the protein. Moreover, the X-ray studies provide a possible explanation for the multiplicity in function exhibited by these compounds as allosteric modulators and/or antisickling agents. Finally, the studies indicate that these compounds bind differently to the R and T states of hemoglobin, and observation of special significance to the original design of these agents

  16. Functional Selectivity of Allosteric Interactions within G Protein–Coupled Receptor Oligomers: The Dopamine D1-D3 Receptor Heterotetramer

    Science.gov (United States)

    Guitart, Xavier; Navarro, Gemma; Moreno, Estefania; Yano, Hideaki; Cai, Ning-Sheng; Sánchez-Soto, Marta; Kumar-Barodia, Sandeep; Naidu, Yamini T.; Mallol, Josefa; Cortés, Antoni; Lluís, Carme; Canela, Enric I.; Casadó, Vicent; McCormick, Peter J.

    2014-01-01

    The dopamine D1 receptor–D3 receptor (D1R-D3R) heteromer is being considered as a potential therapeutic target for neuropsychiatric disorders. Previous studies suggested that this heteromer could be involved in the ability of D3R agonists to potentiate locomotor activation induced by D1R agonists. It has also been postulated that its overexpression plays a role in L-dopa–induced dyskinesia and in drug addiction. However, little is known about its biochemical properties. By combining bioluminescence resonance energy transfer, bimolecular complementation techniques, and cell-signaling experiments in transfected cells, evidence was obtained for a tetrameric stoichiometry of the D1R–D3R heteromer, constituted by two interacting D1R and D3R homodimers coupled to Gs and Gi proteins, respectively. Coactivation of both receptors led to the canonical negative interaction at the level of adenylyl cyclase signaling, to a strong recruitment of β-arrestin-1, and to a positive cross talk of D1R and D3R agonists at the level of mitogen-activated protein kinase (MAPK) signaling. Furthermore, D1R or D3R antagonists counteracted β-arrestin-1 recruitment and MAPK activation induced by D3R and D1R agonists, respectively (cross-antagonism). Positive cross talk and cross-antagonism at the MAPK level were counteracted by specific synthetic peptides with amino acid sequences corresponding to D1R transmembrane (TM) domains TM5 and TM6, which also selectively modified the quaternary structure of the D1R-D3R heteromer, as demonstrated by complementation of hemiproteins of yellow fluorescence protein fused to D1R and D3R. These results demonstrate functional selectivity of allosteric modulations within the D1R-D3R heteromer, which can be involved with the reported behavioral synergism of D1R and D3R agonists. PMID:25097189

  17. Allosteric activation of the follicle-stimulating hormone (FSH) receptor by selective, nonpeptide agonists.

    Science.gov (United States)

    Yanofsky, Stephen D; Shen, Emily S; Holden, Frank; Whitehorn, Erik; Aguilar, Barbara; Tate, Emily; Holmes, Christopher P; Scheuerman, Randall; MacLean, Derek; Wu, May M; Frail, Donald E; López, Francisco J; Winneker, Richard; Arey, Brian J; Barrett, Ronald W

    2006-05-12

    The pituitary glycoprotein hormones, luteinizing hormone and follicle-stimulating hormone (FSH), act through their cognate receptors to initiate a series of coordinated physiological events that results in germ cell maturation. Given the importance of FSH in regulating folliculogenesis and fertility, the development of FSH mimetics has been sought to treat infertility. Currently, purified and recombinant human FSH are the only FSH receptor (FSH-R) agonists available for infertility treatment. By screening unbiased combinatorial chemistry libraries, using a cAMP-responsive luciferase reporter assay, we discovered thiazolidinone agonists (EC50's = 20 microm) of the human FSH-R. Subsequent analog library screening and parallel synthesis optimization resulted in the identification of a potent agonist (EC50 = 2 nm) with full efficacy compared with FSH that was FSH-R-selective and -dependent. The compound mediated progesterone production in Y1 cells transfected with the human FSH-R (EC50 = 980 nm) and estradiol production from primary rat ovarian granulosa cells (EC50 = 10.5 nm). This and related compounds did not compete with FSH for binding to the FSH-R. Use of human FSH/thyroid-stimulating hormone (TSH) receptor chimeras suggested a novel mechanism for receptor activation through a binding site independent of the natural hormone binding site. This study is the first report of a high affinity small molecule agonist that activates a glycoprotein hormone receptor through an allosteric mechanism. The small molecule FSH receptor agonists described here could lead to an oral alternative to the current parenteral FSH treatments used clinically to induce ovarian stimulation for both in vivo and in vitro fertilization therapy.

  18. Structural changes at the myrtenol backbone reverse its positive allosteric potential into inhibitory GABAA receptor modulation

    DEFF Research Database (Denmark)

    Milanos, Sinem; Kuenzel, Katharina; Gilbert, Daniel F

    2017-01-01

    monoterpenes, e.g. myrtenol as positive allosteric modulator at α1β2 GABAA receptors. Here, along with pharmacophore-based virtual screening studies, we demonstrate that scaffold modifications of myrtenol resulted in loss of modulatory activity. Two independent approaches, fluorescence-based compound analysis...

  19. Functional selectivity of allosteric interactions within G protein-coupled receptor oligomers: the dopamine D1-D3 receptor heterotetramer.

    Science.gov (United States)

    Guitart, Xavier; Navarro, Gemma; Moreno, Estefania; Yano, Hideaki; Cai, Ning-Sheng; Sánchez-Soto, Marta; Kumar-Barodia, Sandeep; Naidu, Yamini T; Mallol, Josefa; Cortés, Antoni; Lluís, Carme; Canela, Enric I; Casadó, Vicent; McCormick, Peter J; Ferré, Sergi

    2014-10-01

    The dopamine D1 receptor-D3 receptor (D1R-D3R) heteromer is being considered as a potential therapeutic target for neuropsychiatric disorders. Previous studies suggested that this heteromer could be involved in the ability of D3R agonists to potentiate locomotor activation induced by D1R agonists. It has also been postulated that its overexpression plays a role in L-dopa-induced dyskinesia and in drug addiction. However, little is known about its biochemical properties. By combining bioluminescence resonance energy transfer, bimolecular complementation techniques, and cell-signaling experiments in transfected cells, evidence was obtained for a tetrameric stoichiometry of the D1R-D3R heteromer, constituted by two interacting D1R and D3R homodimers coupled to Gs and Gi proteins, respectively. Coactivation of both receptors led to the canonical negative interaction at the level of adenylyl cyclase signaling, to a strong recruitment of β-arrestin-1, and to a positive cross talk of D1R and D3R agonists at the level of mitogen-activated protein kinase (MAPK) signaling. Furthermore, D1R or D3R antagonists counteracted β-arrestin-1 recruitment and MAPK activation induced by D3R and D1R agonists, respectively (cross-antagonism). Positive cross talk and cross-antagonism at the MAPK level were counteracted by specific synthetic peptides with amino acid sequences corresponding to D1R transmembrane (TM) domains TM5 and TM6, which also selectively modified the quaternary structure of the D1R-D3R heteromer, as demonstrated by complementation of hemiproteins of yellow fluorescence protein fused to D1R and D3R. These results demonstrate functional selectivity of allosteric modulations within the D1R-D3R heteromer, which can be involved with the reported behavioral synergism of D1R and D3R agonists. U.S. Government work not protected by U.S. copyright.

  20. A Comparison of the 2/3/5 Selective Positive Allosteric Modulators L-838,417 and TPA023 in Preclinical Models of Inflammatory and Neuropathic Pain

    Directory of Open Access Journals (Sweden)

    Sarah Nickolls

    2011-01-01

    Full Text Available GABAA receptors containing α2/3 subunits are current targets in the battle to develop new pain medications, as they are expressed in the spinal cord where increasing inhibitory drive should result in analgesia. However, this approach is prone to a range of side effects including sedation, cognitive impairment, and abuse as a consequence of the widespread influence of GABA. The ability to make subtype selective low-efficacy benzodiazepine compounds, which potentiate the action of GABA at specific α subunits, has the potential to reduce this side effect profile. In this study, we have investigated the effects of the medium-efficacy positive allosteric modulator (PAM L-838,417 and the low-efficacy PAM TPA023 in a number of preclinical inflammatory and neuropathic pain models. We conclude that either the higher level of efficacy at α2/3 or efficacy at α5 is required for compounds to have a significant analgesic effect in a range of models, and, therefore, although the side-effect profile of compounds can be reduced compared to typical benzodiazepines, it is unlikely that it can be completely eliminated.

  1. The selective positive allosteric M1 muscarinic receptor modulator PQCA attenuates learning and memory deficits in the Tg2576 Alzheimer's disease mouse model.

    Science.gov (United States)

    Puri, Vanita; Wang, Xiaohai; Vardigan, Joshua D; Kuduk, Scott D; Uslaner, Jason M

    2015-01-01

    We have recently shown that the M1 muscarinic receptor positive allosteric modulator, PQCA, improves cognitive performance in rodents and non-human primates administered the muscarinic receptor antagonist scopolamine. The purpose of the present experiments was to characterize the effects of PQCA in a model more relevant to the disease pathology of Alzheimer's disease. Tg2576 transgenic mice that have elevated Aβ were tested in the novel object recognition task to characterize recognition memory as a function of age and treatment with the PQCA. The effects of PQCA were compared to the acetylcholinesterase inhibitor donepezil, the standard of care for Alzheimer's disease. In addition, the effect of co-administering PQCA and donepezil was evaluated. Aged Tg2576 mice demonstrated a deficit in recognition memory that was significantly attenuated by PQCA. The positive control donepezil also reversed the deficit. Furthermore, doses of PQCA and donepezil that were inactive on their own were found to improve recognition memory when given together. These studies suggest that M1 muscarinic receptor positive allosteric modulation can ameliorate memory deficits in disease relevant models of Alzheimer's disease. These data, combined with our previous findings demonstrating PQCA improves scopolamine-induced cognitive deficits in both rodents and non-human primates, suggest that M1 positive allosteric modulators have therapeutic potential for the treatment of Alzheimer's disease. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Identification of potential small molecule allosteric modulator sites on IL-1R1 ectodomain using accelerated conformational sampling method.

    Directory of Open Access Journals (Sweden)

    Chao-Yie Yang

    Full Text Available The interleukin-1 receptor (IL-1R is the founding member of the interleukin 1 receptor family which activates innate immune response by its binding to cytokines. Reports showed dysregulation of cytokine production leads to aberrant immune cells activation which contributes to auto-inflammatory disorders and diseases. Current therapeutic strategies focus on utilizing antibodies or chimeric cytokine biologics. The large protein-protein interaction interface between cytokine receptor and cytokine poses a challenge in identifying binding sites for small molecule inhibitor development. Based on the significant conformational change of IL-1R type 1 (IL-1R1 ectodomain upon binding to different ligands observed in crystal structures, we hypothesized that transient small molecule binding sites may exist when IL-1R1 undergoes conformational transition and thus suitable for inhibitor development. Here, we employed accelerated molecular dynamics (MD simulation to efficiently sample conformational space of IL-1R1 ectodomain. Representative IL-1R1 ectodomain conformations determined from the hierarchy cluster analysis were analyzed by the SiteMap program which leads to identify small molecule binding sites at the protein-protein interaction interface and allosteric modulator locations. The cosolvent mapping analysis using phenol as the probe molecule further confirms the allosteric modulator site as a binding hotspot. Eight highest ranked fragment molecules identified from in silico screening at the modulator site were evaluated by MD simulations. Four of them restricted the IL-1R1 dynamical motion to inactive conformational space. The strategy from this study, subject to in vitro experimental validation, can be useful to identify small molecule compounds targeting the allosteric modulator sites of IL-1R and prevent IL-1R from binding to cytokine by trapping IL-1R in inactive conformations.

  3. The future of type 1 cannabinoid receptor allosteric ligands.

    Science.gov (United States)

    Alaverdashvili, Mariam; Laprairie, Robert B

    2018-02-01

    Allosteric modulation of the type 1 cannabinoid receptor (CB1R) holds great therapeutic potential. This is because allosteric modulators do not possess intrinsic efficacy, but instead augment (positive allosteric modulation) or diminish (negative allosteric modulation) the receptor's response to endogenous ligand. Consequently, CB1R allosteric modulators have an effect ceiling which allows for the tempering of CB1R signaling without the desensitization, tolerance, dependence, and psychoactivity associated with orthosteric compounds. Pain, movement disorders, epilepsy, obesity are all potential therapeutic targets for CB1R allosteric modulation. Several challenges exist for the development of CB1R allosteric modulators, such as receptor subtype specificity, translation to in vivo systems, and mixed allosteric/agonist/inverse agonist activity. Despite these challenges, elucidation of crystal structures of CB1R and compound design based on structure-activity relationships will advance the field. In this review, we will cover recent progress for CB1R allosteric modulators and discuss the future promise of this research.

  4. Exploiting protein flexibility to predict the location of allosteric sites

    Directory of Open Access Journals (Sweden)

    Panjkovich Alejandro

    2012-10-01

    Full Text Available Abstract Background Allostery is one of the most powerful and common ways of regulation of protein activity. However, for most allosteric proteins identified to date the mechanistic details of allosteric modulation are not yet well understood. Uncovering common mechanistic patterns underlying allostery would allow not only a better academic understanding of the phenomena, but it would also streamline the design of novel therapeutic solutions. This relatively unexplored therapeutic potential and the putative advantages of allosteric drugs over classical active-site inhibitors fuel the attention allosteric-drug research is receiving at present. A first step to harness the regulatory potential and versatility of allosteric sites, in the context of drug-discovery and design, would be to detect or predict their presence and location. In this article, we describe a simple computational approach, based on the effect allosteric ligands exert on protein flexibility upon binding, to predict the existence and position of allosteric sites on a given protein structure. Results By querying the literature and a recently available database of allosteric sites, we gathered 213 allosteric proteins with structural information that we further filtered into a non-redundant set of 91 proteins. We performed normal-mode analysis and observed significant changes in protein flexibility upon allosteric-ligand binding in 70% of the cases. These results agree with the current view that allosteric mechanisms are in many cases governed by changes in protein dynamics caused by ligand binding. Furthermore, we implemented an approach that achieves 65% positive predictive value in identifying allosteric sites within the set of predicted cavities of a protein (stricter parameters set, 0.22 sensitivity, by combining the current analysis on dynamics with previous results on structural conservation of allosteric sites. We also analyzed four biological examples in detail, revealing

  5. Allosteric small-molecule kinase inhibitors

    DEFF Research Database (Denmark)

    Wu, Peng; Clausen, Mads Hartvig; Nielsen, Thomas E.

    2015-01-01

    current barriers of kinase inhibitors, including poor selectivity and emergence of drug resistance. In spite of the small number of identified allosteric inhibitors in comparison with that of inhibitors targeting the ATP pocket, encouraging results, such as the FDA-approval of the first small...

  6. Selective and interactive effects of D2 receptor antagonism and positive allosteric mGluR4 modulation on waiting impulsivity.

    Science.gov (United States)

    Isherwood, Sarah N; Robbins, Trevor W; Nicholson, Janet R; Dalley, Jeffrey W; Pekcec, Anton

    2017-09-01

    Metabotropic glutamate receptor 4 (mGluR4) and dopamine D 2 receptors are specifically expressed within the indirect pathway neurons of the striato-pallidal-subthalamic pathway. This unique expression profile suggests that mGluR4 and D 2 receptors may play a cooperative role in the regulation and inhibitory control of behaviour. We investigated this possibility by testing the effects of a functionally-characterised positive allosteric mGluR4 modulator, 4-((E)-styryl)-pyrimidin-2-ylamine (Cpd11), both alone and in combination with the D 2 receptor antagonist eticlopride, on two distinct forms of impulsivity. Rats were trained on the five-choice serial reaction time task (5-CSRTT) of sustained visual attention and segregated according to low, mid, and high levels of motor impulsivity (LI, MI and HI, respectively), with unscreened rats used as an additional control group. A separate group of rats was trained on a delay discounting task (DDT) to assess choice impulsivity. Systemic administration of Cpd11 dose-dependently increased motor impulsivity and impaired attentional accuracy on the 5-CSRTT in all groups tested. Eticlopride selectively attenuated the increase in impulsivity induced by Cpd11, but not the accompanying attentional impairment, at doses that had no significant effect on behavioural performance when administered alone. Cpd11 also decreased choice impulsivity on the DDT (i.e. increased preference for the large, delayed reward) and decreased locomotor activity. These findings demonstrate that mGluR4s, in conjunction with D 2 receptors, affect motor- and choice-based measures of impulsivity, and therefore may be novel targets to modulate impulsive behaviour associated with a number of neuropsychiatric syndromes. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  7. Allosteric regulation of epigenetic modifying enzymes.

    Science.gov (United States)

    Zucconi, Beth E; Cole, Philip A

    2017-08-01

    Epigenetic enzymes including histone modifying enzymes are key regulators of gene expression in normal and disease processes. Many drug development strategies to target histone modifying enzymes have focused on ligands that bind to enzyme active sites, but allosteric pockets offer potentially attractive opportunities for therapeutic development. Recent biochemical studies have revealed roles for small molecule and peptide ligands binding outside of the active sites in modulating the catalytic activities of histone modifying enzymes. Here we highlight several examples of allosteric regulation of epigenetic enzymes and discuss the biological significance of these findings. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Discovery of a highly selective chemical inhibitor of matrix metalloproteinase-9 (MMP-9) that allosterically inhibits zymogen activation.

    Science.gov (United States)

    Scannevin, Robert H; Alexander, Richard; Haarlander, Tara Mezzasalma; Burke, Sharon L; Singer, Monica; Huo, Cuifen; Zhang, Yue-Mei; Maguire, Diane; Spurlino, John; Deckman, Ingrid; Carroll, Karen I; Lewandowski, Frank; Devine, Eric; Dzordzorme, Keli; Tounge, Brett; Milligan, Cindy; Bayoumy, Shariff; Williams, Robyn; Schalk-Hihi, Celine; Leonard, Kristi; Jackson, Paul; Todd, Matthew; Kuo, Lawrence C; Rhodes, Kenneth J

    2017-10-27

    Aberrant activation of matrix metalloproteinases (MMPs) is a common feature of pathological cascades observed in diverse disorders, such as cancer, fibrosis, immune dysregulation, and neurodegenerative diseases. MMP-9, in particular, is highly dynamically regulated in several pathological processes. Development of MMP inhibitors has therefore been an attractive strategy for therapeutic intervention. However, a long history of failed clinical trials has demonstrated that broad-spectrum MMP inhibitors have limited clinical utility, which has spurred the development of inhibitors selective for individual MMPs. Attaining selectivity has been technically challenging because of sequence and structural conservation across the various MMPs. Here, through a biochemical and structural screening paradigm, we have identified JNJ0966, a highly selective compound that inhibited activation of MMP-9 zymogen and subsequent generation of catalytically active enzyme. JNJ0966 had no effect on MMP-1, MMP-2, MMP-3, MMP-9, or MMP-14 catalytic activity and did not inhibit activation of the highly related MMP-2 zymogen. The molecular basis for this activity was characterized as an interaction of JNJ0966 with a structural pocket in proximity to the MMP-9 zymogen cleavage site near Arg-106, which is distinct from the catalytic domain. JNJ0966 was efficacious in reducing disease severity in a mouse experimental autoimmune encephalomyelitis model, demonstrating the viability of this therapeutic approach. This discovery reveals an unprecedented pharmacological approach to MMP inhibition, providing an opportunity to improve selectivity of future clinical drug candidates. Targeting zymogen activation in this manner may also allow for pharmaceutical exploration of other enzymes previously viewed as intractable drug targets. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Selective Allosteric Antagonists for the G Protein-Coupled Receptor GPRC6A Based on the 2-Phenylindole Privileged Structure Scaffold

    DEFF Research Database (Denmark)

    Johansson, Henrik; Boesgaard, Michael Worch; Nørskov-Lauritsen, Lenea

    2015-01-01

    G protein-coupled receptors (GPCRs) represent a biological target class of fundamental importance in drug therapy. The GPRC6A receptor is a newly deorphanized class C GPCR that we recently reported for the first allosteric antagonists based on the 2-arylindole privileged structure scaffold (e.g., 1...

  10. Allosteric Regulation of Proteins

    Indian Academy of Sciences (India)

    ... Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Resonance – Journal of Science Education; Volume 22; Issue 1. Allosteric Regulation of Proteins: A Historical Perspective on the Development of Concepts and Techniques. General Article Volume 22 Issue 1 January 2017 pp 37-50 ...

  11. Nootropic α7 nicotinic receptor allosteric modulator derived from GABAA receptor modulators

    Science.gov (United States)

    Ng, Herman J.; Whittemore, Edward R.; Tran, Minhtam B.; Hogenkamp, Derk J.; Broide, Ron S.; Johnstone, Timothy B.; Zheng, Lijun; Stevens, Karen E.; Gee, Kelvin W.

    2007-01-01

    Activation of brain α7 nicotinic acetylcholine receptors (α7 nAChRs) has broad therapeutic potential in CNS diseases related to cognitive dysfunction, including Alzheimer's disease and schizophrenia. In contrast to direct agonist activation, positive allosteric modulation of α7 nAChRs would deliver the clinically validated benefits of allosterism to these indications. We have generated a selective α7 nAChR-positive allosteric modulator (PAM) from a library of GABAA receptor PAMs. Compound 6 (N-(4-chlorophenyl)-α-[[(4-chloro-phenyl)amino]methylene]-3-methyl-5-isoxazoleacet-amide) evokes robust positive modulation of agonist-induced currents at α7 nAChRs, while preserving the rapid native characteristics of desensitization, and has little to no efficacy at other ligand-gated ion channels. In rodent models, it corrects sensory-gating deficits and improves working memory, effects consistent with cognitive enhancement. Compound 6 represents a chemotype for allosteric activation of α7 nAChRs, with therapeutic potential in CNS diseases with cognitive dysfunction. PMID:17470817

  12. Positive allosteric modulators of the α7 nicotinic acetylcholine receptor potentiate glutamate release in the prefrontal cortex of freely-moving rats

    DEFF Research Database (Denmark)

    Bortz, D M; Upton, B A; Mikkelsen, J D

    2016-01-01

    Positive allosteric modulators (PAMs) of α7 nicotinic acetylcholine receptors (α7nAChRs) exhibit pro-cognitive effects in animal models of schizophrenia and are targets for the discovery of cognition-enhancing drugs. However, little is known about their in vivo mechanism of action because...

  13. The different ways through which specificity works in orthosteric and allosteric drugs.

    Science.gov (United States)

    Nussinov, Ruth; Tsai, Chung-Jung

    2012-01-01

    Currently, there are two types of drugs on the market: orthosteric, which bind at the active site; and allosteric, which bind elsewhere on the protein surface, and allosterically change the conformation of the protein binding site. In this perspective we argue that the different mechanisms through which the two drug types affect protein activity and their potential pitfalls call for different considerations in drug design. The key problem facing orthosteric drugs is side effects which can occur by drug binding to homologous proteins sharing a similar binding site. Hence, orthosteric drugs should have very high affinity to the target; this would allow a low dosage to selectively achieve the goal of target-only binding. By contrast, allosteric drugs work by shifting the free energy landscape. Their binding to the protein surface perturbs the protein surface atoms, and the perturbation propagates like waves, finally reaching the binding site. Effective drugs should have atoms in good contact with the 'right' protein atoms; that is, the contacts should elicit propagation waves optimally reaching the protein binding site target. While affinity is important, the design should consider the protein conformational ensemble and the preferred propagation states. We provide examples from functional in vivo scenarios for both types of cases, and suggest how high potency can be achieved in allosteric drug development.

  14. 2013 Philip S. Portoghese Medicinal Chemistry Lectureship: Drug Discovery Targeting Allosteric Sites†

    Science.gov (United States)

    2015-01-01

    The identification of sites on receptors topographically distinct from the orthosteric sites, so-called allosteric sites, has heralded novel approaches and modes of pharmacology for target modulation. Over the past 20 years, our understanding of allosteric modulation has grown significantly, and numerous advantages, as well as caveats (e.g., flat structure–activity relationships, species differences, “molecular switches”), have been identified. For multiple receptors and proteins, numerous examples have been described where unprecedented levels of selectivity are achieved along with improved physiochemical properties. While not a panacea, these novel approaches represent exciting opportunities for tool compound development to probe the pharmacology and therapeutic potential of discrete molecular targets, as well as new medicines. In this Perspective, in commemoration of the 2013 Philip S. Portoghese Medicinal Chemistry Lectureship (LindsleyC. W.Adventures in allosteric drug discovery. Presented at the 246th National Meeting of the American Chemical Society, Indianapolis, IN, September 10, 2013; The 2013 Portoghese Lectureship), several vignettes of drug discovery campaigns targeting novel allosteric mechanisms will be recounted, along with lessons learned and guidelines that have emerged for successful lead optimization. PMID:25180768

  15. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.

    Science.gov (United States)

    Wagner, Jeffrey R; Lee, Christopher T; Durrant, Jacob D; Malmstrom, Robert D; Feher, Victoria A; Amaro, Rommie E

    2016-06-08

    Allosteric drug development holds promise for delivering medicines that are more selective and less toxic than those that target orthosteric sites. To date, the discovery of allosteric binding sites and lead compounds has been mostly serendipitous, achieved through high-throughput screening. Over the past decade, structural data has become more readily available for larger protein systems and more membrane protein classes (e.g., GPCRs and ion channels), which are common allosteric drug targets. In parallel, improved simulation methods now provide better atomistic understanding of the protein dynamics and cooperative motions that are critical to allosteric mechanisms. As a result of these advances, the field of predictive allosteric drug development is now on the cusp of a new era of rational structure-based computational methods. Here, we review algorithms that predict allosteric sites based on sequence data and molecular dynamics simulations, describe tools that assess the druggability of these pockets, and discuss how Markov state models and topology analyses provide insight into the relationship between protein dynamics and allosteric drug binding. In each section, we first provide an overview of the various method classes before describing relevant algorithms and software packages.

  16. The allosteric site regulates the voltage sensitivity of muscarinic receptors.

    Science.gov (United States)

    Hoppe, Anika; Marti-Solano, Maria; Drabek, Matthäus; Bünemann, Moritz; Kolb, Peter; Rinne, Andreas

    2018-01-01

    Muscarinic receptors (M-Rs) for acetylcholine (ACh) belong to the class A of G protein-coupled receptors. M-Rs are activated by orthosteric agonists that bind to a specific site buried in the M-R transmembrane helix bundle. In the active conformation, receptor function can be modulated either by allosteric modulators, which bind to the extracellular receptor surface or by the membrane potential via an unknown mechanism. Here, we compared the modulation of M 1 -Rs and M 3 -Rs induced by changes in voltage to their allosteric modulation by chemical compounds. We quantified changes in receptor signaling in single HEK 293 cells with a FRET biosensor for the G q protein cycle. In the presence of ACh, M 1 -R signaling was potentiated by voltage, similarly to positive allosteric modulation by benzyl quinolone carboxylic acid. Conversely, signaling of M 3 -R was attenuated by voltage or the negative allosteric modulator gallamine. Because the orthosteric site is highly conserved among M-Rs, but allosteric sites vary, we constructed "allosteric site" M 3 /M 1 -R chimeras and analyzed their voltage dependencies. Exchanging the entire allosteric sites eliminated the voltage sensitivity of ACh responses for both receptors, but did not affect their modulation by allosteric compounds. Furthermore, a point mutation in M 3 -Rs caused functional uncoupling of the allosteric and orthosteric sites and abolished voltage dependence. Molecular dynamics simulations of the receptor variants indicated a subtype-specific crosstalk between both sites, involving the conserved tyrosine lid structure of the orthosteric site. This molecular crosstalk leads to receptor subtype-specific voltage effects. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Bitropic D3 Dopamine Receptor Selective Compounds as Potential Antipsychotics.

    Science.gov (United States)

    Luedtke, Robert R; Rangel-Barajas, Claudia; Malik, Mahinder; Reichert, David E; Mach, R H

    2015-01-01

    Neuropsychiatric disorders represent a substantial social and health care issue. The National Institutes of Health estimates that greater than 2 million adults suffer from neuropsychiatric disorders in the USA. These individuals experience symptoms that can include auditory hallucinations, delusions, unrealistic beliefs and cognitive dysfunction. Although antipsychotic medications are available, suboptimal therapeutic responses are observed for approximately one-third of patients. Therefore, there is still a need to explore new pharmacotherapeutic strategies for the treatment of neuropsychiatric disorders. Many of the medications that are used clinically to treat neuropsychiatric disorders have a pharmacological profile that includes being an antagonist at D2-like (D2, D3 and D4) dopamine receptor subtypes. However, dopamine receptor subtypes are involved in a variety of neuronal circuits that include movement coordination, cognition, emotion, affect, memory and the regulation of prolactin. Consequently, antagonism at D2-like receptors can also contribute to some of the adverse side effects associated with the long-term use of antipsychotics including the a) adverse extrapyramidal symptoms associated with the use of typical antipsychotics and b) metabolic side effects (weight gain, hyperglycemia, increased risk of diabetes mellitus, dyslipidemia and gynecomastia) associated with atypical antipsychotic use. Preclinical studies suggest that D3 versus D2 dopamine receptor selective compounds might represent an alternative strategy for the treatment of the symptoms of schizophrenia. In this review we discuss a) how bitropic Nphenylpiperazine D3 dopamine receptor selective compounds have been developed by modification of the primary (orthosteric) and secondary (allosteric or modulatory) pharmacophores to optimize D3 receptor affinity and D2/D3 binding selectivity ratios and b) the functional selectivity of these compounds. Examples of how these compounds might be

  18. Molecular sites for the positive allosteric modulation of glycine receptors by endocannabinoids.

    Directory of Open Access Journals (Sweden)

    Gonzalo E Yévenes

    Full Text Available Glycine receptors (GlyRs are transmitter-gated anion channels of the Cys-loop superfamily which mediate synaptic inhibition at spinal and selected supraspinal sites. Although they serve pivotal functions in motor control and sensory processing, they have yet to be exploited as drug targets partly because of hitherto limited possibilities for allosteric control. Endocannabinoids (ECs have recently been characterized as direct allosteric GlyR modulators, but the underlying molecular sites have remained unknown. Here, we show that chemically neutral ECs (e.g. anandamide, AEA are positive modulators of α(1, α(2 and α(3 GlyRs, whereas acidic ECs (e.g. N-arachidonoyl-glycine; NA-Gly potentiate α(1 GlyRs but inhibit α(2 and α(3. This subunit-specificity allowed us to identify the underlying molecular sites through analysis of chimeric and mutant receptors. We found that alanine 52 in extracellular loop 2, glycine 254 in transmembrane (TM region 2 and intracellular lysine 385 determine the positive modulation of α(1 GlyRs by NA-Gly. Successive substitution of non-conserved extracellular and TM residues in α(2 converted NA-Gly-mediated inhibition into potentiation. Conversely, mutation of the conserved lysine within the intracellular loop between TM3 and TM4 attenuated NA-Gly-mediated potentiation of α(1 GlyRs, without affecting inhibition of α(2 and α(3. Notably, this mutation reduced modulation by AEA of all three GlyRs. These results define molecular sites for allosteric control of GlyRs by ECs and reveal an unrecognized function for the TM3-4 intracellular loop in the allosteric modulation of Cys-loop ion channels. The identification of these sites may help to understand the physiological role of this modulation and facilitate the development of novel therapeutic approaches to diseases such as spasticity, startle disease and possibly chronic pain.

  19. Pharmacological characterization and modeling of the binding sites of novel 1,3-bis(pyridinylethynyl)benzenes as metabotropic glutamate receptor 5-selective negative allosteric modulators

    DEFF Research Database (Denmark)

    Mølck, Christina; Harpsøe, Kasper; Gloriam, David E

    2012-01-01

    )pyridine (MPEP)-derived negative allosteric modulators, 2-, 3-, and 4-BisPEB, have been characterized. 2-, 3-, and 4-BisPEB are 1,3-bis(pyridinylethynyl)-benzenes and differ only by the position of the nitrogen atoms in the pyridine rings. Despite their high structural similarity, 2-BisPEB [1,3-bis(pyridin-2......-ylethynyl)-benzene, nitrogen atoms in ortho positions], with an IC(50) value in the nanomolar range, is significantly more potent than the 3- and 4-pyridyl analogs. Mutational analysis, directed by a previously published mGluR5 homology model, was used to determine key residues for the ligand...... that the higher potency of 2-BisPEB is due to hydrogen bonding to Ser809 because the S809A mutation made 2-BisPEB equipotent to 3- and 4-BisPEB (IC(50), 1-2.5 µM). The potency of MPEP was also greatly affected by S809A (52-fold), suggesting that a Ser809-mediated hydrogen bond is also a key interaction between...

  20. Can a Positive Allosteric Modulation of GABAergic Receptors Improve Motor Symptoms in Patients with Parkinson's Disease? The Potential Role of Zolpidem in the Treatment of Parkinson's Disease

    Science.gov (United States)

    Daniele, Antonio; Panza, Francesco; Greco, Antonio; Logroscino, Giancarlo; Seripa, Davide

    2016-01-01

    At present, patients with advanced Parkinson's disease (PD) are unsatisfactorily controlled by currently used anti-Parkinsonian dopaminergic drugs. Various studies suggest that therapeutic strategies based on nondopaminergic drugs might be helpful in PD. Zolpidem, an imidazopyridine widely used as sleep inducer, shows high affinity only for GABAA receptors containing the α-1 subunit and facilitates GABAergic neurotransmission through a positive allosteric modulation of GABAA receptors. Various observations, although preliminary, consistently suggest that in PD patients zolpidem may induce beneficial (and sometimes remarkable) effects on motor symptoms even after single doses and may also improve dyskinesias. Since a high density of zolpidem binding sites is in the two main output structures of the basal ganglia which are abnormally overactive in PD (internal globus pallidus, GPi, and substantia nigra pars reticulata, SNr), it was hypothesized that in PD patients zolpidem may induce through GABAA receptors an inhibition of GPi and SNr (and, possibly, of the subthalamic nucleus also), resulting in an increased activity of motor cortical areas (such as supplementary motor area), which may give rise to improvement of motor symptoms of PD. Randomized clinical trials are needed in order to assess the efficacy, safety, and tolerability of zolpidem in treating motor symptoms of PD. PMID:27293955

  1. Crystal structure of the adenosine A 2A receptor bound to an antagonist reveals a potential allosteric pocket

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Bingfa; Bachhawat, Priti; Chu, Matthew Ling-Hon; Wood, Martyn; Ceska, Tom; Sands, Zara A.; Mercier, Joel; Lebon, Florence; Kobilka, Tong Sun; Kobilka, Brian K. (Stanford-MED); (ConfometRx); (UCB Pharma)

    2017-02-06

    The adenosine A2A receptor (A2AR) has long been implicated in cardiovascular disorders. As more selective A2AR ligands are being identified, its roles in other disorders, such as Parkinson’s disease, are starting to emerge, and A2AR antagonists are important drug candidates for nondopaminergic anti-Parkinson treatment. Here we report the crystal structure of A2A receptor bound to compound 1 (Cmpd-1), a novel A2AR/N-methyl D-aspartate receptor subtype 2B (NR2B) dual antagonist and potential anti-Parkinson candidate compound, at 3.5 Å resolution. The A2A receptor with a cytochrome b562-RIL (BRIL) fusion (A2AR–BRIL) in the intracellular loop 3 (ICL3) was crystallized in detergent micelles using vapor-phase diffusion. Whereas A2AR–BRIL bound to the antagonist ZM241385 has previously been crystallized in lipidic cubic phase (LCP), structural differences in the Cmpd-1–bound A2AR–BRIL prevented formation of the lattice observed with the ZM241385–bound receptor. The crystals grew with a type II crystal lattice in contrast to the typical type I packing seen from membrane protein structures crystallized in LCP. Cmpd-1 binds in a position that overlaps with the native ligand adenosine, but its methoxyphenyl group extends to an exosite not previously observed in other A2AR structures. Structural analysis revealed that Cmpd-1 binding results in the unique conformations of two tyrosine residues, Tyr91.35 and Tyr2717.36, which are critical for the formation of the exosite. The structure reveals insights into antagonist binding that are not observed in other A2AR structures, highlighting flexibility in the binding pocket that may facilitate the development of A2AR-selective compounds for the treatment of Parkinson’s disease.

  2. Steric hindrance mutagenesis in the conserved extracellular vestibule impedes allosteric binding of antidepressants to the serotonin transporter

    DEFF Research Database (Denmark)

    Plenge, Per; Shi, Lei; Beuming, Thijs

    2012-01-01

    be involved in the allosteric binding in the extracellular vestibule located above the central substrate binding (S1) site. Indeed, mutagenesis of selected residues in the vestibule reduces the allosteric potency of (S)-citalopram and clomipramine. The identified site is further supported by the inhibitory...

  3. Antioxidant potential of selected Spirulina platensis preparations.

    Science.gov (United States)

    Dartsch, Peter C

    2008-05-01

    Recent studies suggest that Spirulina, a unicellular blue-green alga, may have a variety of health benefits and therapeutic properties and is also capable of acting as an antioxidant and antiinflammatory agent. In this study, a cell-free and a cell-based test assay were used to examine the antioxidant and antiinflammatory properties of four selected Spirulina platensis preparations: (1) Biospirulina, (2) SpiruComplex, a preparation with naturally bound selenium, chromium and zinc, (3) SpiruZink, a preparation with naturally bound zinc, (4) Zinkspirulina + Acerola, a preparation with naturally bound zinc and acerola powder. The cell-free test assay used potassium superoxide as a donor for superoxide radicals, whereas the cell-based test assay used the formation of intracellular superoxide radicals of functional neutrophils upon stimulation by phorbol-12-myristate-13-acetate as a model to investigate the potential of Spirulina preparations to inactivate superoxide radicals. In accordance with the recommended daily dosage, test concentrations ranging from 50 to 1000 microg/mL were chosen. The results showed a dose-dependent inactivation of free superoxide radicals (antioxidant effect) as well as an antiinflammatory effect characterized by a dose-dependent reduction of the metabolic activity of functional neutrophils and a dose-dependent inactivation of superoxide radicals generated during an oxidative burst. The results demonstrate that the tested Spirulina preparations have a high antioxidant and antiinflammatory potential. Especially SpiruZink and Zinkspirulina + Acerola might be useful as a supportive therapeutic approach for reducing oxidative stress and/or the generation of oxygen radicals in the course of inflammatory processes.

  4. Use of allosteric targets in the discovery of safer drugs.

    Science.gov (United States)

    Grover, Ashok Kumar

    2013-01-01

    The need for drugs with fewer side effects cannot be overemphasized. Today, most drugs modify the actions of enzymes, receptors, transporters and other molecules by directly binding to their active (orthosteric) sites. However, orthosteric site configuration is similar in several proteins performing related functions and this leads to a lower specificity of a drug for the desired protein. Consequently, such drugs may have adverse side effects. A new basis of drug discovery is emerging based on the binding of the drug molecules to sites away (allosteric) from the orthosteric sites. It is possible to find allosteric sites which are unique and hence more specific as targets for drug discovery. Of many available examples, two are highlighted here. The first is caloxins - a new class of highly specific inhibitors of plasma membrane Ca²⁺ pumps. The second concerns the modulation of receptors for the neurotransmitter acetylcholine, which binds to 12 types of receptors. Exploitation of allosteric sites has led to the discovery of drugs which can selectively modulate the activation of only 1 (M1 muscarinic) out of the 12 different types of acetylcholine receptors. These drugs are being tested for schizophrenia treatment. It is anticipated that the drug discovery exploiting allosteric sites will lead to more effective therapeutic agents with fewer side effects. Copyright © 2013 S. Karger AG, Basel.

  5. In Vivo Investigation of Escitalopram’s Allosteric Site on the Serotonin Transporter

    Science.gov (United States)

    Murray, Karen E.; Ressler, Kerry J.; Owens, Michael J.

    2015-01-01

    Escitalopram is a commonly prescribed antidepressant of the selective serotonin reuptake inhibitor class. Clinical evidence and mapping of the serotonin transporter (SERT) identified that escitalopram, in addition to its binding to a primary uptake-blocking site, is capable of binding to the SERT via an allosteric site that is hypothesized to alter escitalopram’s kinetics at the SERT. The studies reported here examined the in vivo role of the SERT allosteric site in escitalopram action. A knockin mouse model that possesses an allosteric-null SERT was developed. Autoradiographic studies indicated that the knockin protein was expressed at a lower density than endogenous mouse SERT (approximately 10–30% of endogenous mouse SERT), but the knockin mice are a viable tool to study the allosteric site. Microdialysis studies in the ventral hippocampus found no measurable decrease in extracellular serotonin response after local escitalopram challenge in mice without the allosteric site compared to mice with the site (p = 0.297). In marble burying assays there was a modest effect of the absence of the allosteric site, with a larger systemic dose of escitalopram (10-fold) necessary for the same effect as in mice with intact SERT (p = 0.023). However, there was no effect of the allosteric site in the tail suspension test. Together these data suggest that there may be a regional specificity in the role of the allosteric site. The lack of a robust effect overall suggests that the role of the allosteric site for escitalopram on the SERT may not produce meaningful in vivo effects. PMID:26621784

  6. Probe-Dependent Negative Allosteric Modulators of the Long-Chain Free Fatty Acid Receptor FFA4

    DEFF Research Database (Denmark)

    Watterson, Kenneth R; Hansen, Steffen V F; Hudson, Brian D

    2017-01-01

    High-affinity and selective antagonists that are able to block the actions of both endogenous and synthetic agonists of G protein-coupled receptors are integral to analysis of receptor function and to support suggestions of therapeutic potential. Although there is great interest in the potential...... of endogenous and synthetic agonists, clear agonist probe dependence in the nature of allosteric modulation was apparent. Although AH-7614 did not antagonize the second long-chain free fatty acid receptor, free fatty acid receptor 1, the simple chemical structure of AH-7614 containing features found in many...

  7. Human Secreted Ly-6/uPAR Related Protein-1 (SLURP-1) Is a Selective Allosteric Antagonist of α7 Nicotinic Acetylcholine Receptor

    DEFF Research Database (Denmark)

    Lyukmanova, Ekaterina N; Shulepko, Mikhail A; Kudryavtsev, Denis

    2016-01-01

    of nicotinic acetylcholine receptors (nAChRs) and muscarinic acetylcholine receptors, respectively, and anti-α7-nAChRs antibodies revealed α7 type nAChRs as an rSLURP-1 target in keratinocytes. Using affinity purification from human cortical extracts, we confirmed that rSLURP-1 binds selectively to the α7-n...

  8. Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery

    Directory of Open Access Journals (Sweden)

    Daura Xavier

    2010-03-01

    Full Text Available Abstract Background With the classical, active-site oriented drug-development approach reaching its limits, protein ligand-binding sites in general and allosteric sites in particular are increasingly attracting the interest of medicinal chemists in the search for new types of targets and strategies to drug development. Given that allostery represents one of the most common and powerful means to regulate protein function, the traditional drug discovery approach of targeting active sites can be extended by targeting allosteric or regulatory protein pockets that may allow the discovery of not only novel drug-like inhibitors, but activators as well. The wealth of available protein structural data can be exploited to further increase our understanding of allosterism, which in turn may have therapeutic applications. A first step in this direction is to identify and characterize putative effector sites that may be present in already available structural data. Results We performed a large-scale study of protein cavities as potential allosteric and functional sites, by integrating publicly available information on protein sequences, structures and active sites for more than a thousand protein families. By identifying common pockets across different structures of the same protein family we developed a method to measure the pocket's structural conservation. The method was first parameterized using known active sites. We characterized the predicted pockets in terms of sequence and structural conservation, backbone flexibility and electrostatic potential. Although these different measures do not tend to correlate, their combination is useful in selecting functional and regulatory sites, as a detailed analysis of a handful of protein families shows. We finally estimated the numbers of potential allosteric or regulatory pockets that may be present in the data set, finding that pockets with putative functional and effector characteristics are widespread across

  9. Allosteric enhancers, allosteric agonists and ago-allosteric modulators: where do they bind and how do they act?

    DEFF Research Database (Denmark)

    Schwartz, Thue W; Holst, Birgitte

    2007-01-01

    Many small-molecule agonists also display allosteric properties. Such ago-allosteric modulators act as co-agonists, providing additive efficacy--instead of partial antagonism--and they can affect--and often improve--the potency of the endogenous agonist. Surprisingly, the apparent binding sites...... different binding modes. In another, dimeric, receptor scenario, the endogenous agonist binds to one protomer while the ago-allosteric modulator binds to the other, 'allosteric' protomer. It is suggested that testing for ago-allosteric properties should be an integral part of the agonist drug discovery...... process because a compound that acts with--rather than against--the endogenous agonist could be an optimal agonist drug....

  10. GABAA receptor: Positive and negative allosteric modulators.

    Science.gov (United States)

    Olsen, Richard W

    2018-01-31

    gamma-Aminobutyric acid (GABA)-mediated inhibitory neurotransmission and the gene products involved were discovered during the mid-twentieth century. Historically, myriad existing nervous system drugs act as positive and negative allosteric modulators of these proteins, making GABA a major component of modern neuropharmacology, and suggesting that many potential drugs will be found that share these targets. Although some of these drugs act on proteins involved in synthesis, degradation, and membrane transport of GABA, the GABA receptors Type A (GABA A R) and Type B (GABA B R) are the targets of the great majority of GABAergic drugs. This discovery is due in no small part to Professor Norman Bowery. Whereas the topic of GABA B R is appropriately emphasized in this special issue, Norman Bowery also made many insights into GABA A R pharmacology, the topic of this article. GABA A R are members of the ligand-gated ion channel receptor superfamily, a chloride channel family of a dozen or more heteropentameric subtypes containing 19 possible different subunits. These subtypes show different brain regional and subcellular localization, age-dependent expression, and potential for plastic changes with experience including drug exposure. Not only are GABA A R the targets of agonist depressants and antagonist convulsants, but most GABA A R drugs act at other (allosteric) binding sites on the GABA A R proteins. Some anxiolytic and sedative drugs, like benzodiazepine and related drugs, act on GABA A R subtype-dependent extracellular domain sites. General anesthetics including alcohols and neurosteroids act at GABA A R subunit-interface trans-membrane sites. Ethanol at high anesthetic doses acts on GABA A R subtype-dependent trans-membrane domain sites. Ethanol at low intoxicating doses acts at GABA A R subtype-dependent extracellular domain sites. Thus GABA A R subtypes possess pharmacologically specific receptor binding sites for a large group of different chemical classes of

  11. In vitro pharmacological characterization of RXFP3 allosterism: an example of probe dependency.

    Directory of Open Access Journals (Sweden)

    Lily Alvarez-Jaimes

    Full Text Available Recent findings suggest that the relaxin-3 neural network may represent a new ascending arousal pathway able to modulate a range of neural circuits including those affecting circadian rhythm and sleep/wake states, spatial and emotional memory, motivation and reward, the response to stress, and feeding and metabolism. Therefore, the relaxin-3 receptor (RXFP3 is a potential therapeutic target for the treatment of various CNS diseases. Here we describe a novel selective RXFP3 receptor positive allosteric modulator (PAM, 3-[3,5-Bis(trifluoromethylphenyl]-1-(3,4-dichlorobenzyl-1-[2-(5-methoxy-1H-indol-3-ylethyl]urea (135PAM1. Calcium mobilization and cAMP accumulation assays in cell lines expressing the cloned human RXFP3 receptor show the compound does not directly activate RXFP3 receptor but increases functional responses to amidated relaxin-3 or R3/I5, a chimera of the INSL5 A chain and the Relaxin-3 B chain. 135PAM1 increases calcium mobilization in the presence of relaxin-3(NH2 and R3/I5(NH2 with pEC50 values of 6.54 (6.46 to 6.64 and 6.07 (5.94 to 6.20, respectively. In the cAMP accumulation assay, 135PAM1 inhibits the CRE response to forskolin with a pIC50 of 6.12 (5.98 to 6.27 in the presence of a probe (10 nM concentration of relaxin-3(NH2. 135PAM1 does not compete for binding with the orthosteric radioligand, [(125I] R3I5 (amide, in membranes prepared from cells expressing the cloned human RXFP3 receptor. 135PAM1 is selective for RXFP3 over RXFP4, which also responds to relaxin-3. However, when using the free acid (native form of relaxin-3 or R3/I5, 135PAM1 doesn't activate RXFP3 indicating that the compound's effect is probe dependent. Thus one can exchange the entire A-chain of the probe peptide while retaining PAM activity, but the state of the probe's c-terminus is crucial to allosteric activity of the PAM. These data demonstrate the existence of an allosteric site for modulation of this GPCR as well as the subtlety of changes in probe

  12. Interactions between allosteric modulators and 4-DAMP and other antagonists at muscarinic receptors: potential significance of the distance between the N and Carboxyl C atoms in the molecules of antagonists

    Czech Academy of Sciences Publication Activity Database

    Lysíková, Michaela; Havlas, Zdeněk; Tuček, Stanislav

    2001-01-01

    Roč. 26, č. 4 (2001), s. 383-394 ISSN 0364-3190 R&D Projects: GA ČR GA309/99/0214; GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z5011922 Keywords : muscarinic receptors * allosteric modulation * 4-DAMP Subject RIV: ED - Physiology Impact factor: 1.638, year: 2001

  13. Drugability of extracellular targets: discovery of small molecule drugs targeting allosteric, functional, and subunit-selective sites on GPCRs and ion channels.

    Science.gov (United States)

    Grigoriadis, Dimitri E; Hoare, Samuel R J; Lechner, Sandra M; Slee, Deborah H; Williams, John A

    2009-01-01

    Beginning with the discovery of the structure of deoxyribose nucleic acid in 1953, by James Watson and Francis Crick, the sequencing of the entire human genome some 50 years later, has begun to quantify the classes and types of proteins that may have relevance to human disease with the promise of rapidly identifying compounds that can modulate these proteins so as to have a beneficial and therapeutic outcome. This so called 'drugable space' involves a variety of membrane-bound proteins including the superfamily of G-protein-coupled receptors (GPCRs), ion channels, and transporters among others. The recent number of novel therapeutics targeting membrane-bound extracellular proteins that have reached the market in the past 20 years however pales in magnitude when compared, during the same timeframe, to the advancements made in the technologies available to aid in the discovery of these novel therapeutics. This review will consider select examples of extracellular drugable targets and focus on the GPCRs and ion channels highlighting the corticotropin releasing factor (CRF) type 1 and gamma-aminobutyric acid receptors, and the Ca(V)2.2 voltage-gated ion channel. These examples will elaborate current technological advancements in drug discovery and provide a prospective framework for future drug development.

  14. Aryloxyalkanoic Acids as Non-Covalent Modifiers of the Allosteric Properties of Hemoglobin

    Directory of Open Access Journals (Sweden)

    Abdelsattar M. Omar

    2016-08-01

    Full Text Available Hemoglobin (Hb modifiers that stereospecifically inhibit sickle hemoglobin polymer formation and/or allosterically increase Hb affinity for oxygen have been shown to prevent the primary pathophysiology of sickle cell disease (SCD, specifically, Hb polymerization and red blood cell sickling. Several such compounds are currently being clinically studied for the treatment of SCD. Based on the previously reported non-covalent Hb binding characteristics of substituted aryloxyalkanoic acids that exhibited antisickling properties, we designed, synthesized and evaluated 18 new compounds (KAUS II series for enhanced antisickling activities. Surprisingly, select test compounds showed no antisickling effects or promoted erythrocyte sickling. Additionally, the compounds showed no significant effect on Hb oxygen affinity (or in some cases, even decreased the affinity for oxygen. The X-ray structure of deoxygenated Hb in complex with a prototype compound, KAUS-23, revealed that the effector bound in the central water cavity of the protein, providing atomic level explanations for the observed functional and biological activities. Although the structural modification did not lead to the anticipated biological effects, the findings provide important direction for designing candidate antisickling agents, as well as a framework for novel Hb allosteric effectors that conversely, decrease the protein affinity for oxygen for potential therapeutic use for hypoxic- and/or ischemic-related diseases.

  15. Allosteric transition: a comparison of two models

    DEFF Research Database (Denmark)

    Bindslev, Niels

    2013-01-01

    Introduction Two recent models are in use for analysis of allosteric drug action at receptor sites remote from orthosteric binding sites. One is an allosteric two-state mechanical model derived in 2000 by David Hall. The other is an extended operational model developed in 2007 by Arthur...... of model both for simulation and analysis of allosteric concentration-responses at equilibrium or steady-state. Conclusions As detailed knowledge of receptors systems becomes available, systems with several pathways and states and/ or more than two binding sites should be analysed by extended forms...

  16. CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction.

    Science.gov (United States)

    Xu, Youjun; Wang, Shiwei; Hu, Qiwan; Gao, Shuaishi; Ma, Xiaomin; Zhang, Weilin; Shen, Yihang; Chen, Fangjin; Lai, Luhua; Pei, Jianfeng

    2018-05-10

    CavityPlus is a web server that offers protein cavity detection and various functional analyses. Using protein three-dimensional structural information as the input, CavityPlus applies CAVITY to detect potential binding sites on the surface of a given protein structure and rank them based on ligandability and druggability scores. These potential binding sites can be further analysed using three submodules, CavPharmer, CorrSite, and CovCys. CavPharmer uses a receptor-based pharmacophore modelling program, Pocket, to automatically extract pharmacophore features within cavities. CorrSite identifies potential allosteric ligand-binding sites based on motion correlation analyses between cavities. CovCys automatically detects druggable cysteine residues, which is especially useful to identify novel binding sites for designing covalent allosteric ligands. Overall, CavityPlus provides an integrated platform for analysing comprehensive properties of protein binding cavities. Such analyses are useful for many aspects of drug design and discovery, including target selection and identification, virtual screening, de novo drug design, and allosteric and covalent-binding drug design. The CavityPlus web server is freely available at http://repharma.pku.edu.cn/cavityplus or http://www.pkumdl.cn/cavityplus.

  17. Supramolecular Allosteric Cofacial Porphyrin Complexes

    International Nuclear Information System (INIS)

    Oliveri, Christopher G.; Gianneschi, Nathan C.; Nguyen, Son Binh T.; Mirkin, Chad A.; Stern, Charlotte L.; Wawrzak, Zdzislaw; Pink, Maren

    2008-01-01

    Nature routinely uses cooperative interactions to regulate cellular activity. For years, chemists have designed synthetic systems that aim toward harnessing the reactivity common to natural biological systems. By learning how to control these interactions in situ, one begins to allow for the preparation of man-made biomimetic systems that can efficiently mimic the interactions found in Nature. To this end, we have designed a synthetic protocol for the preparation of flexible metal-directed supramolecular cofacial porphyrin complexes which are readily obtained in greater than 90% yield through the use of new hemilabile porphyrin ligands with bifunctional ether-phosphine or thioether-phosphine substituents at the 5 and 15 positions on the porphyrin ring. The resulting architectures contain two hemilabile ligand-metal domains (Rh I or Cu I sites) and two cofacially aligned porphyrins (Zn II sites), offering orthogonal functionalities and allowing these multimetallic complexes to exist in two states, 'condensed' or 'open'. Combining the ether-phosphine ligand with the appropriate Rh I or Cu I transition-metal precursors results in 'open' macrocyclic products. In contrast, reacting the thioether-phosphine ligand with RhI or CuI precursors yields condensed structures that can be converted into their 'open' macrocyclic forms via introduction of additional ancillary ligands. The change in cavity size that occurs allows these structures to function as allosteric catalysts for the acyl transfer reaction between X-pyridylcarbinol (where X = 2, 3, or 4) and 1-acetylimidazole. For 3- and 4-pyridylcarbinol, the 'open' macrocycle accelerates the acyl transfer reaction more than the condensed analogue and significantly more than the porphyrin monomer. In contrast, an allosteric effect was not observed for 2-pyridylcarbinol, which is expected to be a weaker binder and is unfavorably constrained inside the macrocyclic cavity.

  18. First steps in the direction of synthetic, allosteric, direct inhibitors of thrombin and factor Xa.

    Science.gov (United States)

    Verghese, Jenson; Liang, Aiye; Sidhu, Preet Pal Singh; Hindle, Michael; Zhou, Qibing; Desai, Umesh R

    2009-08-01

    Designing non-saccharide functional mimics of heparin is a major challenge. In this work, a library of small, aromatic molecules based on the sulfated DHP scaffold was synthesized and screened against thrombin and factor Xa. The results reveal that (i) selected monomeric benzofuran derivatives inhibit the two enzymes, albeit weakly; (ii) the two enzymes recognize different structural features in the benzofurans studied suggesting significant selectivity of recognition; and (iii) the mechanism of inhibition is allosteric. The molecules represent the first allosteric small molecule inhibitors of the two enzymes.

  19. First Steps in the Direction of Synthetic, Allosteric, Direct Inhibitors of Thrombin and Factor Xa

    Science.gov (United States)

    Verghese, Jenson; Liang, Aiye; Sidhu, Preet Pal Singh; Hindle, Michael; Zhou, Qibing; Desai, Umesh R.

    2009-01-01

    Designing non-saccharide functional mimics of heparin is a major challenge. In this work, a library of small, aromatic molecules based on the sulfated DHP scaffold was synthesized and screened against thrombin and factor Xa. The results reveal that i) selected monomeric benzofuran derivatives inhibit the two enzymes, albeit weakly; ii) the two enzymes recognize different structural features in the benzofurans studied suggesting significant selectivity of recognition; and iii) the mechanism of inhibition is allosteric. The molecules represent the first allosteric small molecule inhibitors of the two enzymes. PMID:19540113

  20. Characterisation of endogenous A2A and A2B receptor-mediated cyclic AMP responses in HEK 293 cells using the GloSensor™ biosensor: Evidence for an allosteric mechanism of action for the A2B-selective antagonist PSB 603.

    Science.gov (United States)

    Goulding, Joelle; May, Lauren T; Hill, Stephen J

    2018-01-01

    Endogenous adenosine A 2B receptors (A 2B AR) mediate cAMP accumulation in HEK 293 cells. Here we have used a biosensor to investigate the mechanism of action of the A 2B AR antagonist PSB 603 in HEK 293 cells. The A 2A agonist CGS 21680 elicited a small response in these cells (circa 20% of that obtained with NECA), suggesting that they also contain a small population of A 2A receptors. The responses to NECA and adenosine were antagonised by PSB 603, but not by the selective A 2A AR antagonist SCH 58261. In contrast, CGS 21680 responses were not antagonised by high concentrations of PSB 603, but were sensitive to inhibition by SCH 58261. Analysis of the effect of increasing concentrations of PSB 603 on the response to NECA indicated a non-competitive mode of action yielding a marked reduction in the NECA E MAX with no significant effect on EC 50 values. Kinetics analysis of the effect of PSB 603 on the A 2B AR-mediated NECA responses confirmed a saturable effect that was consistent with an allosteric mode of antagonism. The possibility that PSB 603 acts as a negative allosteric modulator of A 2B AR suggests new approaches to the development of therapeutic agents to treat conditions where adenosine levels are high. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  1. Allosteric cross-talk in chromatin can mediate drug-drug synergy

    Science.gov (United States)

    Adhireksan, Zenita; Palermo, Giulia; Riedel, Tina; Ma, Zhujun; Muhammad, Reyhan; Rothlisberger, Ursula; Dyson, Paul J.; Davey, Curt A.

    2017-03-01

    Exploitation of drug-drug synergism and allostery could yield superior therapies by capitalizing on the immensely diverse, but highly specific, potential associated with the biological macromolecular landscape. Here we describe a drug-drug synergy mediated by allosteric cross-talk in chromatin, whereby the binding of one drug alters the activity of the second. We found two unrelated drugs, RAPTA-T and auranofin, that yield a synergistic activity in killing cancer cells, which coincides with a substantially greater number of chromatin adducts formed by one of the compounds when adducts from the other agent are also present. We show that this occurs through an allosteric mechanism within the nucleosome, whereby defined histone adducts of one drug promote reaction of the other drug at a distant, specific histone site. This opens up possibilities for epigenetic targeting and suggests that allosteric modulation in nucleosomes may have biological relevance and potential for therapeutic interventions.

  2. Biochemistry and structural studies of kynurenine 3-monooxygenase reveal allosteric inhibition by Ro 61-8048.

    Science.gov (United States)

    Gao, Jingjing; Yao, Licheng; Xia, Tingting; Liao, Xuebin; Zhu, Deyu; Xiang, Ye

    2018-04-01

    The human kynurenine 3-monooxygenase (hKMO) is a potential therapeutic target for neurodegenerative and neurologic disorders. Inhibition of KMO by Ro 61-8048, a potent, selective, and the most widely used inhibitor of KMO, was shown effective in various models of neurodegenerative or neurologic disorders. However, the molecular basis of hKMO inhibition by Ro 61-8048 is not clearly understood. Here, we report biochemistry studies on hKMO and crystal structures of an hKMO homolog, pfKMO from Pseudomonas fluorescens, in complex with the substrate l-kynurenine and Ro 61-8048. We found that the C-terminal ∼110 aa are essential for the enzymatic activity of hKMO and the homologous C-terminal region of pfKMO folds into a distinct, all-α-helical domain, which associates with the N-terminal catalytic domain to form a unique tunnel in proximity to the substrate-binding pocket. The tunnel binds the Ro 61-8048 molecule, which fills most of the tunnel, and Ro 61-8048 is hydrogen bonded with several completely conserved residues, including an essential catalytic residue. Modification of Ro 61-8048 and biochemical studies of the modified Ro 61-8048 derivatives suggested that Ro 61-8048 inhibits the enzyme in an allosteric manner by affecting the conformation of the essential catalytic residue and by blocking entry of the substrate or product release. The unique binding sites distinguish Ro 61-8048 as a noncompetitive and highly selective inhibitor from other competitive inhibitors, which should facilitate further optimization of Ro 61-8048 and the development of new inhibitory drugs to hKMO.-Gao, J., Yao, L., Xia, T., Liao, X., Zhu, D., Xiang, Y. Biochemistry and structural studies of kynurenine 3-monooxygenase reveal allosteric inhibition by Ro 61-8048.

  3. A dynamically coupled allosteric network underlies binding cooperativity in Src kinase.

    Science.gov (United States)

    Foda, Zachariah H; Shan, Yibing; Kim, Eric T; Shaw, David E; Seeliger, Markus A

    2015-01-20

    Protein tyrosine kinases are attractive drug targets because many human diseases are associated with the deregulation of kinase activity. However, how the catalytic kinase domain integrates different signals and switches from an active to an inactive conformation remains incompletely understood. Here we identify an allosteric network of dynamically coupled amino acids in Src kinase that connects regulatory sites to the ATP- and substrate-binding sites. Surprisingly, reactants (ATP and peptide substrates) bind with negative cooperativity to Src kinase while products (ADP and phosphopeptide) bind with positive cooperativity. We confirm the molecular details of the signal relay through the allosteric network by biochemical studies. Experiments on two additional protein tyrosine kinases indicate that the allosteric network may be largely conserved among these enzymes. Our work provides new insights into the regulation of protein tyrosine kinases and establishes a potential conduit by which resistance mutations to ATP-competitive kinase inhibitors can affect their activity.

  4. Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling

    Science.gov (United States)

    Bharatham, Kavitha; Bharatham, Nagakumar; Kwon, Yong Jung; Lee, Keun Woo

    2008-12-01

    Allosteric inhibition of protein tyrosine phosphatase 1B (PTP1B), has paved a new path to design specific inhibitors for PTP1B, which is an important drug target for the treatment of type II diabetes and obesity. The PTP1B1-282-allosteric inhibitor complex crystal structure lacks α7 (287-298) and moreover there is no available 3D structure of PTP1B1-298 in open form. As the interaction between α7 and α6-α3 helices plays a crucial role in allosteric inhibition, α7 was modeled to the PTP1B1-282 in open form complexed with an allosteric inhibitor (compound-2) and a 5 ns MD simulation was performed to investigate the relative orientation of the α7-α6-α3 helices. The simulation conformational space was statistically sampled by clustering analyses. This approach was helpful to reveal certain clues on PTP1B allosteric inhibition. The simulation was also utilized in the generation of receptor based pharmacophore models to include the conformational flexibility of the protein-inhibitor complex. Three cluster representative structures of the highly populated clusters were selected for pharmacophore model generation. The three pharmacophore models were subsequently utilized for screening databases to retrieve molecules containing the features that complement the allosteric site. The retrieved hits were filtered based on certain drug-like properties and molecular docking simulations were performed in two different conformations of protein. Thus, performing MD simulation with α7 to investigate the changes at the allosteric site, then developing receptor based pharmacophore models and finally docking the retrieved hits into two distinct conformations will be a reliable methodology in identifying PTP1B allosteric inhibitors.

  5. Selected soil enzymes: Examples of their potential roles in the ...

    African Journals Online (AJOL)

    Soil enzymes regulate ecosystem functioning and in particular play a key role in nutrient cycling. In this review we briefly summarise potential roles of selected enzymes such as amylase, arylsulphatases, -glucosidase, cellulose, chitinase, dehydrogenase, phosphatase, protease and urease in the ecosystem. We also ...

  6. Evaluation of the Nutritional Potentials of Selected Multipurpose ...

    African Journals Online (AJOL)

    This experiment was conducted to evaluate the nutritional potentials of selected multipurpose fodder trees for use in livestock diets. Fresh leaves from five fodder tree species notably Gmelina arborea, Leucaena leucocephala, Tectona grandis, Persea americana and Dactyledila barteri obtained from the forestry unit of Imo ...

  7. Allosteric Modulation of Muscarinic Acetylcholine Receptors

    Czech Academy of Sciences Publication Activity Database

    Jakubík, Jan; El-Fakahany, E. E.

    2010-01-01

    Roč. 3, č. 9 (2010), s. 2838-2860 ISSN 1424-8247 R&D Projects: GA ČR GA305/09/0681 Institutional research plan: CEZ:AV0Z50110509 Keywords : muscarinic acetylcholine receptors * allosteric modulation * Alzheimer´s disease Subject RIV: CE - Biochemistry

  8. Sniffer patch laser uncaging response (SPLURgE): an assay of regional differences in allosteric receptor modulation and neurotransmitter clearance.

    Science.gov (United States)

    Christian, Catherine A; Huguenard, John R

    2013-10-01

    Allosteric modulators exert actions on neurotransmitter receptors by positively or negatively altering the effective response of these receptors to their respective neurotransmitter. γ-Aminobutyric acid (GABA) type A ionotropic receptors (GABAARs) are major targets for allosteric modulators such as benzodiazepines, neurosteroids, and barbiturates. Analysis of substances that produce similar effects has been hampered by the lack of techniques to assess the localization and function of such agents in brain slices. Here we describe measurement of the sniffer patch laser uncaging response (SPLURgE), which combines the sniffer patch recording configuration with laser photolysis of caged GABA. This methodology enables the detection of allosteric GABAAR modulators endogenously present in discrete areas of the brain slice and allows for the application of exogenous GABA with spatiotemporal control without altering the release and localization of endogenous modulators within the slice. Here we demonstrate the development and use of this technique for the measurement of allosteric modulation in different areas of the thalamus. Application of this technique will be useful in determining whether a lack of modulatory effect on a particular category of neurons or receptors is due to insensitivity to allosteric modulation or a lack of local release of endogenous ligand. We also demonstrate that this technique can be used to investigate GABA diffusion and uptake. This method thus provides a biosensor assay for rapid detection of endogenous GABAAR modulators and has the potential to aid studies of allosteric modulators that exert effects on other classes of neurotransmitter receptors, such as glutamate, acetylcholine, or glycine receptors.

  9. Allosteric inhibitors of Coxsackie virus A24 RNA polymerase.

    Science.gov (United States)

    Schein, Catherine H; Rowold, Diane; Choi, Kyung H

    2016-02-15

    Coxsackie virus A24 (CVA24), a causative agent of acute hemorrhagic conjunctivitis, is a prototype of enterovirus (EV) species C. The RNA polymerase (3D(pol)) of CVA24 can uridylylate the viral peptide linked to the genome (VPg) from distantly related EV and is thus, a good model for studying this reaction. Once UMP is bound, VPgpU primes RNA elongation. Structural and mutation data have identified a conserved binding surface for VPg on the RNA polymerase (3D(pol)), located about 20Å from the active site. Here, computational docking of over 60,000 small compounds was used to select those with the lowest (best) specific binding energies (BE) for this allosteric site. Compounds with varying structures and low BE were assayed for their effect on formation of VPgU by CVA24-3D(pol). Two compounds with the lowest specific BE for the site inhibited both uridylylation and formation of VPgpolyU at 10-20μM. These small molecules can be used to probe the role of this allosteric site in polymerase function, and may be the basis for novel antiviral compounds. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Deprivation selectively modulates brain potentials to food pictures.

    Science.gov (United States)

    Stockburger, Jessica; Weike, Almut I; Hamm, Alfons O; Schupp, Harald T

    2008-08-01

    Event-related brain potentials (ERPs) were used to examine whether the processing of food pictures is selectively modulated by changes in the motivational state of the observer. Sixteen healthy male volunteers were tested twice 1 week apart, either after 24 hr of food deprivation or after normal food intake. ERPs were measured while participants viewed appetitive food pictures as well as standard emotional and neutral control pictures. Results show that the ERPs to food pictures in a hungry, rather than satiated, state were associated with enlarged positive potentials over posterior sensor sites in a time window of 170-310 ms poststimulus. Minimum-norm analysis suggests the enhanced processing of food cues primarily in occipito-temporo-parietal regions. In contrast, processing of standard emotional and neutral pictures was not modulated by food deprivation. Considered from the perspective of motivated attention, the selective change of food cue processing may reflect a state-dependent change in stimulus salience.

  11. Deprivation selectively modulates brain potentials to food pictures

    OpenAIRE

    Stockburger, Jessica; Weike, Almut I.; Hamm, Alfons O.; Schupp, Harald Thomas

    2008-01-01

    Event-related brain potentials (ERPs) were used to examine whether the processing of food pictures is selectively modulated by changes in the motivational state of the observer. Sixteen healthy male volunteers were tested twice 1 week apart, either after 24 hr of food deprivation or after normal food intake. ERPs were measured while participants viewed appetitive food pictures as well as standard emotional and neutral control pictures. Results show that the ERPs to food pictures in a hungry, ...

  12. Can a Positive Allosteric Modulation of GABAergic Receptors Improve Motor Symptoms in Patients with Parkinson’s Disease? The Potential Role of Zolpidem in the Treatment of Parkinson’s Disease

    Directory of Open Access Journals (Sweden)

    Antonio Daniele

    2016-01-01

    Full Text Available At present, patients with advanced Parkinson’s disease (PD are unsatisfactorily controlled by currently used anti-Parkinsonian dopaminergic drugs. Various studies suggest that therapeutic strategies based on nondopaminergic drugs might be helpful in PD. Zolpidem, an imidazopyridine widely used as sleep inducer, shows high affinity only for GABAA receptors containing the α-1 subunit and facilitates GABAergic neurotransmission through a positive allosteric modulation of GABAA receptors. Various observations, although preliminary, consistently suggest that in PD patients zolpidem may induce beneficial (and sometimes remarkable effects on motor symptoms even after single doses and may also improve dyskinesias. Since a high density of zolpidem binding sites is in the two main output structures of the basal ganglia which are abnormally overactive in PD (internal globus pallidus, GPi, and substantia nigra pars reticulata, SNr, it was hypothesized that in PD patients zolpidem may induce through GABAA receptors an inhibition of GPi and SNr (and, possibly, of the subthalamic nucleus also, resulting in an increased activity of motor cortical areas (such as supplementary motor area, which may give rise to improvement of motor symptoms of PD. Randomized clinical trials are needed in order to assess the efficacy, safety, and tolerability of zolpidem in treating motor symptoms of PD.

  13. Exploring allosteric coupling in the α-subunit of Heterotrimeric G proteins using evolutionary and ensemble-based approaches

    Directory of Open Access Journals (Sweden)

    Hilser Vincent J

    2008-05-01

    Full Text Available Abstract Background Allosteric coupling, which can be defined as propagation of a perturbation at one region of the protein molecule (such as ligand binding to distant sites in the same molecule, constitutes the most general mechanism of regulation of protein function. However, unlike molecular details of ligand binding, structural elements involved in allosteric effects are difficult to diagnose. Here, we identified allosteric linkages in the α-subunits of heterotrimeric G proteins, which were evolved to transmit membrane receptor signals by allosteric mechanisms, by using two different approaches that utilize fundamentally different and independent information. Results We analyzed: 1 correlated mutations in the family of G protein α-subunits, and 2 cooperativity of the native state ensemble of the Gαi1 or transducin. The combination of these approaches not only recovered already-known details such as the switch regions that change conformation upon nucleotide exchange, and those regions that are involved in receptor, effector or Gβγ interactions (indicating that the predictions of the analyses can be viewed with a measure of confidence, but also predicted new sites that are potentially involved in allosteric communication in the Gα protein. A summary of the new sites found in the present analysis, which were not apparent in crystallographic data, is given along with known functional and structural information. Implications of the results are discussed. Conclusion A set of residues and/or structural elements that are potentially involved in allosteric communication in Gα is presented. This information can be used as a guide to structural, spectroscopic, mutational, and theoretical studies on the allosteric network in Gα proteins, which will provide a better understanding of G protein-mediated signal transduction.

  14. Recreational fishing selectively captures individuals with the highest fitness potential.

    Science.gov (United States)

    Sutter, David A H; Suski, Cory D; Philipp, David P; Klefoth, Thomas; Wahl, David H; Kersten, Petra; Cooke, Steven J; Arlinghaus, Robert

    2012-12-18

    Fisheries-induced evolution and its impact on the productivity of exploited fish stocks remains a highly contested research topic in applied fish evolution and fisheries science. Although many quantitative models assume that larger, more fecund fish are preferentially removed by fishing, there is no empirical evidence describing the relationship between vulnerability to capture and individual reproductive fitness in the wild. Using males from two lines of largemouth bass (Micropterus salmoides) selectively bred over three generations for either high (HV) or low (LV) vulnerability to angling as a model system, we show that the trait "vulnerability to angling" positively correlates with aggression, intensity of parental care, and reproductive fitness. The difference in reproductive fitness between HV and LV fish was particularly evident among larger males, which are also the preferred mating partners of females. Our study constitutes experimental evidence that recreational angling selectively captures individuals with the highest potential for reproductive fitness. Our study further suggests that selective removal of the fittest individuals likely occurs in many fisheries that target species engaged in parental care. As a result, depending on the ecological context, angling-induced selection may have negative consequences for recruitment within wild populations of largemouth bass and possibly other exploited species in which behavioral patterns that determine fitness, such as aggression or parental care, also affect their vulnerability to fishing gear.

  15. Selection theory of free dendritic growth in a potential flow.

    Science.gov (United States)

    von Kurnatowski, Martin; Grillenbeck, Thomas; Kassner, Klaus

    2013-04-01

    The Kruskal-Segur approach to selection theory in diffusion-limited or Laplacian growth is extended via combination with the Zauderer decomposition scheme. This way nonlinear bulk equations become tractable. To demonstrate the method, we apply it to two-dimensional crystal growth in a potential flow. We omit the simplifying approximations used in a preliminary calculation for the same system [Fischaleck, Kassner, Europhys. Lett. 81, 54004 (2008)], thus exhibiting the capability of the method to extend mathematical rigor to more complex problems than hitherto accessible.

  16. Allosteric modulation of endogenous metabolites as an avenue for drug discovery.

    Science.gov (United States)

    Wootten, Denise; Savage, Emilia E; Valant, Celine; May, Lauren T; Sloop, Kyle W; Ficorilli, James; Showalter, Aaron D; Willard, Francis S; Christopoulos, Arthur; Sexton, Patrick M

    2012-08-01

    G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors and a key drug target class. Recently, allosteric drugs that can co-bind with and modulate the activity of the endogenous ligand(s) for the receptor have become a major focus of the pharmaceutical and biotechnology industry for the development of novel GPCR therapeutic agents. This class of drugs has distinct properties compared with drugs targeting the endogenous (orthosteric) ligand-binding site that include the ability to sculpt cellular signaling and to respond differently in the presence of discrete orthosteric ligands, a behavior termed "probe dependence." Here, using cell signaling assays combined with ex vivo and in vivo studies of insulin secretion, we demonstrate that allosteric ligands can cause marked potentiation of previously "inert" metabolic products of neurotransmitters and peptide hormones, a novel consequence of the phenomenon of probe dependence. Indeed, at the muscarinic M(2) receptor and glucagon-like peptide 1 (GLP-1) receptor, allosteric potentiation of the metabolites, choline and GLP-1(9-36)NH(2), respectively, was ~100-fold and up to 200-fold greater than that seen with the physiological signaling molecules acetylcholine and GLP-1(7-36)NH(2). Modulation of GLP-1(9-36)NH(2) was also demonstrated in ex vivo and in vivo assays of insulin secretion. This work opens up new avenues for allosteric drug discovery by directly targeting modulation of metabolites, but it also identifies a behavior that could contribute to unexpected clinical outcomes if interaction of allosteric drugs with metabolites is not part of their preclinical assessment.

  17. Enhancing NMDA Receptor Function: Recent Progress on Allosteric Modulators

    Directory of Open Access Journals (Sweden)

    Lulu Yao

    2017-01-01

    Full Text Available The N-methyl-D-aspartate receptors (NMDARs are subtype glutamate receptors that play important roles in excitatory neurotransmission and synaptic plasticity. Their hypo- or hyperactivation are proposed to contribute to the genesis or progression of various brain diseases, including stroke, schizophrenia, depression, and Alzheimer’s disease. Past efforts in targeting NMDARs for therapeutic intervention have largely been on inhibitors of NMDARs. In light of the discovery of NMDAR hypofunction in psychiatric disorders and perhaps Alzheimer’s disease, efforts in boosting NMDAR activity/functions have surged in recent years. In this review, we will focus on enhancing NMDAR functions, especially on the recent progress in the generation of subunit-selective, allosteric positive modulators (PAMs of NMDARs. We shall also discuss the usefulness of these newly developed NMDAR-PAMs.

  18. SH2-catalytic domain linker heterogeneity influences allosteric coupling across the SFK family.

    Science.gov (United States)

    Register, A C; Leonard, Stephen E; Maly, Dustin J

    2014-11-11

    Src-family kinases (SFKs) make up a family of nine homologous multidomain tyrosine kinases whose misregulation is responsible for human disease (cancer, diabetes, inflammation, etc.). Despite overall sequence homology and identical domain architecture, differences in SH3 and SH2 regulatory domain accessibility and ability to allosterically autoinhibit the ATP-binding site have been observed for the prototypical SFKs Src and Hck. Biochemical and structural studies indicate that the SH2-catalytic domain (SH2-CD) linker, the intramolecular binding epitope for SFK SH3 domains, is responsible for allosterically coupling SH3 domain engagement to autoinhibition of the ATP-binding site through the conformation of the αC helix. As a relatively unconserved region between SFK family members, SH2-CD linker sequence variability across the SFK family is likely a source of nonredundant cellular functions between individual SFKs via its effect on the availability of SH3 and SH2 domains for intermolecular interactions and post-translational modification. Using a combination of SFKs engineered with enhanced or weakened regulatory domain intramolecular interactions and conformation-selective inhibitors that report αC helix conformation, this study explores how SH2-CD sequence heterogeneity affects allosteric coupling across the SFK family by examining Lyn, Fyn1, and Fyn2. Analyses of Fyn1 and Fyn2, isoforms that are identical but for a 50-residue sequence spanning the SH2-CD linker, demonstrate that SH2-CD linker sequence differences can have profound effects on allosteric coupling between otherwise identical kinases. Most notably, a dampened allosteric connection between the SH3 domain and αC helix leads to greater autoinhibitory phosphorylation by Csk, illustrating the complex effects of SH2-CD linker sequence on cellular function.

  19. Scalable rule-based modelling of allosteric proteins and biochemical networks.

    Directory of Open Access Journals (Sweden)

    Julien F Ollivier

    2010-11-01

    Full Text Available Much of the complexity of biochemical networks comes from the information-processing abilities of allosteric proteins, be they receptors, ion-channels, signalling molecules or transcription factors. An allosteric protein can be uniquely regulated by each combination of input molecules that it binds. This "regulatory complexity" causes a combinatorial increase in the number of parameters required to fit experimental data as the number of protein interactions increases. It therefore challenges the creation, updating, and re-use of biochemical models. Here, we propose a rule-based modelling framework that exploits the intrinsic modularity of protein structure to address regulatory complexity. Rather than treating proteins as "black boxes", we model their hierarchical structure and, as conformational changes, internal dynamics. By modelling the regulation of allosteric proteins through these conformational changes, we often decrease the number of parameters required to fit data, and so reduce over-fitting and improve the predictive power of a model. Our method is thermodynamically grounded, imposes detailed balance, and also includes molecular cross-talk and the background activity of enzymes. We use our Allosteric Network Compiler to examine how allostery can facilitate macromolecular assembly and how competitive ligands can change the observed cooperativity of an allosteric protein. We also develop a parsimonious model of G protein-coupled receptors that explains functional selectivity and can predict the rank order of potency of agonists acting through a receptor. Our methodology should provide a basis for scalable, modular and executable modelling of biochemical networks in systems and synthetic biology.

  20. Colorectal cancer chemoprevention: the potential of a selective approach.

    Science.gov (United States)

    Ben-Amotz, Oded; Arber, Nadir; Kraus, Sarah

    2010-10-01

    Colorectal cancer (CRC) is a leading cause of cancer death, and therefore demands special attention. Novel recent approaches for the chemoprevention of CRC focus on selective targeting of key pathways. We review the study by Zhang and colleagues, evaluating a selective approach targeting APC-deficient premalignant cells using retinoid-based therapy and TNF-related apoptosis-inducing ligand (TRAIL). This study demonstrates that induction of TRAIL-mediated death signaling contributes to the chemopreventive value of all-trans-retinyl acetate (RAc) by sensitizing premalignant adenoma cells for apoptosis without affecting normal cells. We discuss these important findings, raise few points that deserve consideration, and may further contribute to the development of RAc-based combination therapies with improved efficacy. The authors clearly demonstrate a synergistic interaction between TRAIL, RAc and APC, which leads to the specific cell death of premalignant target cells. The study adds to the growing body of literature related to CRC chemoprevention, and provides solid data supporting a potentially selective approach for preventing CRC using RAc and TRAIL.

  1. Positive allosteric modulation of TRPV1 as a novel analgesic mechanism

    Directory of Open Access Journals (Sweden)

    Lebovitz Evan E

    2012-09-01

    Full Text Available Abstract Background The prevalence of long-term opiate use in treating chronic non-cancer pain is increasing, and prescription opioid abuse and dependence are a major public health concern. To explore alternatives to opioid-based analgesia, the present study investigates a novel allosteric pharmacological approach operating through the cation channel TRPV1. This channel is highly expressed in subpopulations of primary afferent unmyelinated C- and lightly-myelinated Aδ-fibers that detect low and high rates of noxious heating, respectively, and it is also activated by vanilloid agonists and low pH. Sufficient doses of exogenous vanilloid agonists, such as capsaicin or resiniferatoxin, can inactivate/deactivate primary afferent endings due to calcium overload, and we hypothesized that positive allosteric modulation of agonist-activated TRPV1 could produce a selective, temporary inactivation of nociceptive nerve terminals in vivo. We previously identified MRS1477, a 1,4-dihydropyridine that potentiates vanilloid and pH activation of TRPV1 in vitro, but displays no detectable intrinsic agonist activity of its own. To study the in vivo effects of MRS1477, we injected the hind paws of rats with a non-deactivating dose of capsaicin, MRS1477, or the combination. An infrared diode laser was used to stimulate TRPV1-expressing nerve terminals and the latency and intensity of paw withdrawal responses were recorded. qRT-PCR and immunohistochemistry were performed on dorsal root ganglia to examine changes in gene expression and the cellular specificity of such changes following treatment. Results Withdrawal responses of the capsaicin-only or MRS1477-only treated paws were not significantly different from the untreated, contralateral paws. However, rats treated with the combination of capsaicin and MRS1477 exhibited increased withdrawal latency and decreased response intensity consistent with agonist potentiation and inactivation or lesion of TRPV1-containing

  2. Generalized Selectivity Description for Polymeric Ion-Selective Electrodes Based on the Phase Boundary Potential Model.

    Science.gov (United States)

    Bakker, Eric

    2010-02-15

    A generalized description of the response behavior of potentiometric polymer membrane ion-selective electrodes is presented on the basis of ion-exchange equilibrium considerations at the sample-membrane interface. This paper includes and extends on previously reported theoretical advances in a more compact yet more comprehensive form. Specifically, the phase boundary potential model is used to derive the origin of the Nernstian response behavior in a single expression, which is valid for a membrane containing any charge type and complex stoichiometry of ionophore and ion-exchanger. This forms the basis for a generalized expression of the selectivity coefficient, which may be used for the selectivity optimization of ion-selective membranes containing electrically charged and neutral ionophores of any desired stoichiometry. It is shown to reduce to expressions published previously for specialized cases, and may be effectively applied to problems relevant in modern potentiometry. The treatment is extended to mixed ion solutions, offering a comprehensive yet formally compact derivation of the response behavior of ion-selective electrodes to a mixture of ions of any desired charge. It is compared to predictions by the less accurate Nicolsky-Eisenman equation. The influence of ion fluxes or any form of electrochemical excitation is not considered here, but may be readily incorporated if an ion-exchange equilibrium at the interface may be assumed in these cases.

  3. Levamisole: A Positive Allosteric Modulator for the α3β4 Nicotinic Acetylcholine Receptors Prevents Weight Gain in the CD-1 Mice on a High Fat Diet.

    Science.gov (United States)

    Lewis, Jeanne A; Yakel, Jerrel L; Pandya, Anshul A

    2017-01-01

    Neuronal nicotinic acetylcholine receptors (nAChRs) regulate the function of multiple neurotransmitter pathways throughout the central nervous system. This includes nAChRs found on the proopiomelanocortin neurons in the hypothalamus. Activation of these nAChRs by nicotine causes a decrease in the consumption of food in rodents. This study tested the effect of subtype selective allosteric modulators for nAChRs on the body weight of CD-1 mice. Levamisole, an allosteric modulator for the α3β4 subtype of nAChRs, prevented weight gain in mice that were fed a high fat diet. PNU-120596 and desformylflustrabromine were observed to be selective PAMs for the α7 and α4β2 nAChR, respectively. Both of these compounds failed to prevent weight gain in the CD-1 mice. These results suggest that the modulation of hypothalamic α3β4 nAChRs is an important factor in regulating food intake, and the PAMs for these receptors need further investigation as potential therapeutic agents for controlling weight gain. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  4. Visual evoked potentials and selective attention to points in space

    Science.gov (United States)

    Van Voorhis, S.; Hillyard, S. A.

    1977-01-01

    Visual evoked potentials (VEPs) were recorded to sequences of flashes delivered to the right and left visual fields while subjects responded promptly to designated stimuli in one field at a time (focused attention), in both fields at once (divided attention), or to neither field (passive). Three stimulus schedules were used: the first was a replication of a previous study (Eason, Harter, and White, 1969) where left- and right-field flashes were delivered quasi-independently, while in the other two the flashes were delivered to the two fields in random order (Bernoulli sequence). VEPs to attended-field stimuli were enhanced at both occipital (O2) and central (Cz) recording sites under all stimulus sequences, but different components were affected at the two scalp sites. It was suggested that the VEP at O2 may reflect modality-specific processing events, while the response at Cz, like its auditory homologue, may index more general aspects of selective attention.

  5. Allosteric modulation of G-protein coupled receptors

    DEFF Research Database (Denmark)

    Jensen, Anders A.; Spalding, Tracy A

    2004-01-01

    are believed to activate (agonists) or inhibit (competitive antagonists) receptor signalling by binding the receptor at the same site as the endogenous agonist, the orthosteric site. In contrast, allosteric ligands modulate receptor function by binding to different regions in the receptor, allosteric sites....... In recent years, combinatorial chemistry and high throughput screening have helped identify several allosteric GPCR modulators with novel structures, several of which already have become valuable pharmacological tools and may be candidates for clinical testing in the near future. This mini review outlines...... the current status and perspectives of allosteric modulation of GPCR function with emphasis on the pharmacology of endogenous and synthesised modulators, their receptor interactions and the therapeutic prospects of allosteric ligands compared to orthosteric ligands....

  6. Selection of potential microorganism for sago starch fermentation

    Directory of Open Access Journals (Sweden)

    RUTH MELLIAWATI

    2006-02-01

    Full Text Available Fermentation process of sago starch for the production of bioproduct requires potential microorganism that have ability to hydrolyze sago starch. The purpose of this research was to get the potential of amylolytic microorganisms for their capability of amyloglucosidase activity and to know the sugar strains of the fermentation result. Eleven amylolytic microorganisms (9 strains of mold and 2 strains of yeast were obtained from the collection Research Centre for Biotechnology – Indonesian Institute of Sciences (LIPI, Cibinong-Bogor were used. The selection step was carried out based on their capability of starch hydrolysis to reducing sugar. The best result indicates that the production of reducing sugar reached the highest 18.485 ppm and amyloglucosidase activities was 3.583 units by KTU-1 strain. The highest total acid obtained was 5.85 mg/mL by Rhizopus IFO.R5442. The cell biomass was obtained between 0.5 to 1.74 g dry weight/100 mL and pH of the final fermentation (72 h were 3.57 to 8.38.

  7. A novel antidiabetic drug, fasiglifam/TAK-875, acts as an ago-allosteric modulator of FFAR1.

    Directory of Open Access Journals (Sweden)

    Chiori Yabuki

    Full Text Available Selective free fatty acid receptor 1 (FFAR1/GPR40 agonist fasiglifam (TAK-875, an antidiabetic drug under phase 3 development, potentiates insulin secretion in a glucose-dependent manner by activating FFAR1 expressed in pancreatic β cells. Although fasiglifam significantly improved glycemic control in type 2 diabetes patients with a minimum risk of hypoglycemia in a phase 2 study, the precise mechanisms of its potent pharmacological effects are not fully understood. Here we demonstrate that fasiglifam acts as an ago-allosteric modulator with a partial agonistic activity for FFAR1. In both Ca(2+ influx and insulin secretion assays using cell lines and mouse islets, fasiglifam showed positive cooperativity with the FFAR1 ligand γ-linolenic acid (γ-LA. Augmentation of glucose-induced insulin secretion by fasiglifam, γ-LA, or their combination was completely abolished in pancreatic islets of FFAR1-knockout mice. In diabetic rats, the insulinotropic effect of fasiglifam was suppressed by pharmacological reduction of plasma free fatty acid (FFA levels using a lipolysis inhibitor, suggesting that fasiglifam potentiates insulin release in conjunction with plasma FFAs in vivo. Point mutations of FFAR1 differentially affected Ca(2+ influx activities of fasiglifam and γ-LA, further indicating that these agonists may bind to distinct binding sites. Our results strongly suggest that fasiglifam is an ago-allosteric modulator of FFAR1 that exerts its effects by acting cooperatively with endogenous plasma FFAs in human patients as well as diabetic animals. These findings contribute to our understanding of fasiglifam as an attractive antidiabetic drug with a novel mechanism of action.

  8. mGluR5 Positive Allosteric Modulation Enhances Extinction Learning Following Cocaine Self-Administration

    OpenAIRE

    Cleva, Richard M.; Hicks, Megan P.; Gass, Justin T.; Wischerath, Kelly C.; Plasters, Elizabeth T.; Widholm, John J.; Olive, M. Foster

    2011-01-01

    Extinction of classically and instrumentally conditioned behaviors, such as conditioned fear and drug-seeking behavior, is a process of active learning, and recent studies indicate that potentiation of glutamatergic transmission facilitates extinction learning. In this study we investigated the effects of the type 5 metabotropic glutamate receptors (mGluR5) positive allosteric modulator 3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide (CDPPB) on the extinction of cocaine-seeking behavior in ...

  9. Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors.

    Science.gov (United States)

    Rodgers, Thomas L; Townsend, Philip D; Burnell, David; Jones, Matthew L; Richards, Shane A; McLeish, Tom C B; Pohl, Ehmke; Wilson, Mark R; Cann, Martin J

    2013-09-01

    Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distinct site. There is growing evidence that allosteric cooperativity can be communicated by modulation of protein dynamics without conformational change. The mechanisms, however, for communicating dynamic fluctuations between sites are debated. We provide a foundational theory for how allostery can occur as a function of low-frequency dynamics without a change in structure. We have generated coarse-grained models that describe the protein backbone motions of the CRP/FNR family transcription factors, CAP of Escherichia coli and GlxR of Corynebacterium glutamicum. The latter we demonstrate as a new exemplar for allostery without conformation change. We observe that binding the first molecule of cAMP ligand is correlated with modulation of the global normal modes and negative cooperativity for binding the second cAMP ligand without a change in mean structure. The theory makes key experimental predictions that are tested through an analysis of variant proteins by structural biology and isothermal calorimetry. Quantifying allostery as a free energy landscape revealed a protein "design space" that identified the inter- and intramolecular regulatory parameters that frame CRP/FNR family allostery. Furthermore, through analyzing CAP variants from diverse species, we demonstrate an evolutionary selection pressure to conserve residues crucial for allosteric control. This finding provides a link between the position of CRP/FNR transcription factors within the allosteric free energy landscapes and evolutionary selection pressures. Our study therefore reveals significant features of the mechanistic basis for allostery. Changes in low-frequency dynamics correlate with allosteric effects on ligand binding without the requirement for a defined spatial pathway. In addition to evolving suitable three-dimensional structures, CRP/FNR family transcription factors have been selected to

  10. Allosteric Inhibition of Factor XIIIa. Non-Saccharide Glycosaminoglycan Mimetics, but Not Glycosaminoglycans, Exhibit Promising Inhibition Profile.

    Directory of Open Access Journals (Sweden)

    Rami A Al-Horani

    Full Text Available Factor XIIIa (FXIIIa is a transglutaminase that catalyzes the last step in the coagulation process. Orthostery is the only approach that has been exploited to design FXIIIa inhibitors. Yet, allosteric inhibition of FXIIIa is a paradigm that may offer a key advantage of controlled inhibition over orthosteric inhibition. Such an approach is likely to lead to novel FXIIIa inhibitors that do not carry bleeding risks. We reasoned that targeting a collection of basic amino acid residues distant from FXIIIa's active site by using sulfated glycosaminoglycans (GAGs or non-saccharide GAG mimetics (NSGMs would lead to the discovery of the first allosteric FXIIIa inhibitors. We tested a library of 22 variably sulfated GAGs and NSGMs against human FXIIIa to discover promising hits. Interestingly, although some GAGs bound to FXIIIa better than NSGMs, no GAG displayed any inhibition. An undecasulfated quercetin analog was found to inhibit FXIIIa with reasonable potency (efficacy of 98%. Michaelis-Menten kinetic studies revealed an allosteric mechanism of inhibition. Fluorescence studies confirmed close correspondence between binding affinity and inhibition potency, as expected for an allosteric process. The inhibitor was reversible and at least 9-fold- and 26-fold selective over two GAG-binding proteins factor Xa (efficacy of 71% and thrombin, respectively, and at least 27-fold selective over a cysteine protease papain. The inhibitor also inhibited the FXIIIa-mediated polymerization of fibrin in vitro. Overall, our work presents the proof-of-principle that FXIIIa can be allosterically modulated by sulfated non-saccharide agents much smaller than GAGs, which should enable the design of selective and safe anticoagulants.

  11. Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors.

    Directory of Open Access Journals (Sweden)

    Thomas L Rodgers

    2013-09-01

    Full Text Available Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distinct site. There is growing evidence that allosteric cooperativity can be communicated by modulation of protein dynamics without conformational change. The mechanisms, however, for communicating dynamic fluctuations between sites are debated. We provide a foundational theory for how allostery can occur as a function of low-frequency dynamics without a change in structure. We have generated coarse-grained models that describe the protein backbone motions of the CRP/FNR family transcription factors, CAP of Escherichia coli and GlxR of Corynebacterium glutamicum. The latter we demonstrate as a new exemplar for allostery without conformation change. We observe that binding the first molecule of cAMP ligand is correlated with modulation of the global normal modes and negative cooperativity for binding the second cAMP ligand without a change in mean structure. The theory makes key experimental predictions that are tested through an analysis of variant proteins by structural biology and isothermal calorimetry. Quantifying allostery as a free energy landscape revealed a protein "design space" that identified the inter- and intramolecular regulatory parameters that frame CRP/FNR family allostery. Furthermore, through analyzing CAP variants from diverse species, we demonstrate an evolutionary selection pressure to conserve residues crucial for allosteric control. This finding provides a link between the position of CRP/FNR transcription factors within the allosteric free energy landscapes and evolutionary selection pressures. Our study therefore reveals significant features of the mechanistic basis for allostery. Changes in low-frequency dynamics correlate with allosteric effects on ligand binding without the requirement for a defined spatial pathway. In addition to evolving suitable three-dimensional structures, CRP/FNR family transcription factors have

  12. An evolution-based strategy for engineering allosteric regulation

    Science.gov (United States)

    Pincus, David; Resnekov, Orna; Reynolds, Kimberly A.

    2017-04-01

    Allosteric regulation provides a way to control protein activity at the time scale of milliseconds to seconds inside the cell. An ability to engineer synthetic allosteric systems would be of practical utility for the development of novel biosensors, creation of synthetic cell signaling pathways, and design of small molecule pharmaceuticals with regulatory impact. To this end, we outline a general approach—termed rational engineering of allostery at conserved hotspots (REACH)—to introduce novel regulation into a protein of interest by exploiting latent allostery that has been hard-wired by evolution into its structure. REACH entails the use of statistical coupling analysis (SCA) to identify ‘allosteric hotspots’ on protein surfaces, the development and implementation of experimental assays to test hotspots for functionality, and a toolkit of allosteric modulators to impinge on endogenous cellular circuitry. REACH can be broadly applied to rewire cellular processes to respond to novel inputs.

  13. The structure of brain glycogen phosphorylase-from allosteric regulation mechanisms to clinical perspectives.

    Science.gov (United States)

    Mathieu, Cécile; Dupret, Jean-Marie; Rodrigues Lima, Fernando

    2017-02-01

    Glycogen phosphorylase (GP) is the key enzyme that regulates glycogen mobilization in cells. GP is a complex allosteric enzyme that comprises a family of three isozymes: muscle GP (mGP), liver GP (lGP), and brain GP (bGP). Although the three isozymes display high similarity and catalyze the same reaction, they differ in their sensitivity to the allosteric activator adenosine monophosphate (AMP). Moreover, inactivating mutations in mGP and lGP have been known to be associated with glycogen storage diseases (McArdle and Hers disease, respectively). The determination, decades ago, of the structure of mGP and lGP have allowed to better understand the allosteric regulation of these two isoforms and the development of specific inhibitors. Despite its important role in brain glycogen metabolism, the structure of the brain GP had remained elusive. Here, we provide an overview of the human brain GP structure and its relationship with the two other members of this key family of the metabolic enzymes. We also summarize how this structure provides valuable information to understand the regulation of bGP and to design specific ligands of potential pharmacological interest. © 2016 Federation of European Biochemical Societies.

  14. PATTERN BASED DETECTION OF POTENTIALLY DRUGGABLE BINDING SITES BY LIGAND SCREENING

    Directory of Open Access Journals (Sweden)

    Uttam Pal

    2018-03-01

    Full Text Available This article describes an innovative way of finding the potentially druggable sites on a target protein, which can be used for orthosteric and allosteric lead detection in a single virtual screening setup. Druggability estimation for an alternate binding site other than the canonical ligand-binding pocket of an enzyme is rewarding for several inherent benefits. Allostery is a direct and efficient way of regulating biomacromolecule function. The allosteric modulators can fine-tune protein mechanics. Besides, allosteric sites are evolutionarily less conserved/more diverse even in very similarly related proteins, thus, provides high degree of specificity in targeting a particular protein. Therefore, targeting of allosteric sites is gaining attention as an emerging strategy in rational drug design. However, the experimental approaches provide a limited degree of characterization of new allosteric sites. Computational approaches are useful to analyze and select potential allosteric sites for drug discovery. Here, the use of molecular docking, which has become an integral part of the drug discovery process, has been discussed to predict the druggability of novel allosteric sites as well as the active site on target proteins by ligand screening. Genetic algorithm was used for docking and the whole protein was placed in the search space. For each ligand in the library of small molecules, the genetic algorithm was run for multiple times to populate all the druggable sites in the target protein, which was then translated into two dimensional density maps or “patterns”. High density clusters were observed for lead like molecules in these pattern diagrams. Each cluster in such a pattern diagram indicated a plausible binding site and the density gave its druggability score in terms of weighted probabilities. The patterns were filtered to find the leads for each of the druggable sites on the target protein. Such a novel pattern based analysis of the

  15. Allosteric modulation of Ras and the PI3K/AKT/mTOR pathway: emerging therapeutic opportunities

    Science.gov (United States)

    Hubbard, Paul A.; Moody, Colleen L.; Murali, Ramachandran

    2014-01-01

    GTPases and kinases are two predominant signaling modules that regulate cell fate. Dysregulation of Ras, a GTPase, and the three eponymous kinases that form key nodes of the associated phosphatidylinositol 4,5-bisphosphate 3-kinase (PI3K)/AKT/mTOR pathway have been implicated in many cancers, including pancreatic cancer, a disease noted for its current lack of effective therapeutics. The K-Ras isoform of Ras is mutated in over 90% of pancreatic ductal adenocarcinomas (PDAC) and there is growing evidence linking aberrant PI3K/AKT/mTOR pathway activity to PDAC. Although these observations suggest that targeting one of these nodes might lead to more effective treatment options for patients with pancreatic and other cancers, the complex regulatory mechanisms and the number of sequence-conserved isoforms of these proteins have been viewed as significant barriers in drug development. Emerging insights into the allosteric regulatory mechanisms of these proteins suggest novel opportunities for development of selective allosteric inhibitors with fragment-based drug discovery (FBDD) helping make significant inroads. The fact that allosteric inhibitors of Ras and AKT are currently in pre-clinical development lends support to this approach. In this article, we will focus on the recent advances and merits of developing allosteric drugs targeting these two inter-related signaling pathways. PMID:25566081

  16. Selective effects of an octopus toxin on action potentials

    Science.gov (United States)

    Dulhunty, Angela; Gage, Peter W.

    1971-01-01

    1. A lethal, water soluble toxin (Maculotoxin, MTX) with a molecular weight less than 540, can be extracted from the salivary glands of an octopus (Hapalochlaena maculosa). 2. MTX blocks action potentials in sartorius muscle fibres of toads without affecting the membrane potential. Delayed rectification is not inhibited by the toxin. 3. At low concentrations (10-6-10-5 g/ml.) MTX blocks action potentials only after a certain number have been elicited. The number of action potentials, which can be defined accurately, depends on the concentration of MTX and the concentration of sodium ions in the extracellular solution. 4. The toxin has no post-synaptic effect at the neuromuscular junction and it is concluded that it blocks neuromuscular transmission by inhibiting action potentials in motor nerve terminals. PMID:4330930

  17. Potential of marker-assisted selection for Tobacco mosaic ...

    African Journals Online (AJOL)

    Tobacco mosaic tobamovirus (TMV) is one of the most destructive virus threatening worldwide tobacco production. Use of host resistance is the best method of control. The N-gene was introgressed into tobacco from Nicotiana glutinosa to confer hypersensitive resistance to TMV. Phenotypic selection of TMV resistant ...

  18. Protection from potential exposures: application to selected radiation sources

    International Nuclear Information System (INIS)

    1997-09-01

    This ICRP Report begins with the general principles of radiation protection in the case of potential exposures, followed by special issues in application and compliance with regulatory aims. The rest of the report uses event trees or fault trees to derive the logical structure of six scenarios of potential exposure, i.e. two irradiators, a large research accelerator, an accelerator for industrial isotope production, an industrial radiography device using a mobile source of radiation, and finally a medical gamma radiotherapy device. (UK)

  19. Allosteric mechanism controls traffic in the chaperone/usher pathway.

    Science.gov (United States)

    Di Yu, Xiao; Dubnovitsky, Anatoly; Pudney, Alex F; Macintyre, Sheila; Knight, Stefan D; Zavialov, Anton V

    2012-11-07

    Many virulence organelles of Gram-negative bacterial pathogens are assembled via the chaperone/usher pathway. The chaperone transports organelle subunits across the periplasm to the outer membrane usher, where they are released and incorporated into growing fibers. Here, we elucidate the mechanism of the usher-targeting step in assembly of the Yersinia pestis F1 capsule at the atomic level. The usher interacts almost exclusively with the chaperone in the chaperone:subunit complex. In free chaperone, a pair of conserved proline residues at the beginning of the subunit-binding loop form a "proline lock" that occludes the usher-binding surface and blocks usher binding. Binding of the subunit to the chaperone rotates the proline lock away from the usher-binding surface, allowing the chaperone-subunit complex to bind to the usher. We show that the proline lock exists in other chaperone/usher systems and represents a general allosteric mechanism for selective targeting of chaperone:subunit complexes to the usher and for release and recycling of the free chaperone. Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. Allosteric conformational barcodes direct signaling in the cell.

    Science.gov (United States)

    Nussinov, Ruth; Ma, Buyong; Tsai, Chung-Jung; Csermely, Peter

    2013-09-03

    The cellular network is highly interconnected. Pathways merge and diverge. They proceed through shared proteins and may change directions. How are cellular pathways controlled and their directions decided, coded, and read? These questions become particularly acute when we consider that a small number of pathways, such as signaling pathways that regulate cell fates, cell proliferation, and cell death in development, are extensively exploited. This review focuses on these signaling questions from the structural standpoint and discusses the literature in this light. All co-occurring allosteric events (including posttranslational modifications, pathogen binding, and gain-of-function mutations) collectively tag the protein functional site with a unique barcode. The barcode shape is read by an interacting molecule, which transmits the signal. A conformational barcode provides an intracellular address label, which selectively favors binding to one partner and quenches binding to others, and, in this way, determines the pathway direction, and, eventually, the cell's response and fate. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. A study of algal biomass potential in selected Canadian regions.

    Energy Technology Data Exchange (ETDEWEB)

    Passell, Howard David; Roach, Jesse Dillon; Klise, Geoffrey T.

    2011-11-01

    A dynamic assessment model has been developed for evaluating the potential algal biomass and extracted biocrude productivity and costs, using nutrient and water resources available from waste streams in four regions of Canada (western British Columbia, Alberta oil fields, southern Ontario, and Nova Scotia). The purpose of this model is to help identify optimal locations in Canada for algae cultivation and biofuel production. The model uses spatially referenced data across the four regions for nitrogen and phosphorous loads in municipal wastewaters, and CO{sub 2} in exhaust streams from a variety of large industrial sources. Other data inputs include land cover, and solar insolation. Model users can develop estimates of resource potential by manipulating model assumptions in a graphic user interface, and updated results are viewed in real time. Resource potential by location can be viewed in terms of biomass production potential, potential CO{sub 2} fixed, biocrude production potential, and area required. The cost of producing algal biomass can be estimated using an approximation of the distance to move CO{sub 2} and water to the desired land parcel and an estimation of capital and operating costs for a theoretical open pond facility. Preliminary results suggest that in most cases, the CO{sub 2} resource is plentiful compared to other necessary nutrients (especially nitrogen), and that siting and prospects for successful large-scale algae cultivation efforts in Canada will be driven by availability of those other nutrients and the efficiency with which they can be used and re-used. Cost curves based on optimal possible siting of an open pond system are shown. The cost of energy for maintaining optimal growth temperatures is not considered in this effort, and additional research in this area, which has not been well studied at these latitudes, will be important in refining the costs of algal biomass production. The model will be used by NRC-IMB Canada to identify

  2. Allosteric regulation of rhomboid intramembrane proteolysis.

    Science.gov (United States)

    Arutyunova, Elena; Panwar, Pankaj; Skiba, Pauline M; Gale, Nicola; Mak, Michelle W; Lemieux, M Joanne

    2014-09-01

    Proteolysis within the lipid bilayer is poorly understood, in particular the regulation of substrate cleavage. Rhomboids are a family of ubiquitous intramembrane serine proteases that harbour a buried active site and are known to cleave transmembrane substrates with broad specificity. In vitro gel and Förster resonance energy transfer (FRET)-based kinetic assays were developed to analyse cleavage of the transmembrane substrate psTatA (TatA from Providencia stuartii). We demonstrate significant differences in catalytic efficiency (kcat/K0.5) values for transmembrane substrate psTatA (TatA from Providencia stuartii) cleavage for three rhomboids: AarA from P. stuartii, ecGlpG from Escherichia coli and hiGlpG from Haemophilus influenzae demonstrating that rhomboids specifically recognize this substrate. Furthermore, binding of psTatA occurs with positive cooperativity. Competitive binding studies reveal an exosite-mediated mode of substrate binding, indicating allostery plays a role in substrate catalysis. We reveal that exosite formation is dependent on the oligomeric state of rhomboids, and when dimers are dissociated, allosteric substrate activation is not observed. We present a novel mechanism for specific substrate cleavage involving several dynamic processes including positive cooperativity and homotropic allostery for this interesting class of intramembrane proteases. © 2014 The Authors.

  3. Potential application of palladium nanoparticles as selective recyclable hydrogenation catalysts

    International Nuclear Information System (INIS)

    Mukherjee, DebKumar

    2008-01-01

    The search for more efficient catalytic systems that might combine the advantages of both homogeneous (catalyst modulation) and heterogeneous (catalyst recycling) catalysis is one of the most exciting challenges of modern chemistry. More recently with the advances of nanochemistry, it has been possible to prepare soluble analogues of heterogeneous catalysts. These nanoparticles are generally stabilized against aggregation into larger particles by electrostatic or steric protection. Herein we demonstrate the use of room temperature ionic liquid for the stabilization of palladium nanoparticles that are recyclable catalysts for the hydrogenation of carbon-carbon double bonds and application of these catalysts to the selective hydrogenation of internal or terminal C=C bonds in unsaturated primary alcohols. The particles suspended in room temperature ionic liquid show no metal aggregation or loss of catalytic activity even on prolonged use

  4. Potential Study of Water Extraction from Selected Plants

    Directory of Open Access Journals (Sweden)

    Musa S.

    2017-01-01

    Full Text Available Water is absorbed by the roots of a plant and transported subsequently as a liquid to all parts of the plant before being released into the atmosphere as transpiration. In this study, seven(7selected plant species collected from urban, rural and forested areas were studied and characterized. The water was collected using transparent plastic bag that being tied to the tree branches. Then, the vapouris water trapped inside the plastic bag and through the condensation process, it become water droplets. Water quality parameters such as temperature, pH value, DO, turbidity, colour, magnesium, calcium, nitrate and chloride were analyzed. The analysis was compared to drinking water quality standard set by the Ministry of Health Malaysia. Based on the results, it shows that banana leaf has a higher rate of water extraction compared to others. Thus, the plant can be categorised as a helpful guide for emergency use of water or as an alternative source to survival.

  5. Chemogenomic discovery of allosteric antagonists at the GPRC6A receptor

    DEFF Research Database (Denmark)

    Gloriam, David E.; Wellendorph, Petrine; Johansen, Lars Dan

    2011-01-01

    and pharmacological character: (1) chemogenomic lead identification through the first, to our knowledge, ligand inference between two different GPCR families, Families A and C; and (2) the discovery of the most selective GPRC6A allosteric antagonists discovered to date. The unprecedented inference of...... pharmacological activity across GPCR families provides proof-of-concept for in silico approaches against Family C targets based on Family A templates, greatly expanding the prospects of successful drug design and discovery. The antagonists were tested against a panel of seven Family A and C G protein-coupled receptors...

  6. Conopeptide ρ-TIA defines a new allosteric site on the extracellular surface of the α1B-adrenoceptor.

    Science.gov (United States)

    Ragnarsson, Lotten; Wang, Ching-I Anderson; Andersson, Åsa; Fajarningsih, Dewi; Monks, Thea; Brust, Andreas; Rosengren, K Johan; Lewis, Richard J

    2013-01-18

    The G protein-coupled receptor (GPCR) superfamily is an important drug target that includes over 1000 membrane receptors that functionally couple extracellular stimuli to intracellular effectors. Despite the potential of extracellular surface (ECS) residues in GPCRs to interact with subtype-specific allosteric modulators, few ECS pharmacophores for class A receptors have been identified. Using the turkey β(1)-adrenergic receptor crystal structure, we modeled the α(1B)-adrenoceptor (α(1B)-AR) to help identify the allosteric site for ρ-conopeptide TIA, an inverse agonist at this receptor. Combining mutational radioligand binding and inositol 1-phosphate signaling studies, together with molecular docking simulations using a refined NMR structure of ρ-TIA, we identified 14 residues on the ECS of the α(1B)-AR that influenced ρ-TIA binding. Double mutant cycle analysis and docking confirmed that ρ-TIA binding was dominated by a salt bridge and cation-π between Arg-4-ρ-TIA and Asp-327 and Phe-330, respectively, and a T-stacking-π interaction between Trp-3-ρ-TIA and Phe-330. Water-bridging hydrogen bonds between Asn-2-ρ-TIA and Val-197, Trp-3-ρ-TIA and Ser-318, and the positively charged N terminus and Glu-186, were also identified. These interactions reveal that peptide binding to the ECS on transmembrane helix 6 (TMH6) and TMH7 at the base of extracellular loop 3 (ECL3) is sufficient to allosterically inhibit agonist signaling at a GPCR. The ligand-accessible ECS residues identified provide the first view of an allosteric inhibitor pharmacophore for α(1)-adrenoceptors and mechanistic insight and a new set of structural constraints for the design of allosteric antagonists at related GPCRs.

  7. Selection of materials with potential in sensible thermal energy storage

    International Nuclear Information System (INIS)

    Fernandez, A.I.; Martinez, M.; Segarra, M.; Martorell, I.; Cabeza, L.F.

    2010-01-01

    Thermal energy storage is a technology under investigation since the early 1970s. Since then, numerous new applications have been found and much work has been done to bring this technology to the market. Nevertheless, the materials used either for latent or for sensible storage were mostly investigated 30 years ago, and the research has lead to improvement in their performance under different conditions of applications. In those years a significant number of new materials were developed in many fields other than storage and energy, but a great effort to characterize and classify these materials was done. Taking into account the fact that thousands of materials are known and a large number of new materials are developed every year, the authors use the methodology for materials selection developed by Prof. Ashby to give an overview of other materials suitable to be used in thermal energy storage. Sensible heat storage at temperatures between 150 and 200 C is defined as a case study and two different scenarios were considered: long term sensible heat storage and short term sensible heat storage. (author)

  8. [Potential selection bias in telephone surveys: landline and mobile phones].

    Science.gov (United States)

    Garcia-Continente, Xavier; Pérez-Giménez, Anna; López, María José; Nebot, Manel

    2014-01-01

    The increasing use of mobile phones in the last decade has decreased landline telephone coverage in Spanish households. This study aimed to analyze sociodemographic characteristics and health indicators by type of telephone service (mobile phone vs. landline or landline and mobile phone). Two telephone surveys were conducted in Spanish samples (February 2010 and February 2011). Multivariate logistic regression analyses were performed to analyze differences in the main sociodemographic characteristics and health indicators according to the type of telephone service available in Spanish households. We obtained 2027 valid responses (1627 landline telephones and 400 mobile phones). Persons contacted through a mobile phone were more likely to be a foreigner, to belong to the manual social class, to have a lower educational level, and to be a smoker than those contacted through a landline telephone. The profile of the population that has only a mobile phone differs from that with a landline telephone. Therefore, telephone surveys that exclude mobile phones could show a selection bias. Copyright © 2013 SESPAS. Published by Elsevier Espana. All rights reserved.

  9. Allosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Ying-Nan P.; LaMarche, Matthew J.; Chan, Ho Man; Fekkes, Peter; Garcia-Fortanet, Jorge; Acker, Michael G.; Antonakos, Brandon; Chen, Christine Hiu-Tung; Chen, Zhouliang; Cooke, Vesselina G.; Dobson, Jason R.; Deng, Zhan; Fei, Feng; Firestone, Brant; Fodor, Michelle; Fridrich, Cary; Gao, Hui; Grunenfelder, Denise; Hao, Huai-Xiang; Jacob, Jaison; Ho, Samuel; Hsiao, Kathy; Kang, Zhao B.; Karki, Rajesh; Kato, Mitsunori; Larrow, Jay; La Bonte, Laura R.; Lenoir, Francois; Liu, Gang; Liu, Shumei; Majumdar, Dyuti; Meyer, Matthew J.; Palermo, Mark; Perez, Lawrence; Pu, Minying; Price, Edmund; Quinn, Christopher; Shakya, Subarna; Shultz, Michael D.; Slisz, Joanna; Venkatesan, Kavitha; Wang, Ping; Warmuth, Markus; Williams, Sarah; Yang, Guizhi; Yuan, Jing; Zhang, Ji-Hu; Zhu, Ping; Ramsey, Timothy; Keen, Nicholas J.; Sellers, William R.; Stams, Travis; Fortin , Pascal D. (Novartis)

    2016-06-29

    The non-receptor protein tyrosine phosphatase SHP2, encoded by PTPN11, has an important role in signal transduction downstream of growth factor receptor signalling and was the first reported oncogenic tyrosine phosphatase1. Activating mutations of SHP2 have been associated with developmental pathologies such as Noonan syndrome and are found in multiple cancer types, including leukaemia, lung and breast cancer and neuroblastoma1, 2, 3, 4, 5. SHP2 is ubiquitously expressed and regulates cell survival and proliferation primarily through activation of the RAS–ERK signalling pathway2, 3. It is also a key mediator of the programmed cell death 1 (PD-1) and B- and T-lymphocyte attenuator (BTLA) immune checkpoint pathways6, 7. Reduction of SHP2 activity suppresses tumour cell growth and is a potential target of cancer therapy8, 9. Here we report the discovery of a highly potent (IC50 = 0.071 μM), selective and orally bioavailable small-molecule SHP2 inhibitor, SHP099, that stabilizes SHP2 in an auto-inhibited conformation. SHP099 concurrently binds to the interface of the N-terminal SH2, C-terminal SH2, and protein tyrosine phosphatase domains, thus inhibiting SHP2 activity through an allosteric mechanism. SHP099 suppresses RAS–ERK signalling to inhibit the proliferation of receptor-tyrosine-kinase-driven human cancer cells in vitro and is efficacious in mouse tumour xenograft models. Together, these data demonstrate that pharmacological inhibition of SHP2 is a valid therapeutic approach for the treatment of cancers.

  10. Antioxidant Potential of Selected Korean Edible Plant Extracts

    Directory of Open Access Journals (Sweden)

    Yaejin Woo

    2017-01-01

    Full Text Available This study aimed to evaluate the antioxidant activity of various plant extracts. A total of 94 kinds of edible plant extracts obtained from the Korea Plant Extract Bank were screened for cytotoxicity, following which the total phenolic content of 24 shortlisted extracts was determined. Of these, extracts from three plants, namely, Castanea crenata (CC leaf, Camellia japonica (CJ fruit, and Viburnum dilatatum (VD leaf, were examined for antioxidant capabilities by measuring radical scavenging activity, ferric reducing/antioxidant power, and lipid peroxidation inhibitory activity. In addition, cellular antioxidant activities of the three extracts were assessed by a cell-based dichlorofluorescein assay and antioxidant response element (ARE reporter activity assay. The results demonstrated that all three extracts concentration-dependently scavenged free radicals, inhibited lipid peroxidation, reduced the cellular level of reactive oxygen species, and increased ARE-luciferase activity, indicating antioxidant enzyme-inducing potential. In particular, CJ extract showed significantly greater antioxidative activity and antimigratory effect in a breast cancer cell line compared to CC and VD extracts. Hence, CJ extract deserves further study for its in vivo functionality or biologically active constituents.

  11. Pyrometallurgical slags as a potential source of selected metals recovery

    Directory of Open Access Journals (Sweden)

    K. Nowińska

    2014-10-01

    Full Text Available Complex analysis of concentration and form of occurrence such metals as Zn, Pb, Fe and Cu in slags formed during a current zinc production in the Imperial Smelting Process (ISP is a possible basis for development of optimal recovery technology. For this purpose studies of slags from the current production of the Shaft Furnace Unit and of the Lead Refining of the “Miasteczko Śląskie” Zinc Smelting Plant were carried out. The studies results show that slags includes high concentrations of: Zn from 0,064 % to 1,680 %, Pb from 10,56 % to 50,71 %, Fe from 0,015 % to 2,576 %, Cu from 7,48 % to 64,95 %, and change in a broad range. This slags show significant heterogeneity, caused by intermetallic phases (Zn - Pb, Cu - Zn, Cu - Pb formed on the surface thereof. It is so possible that slag can be a potential source of this metals recovery.

  12. Trypanosomosis: Potential driver of selection in African cattle

    Directory of Open Access Journals (Sweden)

    Anamarija eSmetko

    2015-04-01

    Full Text Available Trypanosomosis is a serious cause of reduction in productivity of cattle in tsetse-fly infested areas. Baoule and other local Taurine cattle breeds in Burkina Faso are trypanotolerant. Zebuine cattle, which are also kept there are susceptible to trypanosomosis but bigger in body size. Farmers have continuously been intercrossing Baoule and Zebu animals to increase production and disease tolerance. The aim of this study was to compare levels of zebuine and taurine admixture in genomic regions potentially involved in trypanotolerance with background admixture of composites to identify differences in allelic frequencies of tolerant and non tolerant animals. The study was conducted on 214 animals (90 Baoule, 90 Zebu and 34 composites, genotyped with 25 microsatellites across the genome and with 155 SNPs in 23 candidate regions. Degrees of admixture of composites were analyzed for microsatellite and SNP data separately. Average Baoule admixture based on microsatellites across the genomes of the Baoule-Zebu composites was 0.31, which was smaller than the average Baoule admixture in the trypanosomosis candidate regions of 0.37 (P=0.15. Fixation index FST measured in the overall genome based on microsatellites or with SNPs from candidate regions indicates strong differentiation between breeds. Nine out of 23 regions had FST ≥ 0.20 calculated from haplotypes or individual SNPs. The levels of admixture were significantly different from background admixture, as revealed by microsatellite data, for six out of the nine regions. Five out of the six regions showed an excess of Baoule ancestry. Information about best levels of breed composition would be useful for future breeding activities, aiming at trypanotolerant animals with higher productive capacity.

  13. Structural insight to mutation effects uncover a common allosteric site in class C GPCRs

    DEFF Research Database (Denmark)

    Harpsøe, Kasper; Boesgaard, Michael W; Munk, Christian

    2017-01-01

    MOTIVATION: Class C G protein-coupled receptors (GPCRs) regulate important physiological functions and allosteric modulators binding to the transmembrane domain constitute an attractive and, due to a lack of structural insight, a virtually unexplored potential for therapeutics and the food industry....... Combining pharmacological site-directed mutagenesis data with the recent class C GPCR experimental structures will provide a foundation for rational design of new therapeutics. RESULTS: We uncover one common site for both positive and negative modulators with different amino acid layouts that can...

  14. Substituted 3-Benzylcoumarins as Allosteric MEK1 Inhibitors: Design, Synthesis and Biological Evaluation as Antiviral Agents

    Directory of Open Access Journals (Sweden)

    Ping Xu

    2013-05-01

    Full Text Available In order to find novel antiviral agents, a series of allosteric MEK1 inhibitors were designed and synthesized. Based on docking results, multiple optimizations were made on the coumarin scaffold. Some of the derivatives showed excellent MEK1 binding affinity in the appropriate enzymatic assays and displayed obvious inhibitory effects on the ERK pathway in a cellular assay. These compounds also significantly inhibited virus (EV71 replication in HEK293 and RD cells. Several compounds showed potential as agents for the treatment of viral infective diseases, with the most potent compound 18 showing an IC50 value of 54.57 nM in the MEK1 binding assay.

  15. Convergent transmission of RNAi guide-target mismatch information across Argonaute internal allosteric network.

    Science.gov (United States)

    Joseph, Thomas T; Osman, Roman

    2012-01-01

    In RNA interference, a guide strand derived from a short dsRNA such as a microRNA (miRNA) is loaded into Argonaute, the central protein in the RNA Induced Silencing Complex (RISC) that silences messenger RNAs on a sequence-specific basis. The positions of any mismatched base pairs in an miRNA determine which Argonaute subtype is used. Subsequently, the Argonaute-guide complex binds and silences complementary target mRNAs; certain Argonautes cleave the target. Mismatches between guide strand and the target mRNA decrease cleavage efficiency. Thus, loading and silencing both require that signals about the presence of a mismatched base pair are communicated from the mismatch site to effector sites. These effector sites include the active site, to prevent target cleavage; the binding groove, to modify nucleic acid binding affinity; and surface allosteric sites, to control recruitment of additional proteins to form the RISC. To examine how such signals may be propagated, we analyzed the network of internal allosteric pathways in Argonaute exhibited through correlations of residue-residue interactions. The emerging network can be described as a set of pathways emanating from the core of the protein near the active site, distributed into the bulk of the protein, and converging upon a distributed cluster of surface residues. Nucleotides in the guide strand "seed region" have a stronger relationship with the protein than other nucleotides, concordant with their importance in sequence selectivity. Finally, any of several seed region guide-target mismatches cause certain Argonaute residues to have modified correlations with the rest of the protein. This arises from the aggregation of relatively small interaction correlation changes distributed across a large subset of residues. These residues are in effector sites: the active site, binding groove, and surface, implying that direct functional consequences of guide-target mismatches are mediated through the cumulative effects of

  16. Convergent transmission of RNAi guide-target mismatch information across Argonaute internal allosteric network.

    Directory of Open Access Journals (Sweden)

    Thomas T Joseph

    Full Text Available In RNA interference, a guide strand derived from a short dsRNA such as a microRNA (miRNA is loaded into Argonaute, the central protein in the RNA Induced Silencing Complex (RISC that silences messenger RNAs on a sequence-specific basis. The positions of any mismatched base pairs in an miRNA determine which Argonaute subtype is used. Subsequently, the Argonaute-guide complex binds and silences complementary target mRNAs; certain Argonautes cleave the target. Mismatches between guide strand and the target mRNA decrease cleavage efficiency. Thus, loading and silencing both require that signals about the presence of a mismatched base pair are communicated from the mismatch site to effector sites. These effector sites include the active site, to prevent target cleavage; the binding groove, to modify nucleic acid binding affinity; and surface allosteric sites, to control recruitment of additional proteins to form the RISC. To examine how such signals may be propagated, we analyzed the network of internal allosteric pathways in Argonaute exhibited through correlations of residue-residue interactions. The emerging network can be described as a set of pathways emanating from the core of the protein near the active site, distributed into the bulk of the protein, and converging upon a distributed cluster of surface residues. Nucleotides in the guide strand "seed region" have a stronger relationship with the protein than other nucleotides, concordant with their importance in sequence selectivity. Finally, any of several seed region guide-target mismatches cause certain Argonaute residues to have modified correlations with the rest of the protein. This arises from the aggregation of relatively small interaction correlation changes distributed across a large subset of residues. These residues are in effector sites: the active site, binding groove, and surface, implying that direct functional consequences of guide-target mismatches are mediated through the

  17. Overlapping binding site for the endogenous agonist, small-molecule agonists, and ago-allosteric modulators on the ghrelin receptor

    DEFF Research Database (Denmark)

    Holst, Birgitte; Frimurer, Thomas M; Mokrosinski, Jacek

    2008-01-01

    A library of robust ghrelin receptor mutants with single substitutions at 22 positions in the main ligand-binding pocket was employed to map binding sites for six different agonists: two peptides (the 28-amino-acid octanoylated endogenous ligand ghrelin and the hexapeptide growth hormone......, and PheVI:23 on the opposing face of transmembrane domain (TM) VI. Each of the agonists was also affected selectively by specific mutations. The mutational map of the ability of L-692,429 and GHRP-6 to act as allosteric modulators by increasing ghrelin's maximal efficacy overlapped with the common....... It is concluded that although each of the ligands in addition exploits other parts of the receptor, a large, common binding site for both small-molecule agonists--including ago-allosteric modulators--and the endogenous agonist is found on the opposing faces of TM-III and -VI of the ghrelin receptor....

  18. The allosteric communication pathways in KIX domain of CBP

    Science.gov (United States)

    Palazzesi, Ferruccio; Barducci, Alessandro; Tollinger, Martin; Parrinello, Michele

    2013-01-01

    Allosteric regulation plays an important role in a myriad of biomacromolecular processes. Specifically, in a protein, the process of allostery refers to the transmission of a local perturbation, such as ligand binding, to a distant site. Decades after the discovery of this phenomenon, models built on static images of proteins are being reconsidered with the knowledge that protein dynamics plays an important role in its function. Molecular dynamics simulations are a valuable tool for studying complex biomolecular systems, providing an atomistic description of their structure and dynamics. Unfortunately, their predictive power has been limited by the complexity of the biomolecule free-energy surface and by the length of the allosteric timescale (in the order of milliseconds). In this work, we are able to probe the origins of the allosteric changes that transcription factor mixed lineage leukemia (MLL) causes to the interactions of KIX domain of CREB-binding protein (CBP) with phosphorylated kinase inducible domain (pKID), by combing all-atom molecular dynamics with enhanced sampling methods recently developed in our group. We discuss our results in relation to previous NMR studies. We also develop a general simulations protocol to study allosteric phenomena and many other biological processes that occur in the micro/milliseconds timescale. PMID:23940332

  19. Extracellular loop 2 of the free Fatty Acid receptor 2 mediates allosterism of a phenylacetamide ago-allosteric modulator

    DEFF Research Database (Denmark)

    Smith, Nicola J; Ward, Richard J; Stoddart, Leigh A

    2011-01-01

    Allosteric agonists are powerful tools for exploring the pharmacology of closely related G protein-coupled receptors that have nonselective endogenous ligands, such as the short chain fatty acids at free fatty acid receptors 2 and 3 (FFA2/GPR43 and FFA3/GPR41, respectively). We explored the molec...

  20. Event-related potentials during visual selective attention in children of alcoholics.

    NARCIS (Netherlands)

    van der Stelt, O.; Gunning, W.B.; Snel, J.; Kok, A.

    1998-01-01

    Event-related potentials (ERPs) were recorded from 50 7-18 yr old children of alcoholics (COAs) and 50 age- and sex-matched control children while they performed a visual selective attention task. The task was to attend selectively to stimuli with a specified color (red or blue) in an attempt to

  1. Selecting for Creativity and Innovation Potential: Implications for Practice in Healthcare Education

    Science.gov (United States)

    Patterson, Fiona; Zibarras, Lara Dawn

    2017-01-01

    The ability to innovate is an important requirement in many organisations. Despite this pressing need, few selection systems in healthcare focus on identifying the potential for creativity and innovation and so this area has been vastly under-researched. As a first step towards understanding how we might select for creativity and innovation, this…

  2. Do extra-group fertilizations increase the potential for sexual selection in male mammals?

    Science.gov (United States)

    Isvaran, Kavita; Sankaran, Sumithra

    2017-10-01

    Fertilizations by males outside the social breeding group (extra-group paternity, EGP) are widespread in birds and mammals. EGP is generally proposed to increase male reproductive skew and thereby increase the potential for sexual selection, but the generality of this relationship is unclear. We extracted data from 27 mammals in seven orders and used phylogenetic comparative methods to investigate the influence of EGP and social mating system on measures of inequality in male fertilization success, which are indices of the potential for sexual selection. We find that EGP and social mating system can predict the potential for sexual selection in mammalian populations, but only when considered jointly and not individually. EGP appears to increase the potential for sexual selection but only when the degree of social polygyny is relatively low. When social polygyny is high, EGP appears to result in a more uniform distribution of reproduction and a decrease in the potential for sexual selection. A possible explanation to be investigated is that the phenotype of extra-group fathers differs systematically across social mating systems. Our findings have implications for the use of EGP and social mating system as indices of sexual selection in comparative analyses of trait evolution under sexual selection. © 2017 The Author(s).

  3. [Pharmacological characteristics of drugs targeted on calcium-sensing receptor.-properties of cinacalcet hydrochloride as allosteric modulator].

    Science.gov (United States)

    Nagano, Nobuo; Tsutsui, Takaaki

    2016-06-01

    Calcimimetics act as positive allosteric modulators of the calcium-sensing receptor (CaSR), thereby decreasing parathyroid hormone (PTH) secretion from the parathyroid glands. On the other hand, negative allosteric modulators of the CaSR with stimulatory effect on PTH secretion are termed calcilytics. The calcimimetic cinacalcet hydrochloride (cinacalcet) is the world's first allosteric modulator of G protein-coupled receptor to enter the clinical market. Cinacalcet just tunes the physiological effects of Ca(2+), an endogenous ligand, therefore, shows high selectivity and low side effects. Calcimimetics also increase cell surface CaSR expression by acting as pharmacological chaperones (pharmacoperones). It is considered that the cinacalcet-induced upper gastrointestinal problems are resulted from enhanced physiological responses to Ca(2+) and amino acids via increased sensitivity of digestive tract CaSR by cinacalcet. While clinical developments of calcilytics for osteoporosis were unfortunately halted or terminated due to paucity of efficacy, it is expected that calcilytics may be useful for the treatment of patients with activating CaSR mutations, asthma, and idiopathic pulmonary artery hypertension.

  4. Piracetam Defines a New Binding Site for Allosteric Modulators of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptors§

    Science.gov (United States)

    Ahmed, Ahmed H.; Oswald, Robert E.

    2010-01-01

    Glutamate receptors are the most prevalent excitatory neurotransmitter receptors in the vertebrate central nervous system and are important potential drug targets for cognitive enhancement and the treatment of schizophrenia. Allosteric modulators of AMPA receptors promote dimerization by binding to a dimer interface and reducing desensitization and deactivation. The pyrrolidine allosteric modulators, piracetam and aniracetam, were among the first of this class of drugs to be discovered. We have determined the structure of the ligand binding domain of the AMPA receptor subtypes GluA2 and GluA3 with piracetam and a corresponding structure of GluA3 with aniracetam. Both drugs bind to both GluA2 and GluA3 in a very similar manner, suggesting little subunit specificity. However, the binding sites for piracetam and aniracetam differ considerably. Aniracetam binds to a symmetrical site at the center of the dimer interface. Piracetam binds to multiple sites along the dimer interface with low occupation, one of which is a unique binding site for potential allosteric modulators. This new site may be of importance in the design of new allosteric regulators. PMID:20163115

  5. Piracetam defines a new binding site for allosteric modulators of alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptors.

    Science.gov (United States)

    Ahmed, Ahmed H; Oswald, Robert E

    2010-03-11

    Glutamate receptors are the most prevalent excitatory neurotransmitter receptors in the vertebrate central nervous system and are important potential drug targets for cognitive enhancement and the treatment of schizophrenia. Allosteric modulators of AMPA receptors promote dimerization by binding to a dimer interface and reducing desensitization and deactivation. The pyrrolidine allosteric modulators, piracetam and aniracetam, were among the first of this class of drugs to be discovered. We have determined the structure of the ligand binding domain of the AMPA receptor subtypes GluA2 and GluA3 with piracetam and a corresponding structure of GluA3 with aniracetam. Both drugs bind to GluA2 and GluA3 in a very similar manner, suggesting little subunit specificity. However, the binding sites for piracetam and aniracetam differ considerably. Aniracetam binds to a symmetrical site at the center of the dimer interface. Piracetam binds to multiple sites along the dimer interface with low occupation, one of which is a unique binding site for potential allosteric modulators. This new site may be of importance in the design of new allosteric regulators.

  6. Allosteric mechanism of action of the therapeutic anti-IgE antibody omalizumab.

    Science.gov (United States)

    Davies, Anna M; Allan, Elizabeth G; Keeble, Anthony H; Delgado, Jean; Cossins, Benjamin P; Mitropoulou, Alkistis N; Pang, Marie O Y; Ceska, Tom; Beavil, Andrew J; Craggs, Graham; Westwood, Marta; Henry, Alistair J; McDonnell, James M; Sutton, Brian J

    2017-06-16

    Immunoglobulin E and its interactions with receptors FcϵRI and CD23 play a central role in allergic disease. Omalizumab, a clinically approved therapeutic antibody, inhibits the interaction between IgE and FcϵRI, preventing mast cell and basophil activation, and blocks IgE binding to CD23 on B cells and antigen-presenting cells. We solved the crystal structure of the complex between an omalizumab-derived Fab and IgE-Fc, with one Fab bound to each Cϵ3 domain. Free IgE-Fc adopts an acutely bent structure, but in the complex it is only partially bent, with large-scale conformational changes in the Cϵ3 domains that inhibit the interaction with FcϵRI. CD23 binding is inhibited sterically due to overlapping binding sites on each Cϵ3 domain. Studies of omalizumab Fab binding in solution demonstrate the allosteric basis for FcϵRI inhibition and, together with the structure, reveal how omalizumab may accelerate dissociation of receptor-bound IgE from FcϵRI, exploiting the intrinsic flexibility and allosteric potential of IgE. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Partial mGlu₅ Negative Allosteric Modulators Attenuate Cocaine-Mediated Behaviors and Lack Psychotomimetic-Like Effects.

    Science.gov (United States)

    Gould, Robert W; Amato, Russell J; Bubser, Michael; Joffe, Max E; Nedelcovych, Michael T; Thompson, Analisa D; Nickols, Hilary H; Yuh, Johannes P; Zhan, Xiaoyan; Felts, Andrew S; Rodriguez, Alice L; Morrison, Ryan D; Byers, Frank W; Rook, Jerri M; Daniels, John S; Niswender, Colleen M; Conn, P Jeffrey; Emmitte, Kyle A; Lindsley, Craig W; Jones, Carrie K

    2016-03-01

    Cocaine abuse remains a public health concern for which pharmacotherapies are largely ineffective. Comorbidities between cocaine abuse, depression, and anxiety support the development of novel treatments targeting multiple symptom clusters. Selective negative allosteric modulators (NAMs) targeting the metabotropic glutamate receptor 5 (mGlu5) subtype are currently in clinical trials for the treatment of multiple neuropsychiatric disorders and have shown promise in preclinical models of substance abuse. However, complete blockade or inverse agonist activity by some full mGlu5 NAM chemotypes demonstrated adverse effects, including psychosis in humans and psychotomimetic-like effects in animals, suggesting a narrow therapeutic window. Development of partial mGlu5 NAMs, characterized by their submaximal but saturable levels of blockade, may represent a novel approach to broaden the therapeutic window. To understand potential therapeutic vs adverse effects in preclinical behavioral assays, we examined the partial mGlu5 NAMs, M-5MPEP and Br-5MPEPy, in comparison with the full mGlu5 NAM MTEP across models of addiction and psychotomimetic-like activity. M-5MPEP, Br-5MPEPy, and MTEP dose-dependently decreased cocaine self-administration and attenuated the discriminative stimulus effects of cocaine. M-5MPEP and Br-5MPEPy also demonstrated antidepressant- and anxiolytic-like activity. Dose-dependent effects of partial and full mGlu5 NAMs in these assays corresponded with increasing in vivo mGlu5 occupancy, demonstrating an orderly occupancy-to-efficacy relationship. PCP-induced hyperlocomotion was potentiated by MTEP, but not by M-5MPEP and Br-5MPEPy. Further, MTEP, but not M-5MPEP, potentiated the discriminative-stimulus effects of PCP. The present data suggest that partial mGlu5 NAM activity is sufficient to produce therapeutic effects similar to full mGlu5 NAMs, but with a broader therapeutic index.

  8. Defying c-Abl signaling circuits through small allosteric compounds

    Directory of Open Access Journals (Sweden)

    Stefania eGonfloni

    2014-11-01

    Full Text Available Many extracellular and intracellular signals promote the c-Abl tyrosine kinase activity. c-Abl in turn triggers a multitude of changes either in protein phosphorylation or in gene expression in the cell. Yet, c-Abl takes part in diverse signaling routes because of several domains linked to its catalytic core. Complex conformational changes turn on and off its kinase activity. These changes affect surface features of the c-Abl kinase and likely its capability to bind actin and/or DNA. Two specific inhibitors (ATP-competitive or allosteric compounds regulate the c-Abl kinase through different mechanisms. NMR studies show that a c-Abl fragment (SH3-SH2-linker-SH1 adopts different conformational states upon binding to each inhibitor. This supports an unconventional use for allosteric compounds to unraveling physiological c-Abl signaling circuits.

  9. Evolution of allosteric regulation in chorismate mutases from early plants

    Energy Technology Data Exchange (ETDEWEB)

    Kroll, Kourtney; Holland, Cynthia K.; Starks, Courtney M.; Jez, Joseph M.

    2017-09-28

    Plants, fungi, and bacteria synthesize the aromatic amino acids: l-phenylalanine, l-tyrosine, and l-tryptophan. Chorismate mutase catalyzes the branch point reaction of phenylalanine and tyrosine biosynthesis to generate prephenate. In Arabidopsis thaliana, there are two plastid-localized chorismate mutases that are allosterically regulated (AtCM1 and AtCM3) and one cytosolic isoform (AtCM2) that is unregulated. Previous analysis of plant chorismate mutases suggested that the enzymes from early plants (i.e. bryophytes/moss, lycophytes, and basal angiosperms) formed a clade distinct from the isoforms found in flowering plants; however, no biochemical information on these enzymes is available. To understand the evolution of allosteric regulation in plant chorismate mutases, we analyzed a basal lineage of plant enzymes homologous to AtCM1 based on sequence similarity. The chorismate mutases from the moss/bryophyte Physcomitrella patens (PpCM1 and PpCM2), the lycophyte Selaginella moellendorffii (SmCM), and the basal angiosperm Amborella trichopoda (AmtCM1 and AmtCM2) were characterized biochemically. Tryptophan was a positive effector for each of the five enzymes examined. Histidine was a weak positive effector for PpCM1 and AmtCM1. Neither tyrosine nor phenylalanine altered the activity of SmCM; however, tyrosine was a negative regulator of the other four enzymes. Phenylalanine down-regulates both moss enzymes and AmtCM2. The 2.0 Å X-ray crystal structure of PpCM1 in complex with the tryptophan identified the allosteric effector site and reveals structural differences between the R- (more active) and T-state (less active) forms of plant chorismate mutases. Molecular insight into the basal plant chorismate mutases guides our understanding of the evolution of allosteric regulation in these enzymes.

  10. Phase associations and potential selective extraction methods for selected high-tech metals from ferromanganese nodules and crusts with siderophores

    International Nuclear Information System (INIS)

    Mohwinkel, Dennis; Kleint, Charlotte; Koschinsky, Andrea

    2014-01-01

    Highlights: • Phase associations of metals in marine Fe–Mn nodules and crusts were determined. • Selective leaching experiments with siderophore desferrioxamine B were conducted. • Siderophores selectively mobilize high-tech metals associated with Fe carrier phases. • Base metal liberation including Fe and Mn is limited. • Siderophores have promising potential for application in ore processing industries. - Abstract: Deep-sea ferromanganese deposits contain a wide range of economically important metals. Ferromanganese crusts and nodules represent an important future resource, since they not only contain base metals such as Mn, Ni, Co, Cu and Zn, but are also enriched in critical or rare high-technology elements such as Li, Mo, Nb, W, the rare earth elements and yttrium (REY). These metals could be extracted from nodules and crusts as a by-product to the base metal production. However, there are no proper separation techniques available that selectively extract certain metals out of the carrier phases. By sequential leaching, we demonstrated that, except for Li, which is present in an easily soluble form, all other high-tech metals enriched in ferromanganese nodules and crusts are largely associated with the Fe-oxyhydroxide phases and only to subordinate extents with Mn-oxide phases. Based on this fact, we conducted selective leaching experiments with the Fe-specific organic ligand desferrioxamine-B, a naturally occurring and ubiquitous siderophore. We showed by leaching of ferromanganese nodules and crusts with desferrioxamine-B that a significant and selective extraction of high-tech metals such as Li, Mo, Zr, Hf and Ta is possible, while other elements like Fe and the base metals Mn, Ni, Cu, Co and Zn are not extracted to large extents. The set of selectively extracted elements can be extended to Nb and W if Mn and carbonate phases are stripped from the bulk nodule or crust prior to the siderophore leach by e.g. a sequential leaching technique. This

  11. Identification of the Allosteric Regulatory Site of Insulysin

    Energy Technology Data Exchange (ETDEWEB)

    Noinaj, Nicholas; Bhasin, Sonia K.; Song, Eun Suk; Scoggin, Kirsten E.; Juliano, Maria A.; Juliano, Luiz; Hersh, Louis B.; Rodgers, David W. (U. Sao Paulo); (Kentucky)

    2012-05-25

    Insulin degrading enzyme (IDE) is responsible for the metabolism of insulin and plays a role in clearance of the A{beta} peptide associated with Alzheimer's disease. Unlike most proteolytic enzymes, IDE, which consists of four structurally related domains and exists primarily as a dimer, exhibits allosteric kinetics, being activated by both small substrate peptides and polyphosphates such as ATP. The crystal structure of a catalytically compromised mutant of IDE has electron density for peptide ligands bound at the active site in domain 1 and a distal site in domain 2. Mutating residues in the distal site eliminates allosteric kinetics and activation by a small peptide, as well as greatly reducing activation by ATP, demonstrating that this site plays a key role in allostery. Comparison of the peptide bound IDE structure (using a low activity E111F IDE mutant) with unliganded wild type IDE shows a change in the interface between two halves of the clamshell-like molecule, which may enhance enzyme activity by altering the equilibrium between closed and open conformations. In addition, changes in the dimer interface suggest a basis for communication between subunits. Our findings indicate that a region remote from the active site mediates allosteric activation of insulysin by peptides. Activation may involve a small conformational change that weakens the interface between two halves of the enzyme.

  12. Identification of the Allosteric Regulatory Site of Insulysin

    Energy Technology Data Exchange (ETDEWEB)

    Noinaj, Nicholas; Bhasin, Sonia K.; Song, Eun Suk; Scoggin, Kirsten E.; Juliano, Maria A.; Juliano, Luiz; Hersh, Louis B.; Rodgers, David W.; Gerrard, Juliet Ann

    2011-06-24

    Background Insulin degrading enzyme (IDE) is responsible for the metabolism of insulin and plays a role in clearance of the Aβ peptide associated with Alzheimer's disease. Unlike most proteolytic enzymes, IDE, which consists of four structurally related domains and exists primarily as a dimer, exhibits allosteric kinetics, being activated by both small substrate peptides and polyphosphates such as ATP. Principal Findings The crystal structure of a catalytically compromised mutant of IDE has electron density for peptide ligands bound at the active site in domain 1 and a distal site in domain 2. Mutating residues in the distal site eliminates allosteric kinetics and activation by a small peptide, as well as greatly reducing activation by ATP, demonstrating that this site plays a key role in allostery. Comparison of the peptide bound IDE structure (using a low activity E111F IDE mutant) with unliganded wild type IDE shows a change in the interface between two halves of the clamshell-like molecule, which may enhance enzyme activity by altering the equilibrium between closed and open conformations. In addition, changes in the dimer interface suggest a basis for communication between subunits. Conclusions/Significance Our findings indicate that a region remote from the active site mediates allosteric activation of insulysin by peptides. Activation may involve a small conformational change that weakens the interface between two halves of the enzyme.

  13. Zinc as Allosteric Ion Channel Modulator: Ionotropic Receptors as Metalloproteins

    Science.gov (United States)

    Peralta, Francisco Andrés; Huidobro-Toro, Juan Pablo

    2016-01-01

    Zinc is an essential metal to life. This transition metal is a structural component of many proteins and is actively involved in the catalytic activity of cell enzymes. In either case, these zinc-containing proteins are metalloproteins. However, the amino acid residues that serve as ligands for metal coordination are not necessarily the same in structural proteins compared to enzymes. While crystals of structural proteins that bind zinc reveal a higher preference for cysteine sulfhydryls rather than histidine imidazole rings, catalytic enzymes reveal the opposite, i.e., a greater preference for the histidines over cysteines for catalysis, plus the influence of carboxylic acids. Based on this paradigm, we reviewed the putative ligands of zinc in ionotropic receptors, where zinc has been described as an allosteric modulator of channel receptors. Although these receptors do not strictly qualify as metalloproteins since they do not normally bind zinc in structural domains, they do transitorily bind zinc at allosteric sites, modifying transiently the receptor channel’s ion permeability. The present contribution summarizes current information showing that zinc allosteric modulation of receptor channels occurs by the preferential metal coordination to imidazole rings as well as to the sulfhydryl groups of cysteine in addition to the carboxyl group of acid residues, as with enzymes and catalysis. It is remarkable that most channels, either voltage-sensitive or transmitter-gated receptor channels, are susceptible to zinc modulation either as positive or negative regulators. PMID:27384555

  14. Prediction of allosteric sites on protein surfaces with an elastic-network-model-based thermodynamic method.

    Science.gov (United States)

    Su, Ji Guo; Qi, Li Sheng; Li, Chun Hua; Zhu, Yan Ying; Du, Hui Jing; Hou, Yan Xue; Hao, Rui; Wang, Ji Hua

    2014-08-01

    Allostery is a rapid and efficient way in many biological processes to regulate protein functions, where binding of an effector at the allosteric site alters the activity and function at a distant active site. Allosteric regulation of protein biological functions provides a promising strategy for novel drug design. However, how to effectively identify the allosteric sites remains one of the major challenges for allosteric drug design. In the present work, a thermodynamic method based on the elastic network model was proposed to predict the allosteric sites on the protein surface. In our method, the thermodynamic coupling between the allosteric and active sites was considered, and then the allosteric sites were identified as those where the binding of an effector molecule induces a large change in the binding free energy of the protein with its ligand. Using the proposed method, two proteins, i.e., the 70 kD heat shock protein (Hsp70) and GluA2 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor, were studied and the allosteric sites on the protein surface were successfully identified. The predicted results are consistent with the available experimental data, which indicates that our method is a simple yet effective approach for the identification of allosteric sites on proteins.

  15. Potential site selection for radioactive waste repository using GIS (Study area: Negeri Sembilan) - Phase 1

    International Nuclear Information System (INIS)

    Ahmad Hasnulhadi Che Kamaruddin; Faizal Azrin Abdul Razalim; Mohd Abdul Wahab Yusof; Nik Marzukee Nik Ibrahim; Nazran Harun; Muhammad Fathi Sujan; Karuppiah, T.; Surip, N.; Malik, N.N.A.; Che Musa, R.

    2010-01-01

    The main purpose in this paper is to create the Geographic Information System (GIS) based analysis on the potential site area for near-surface radioactive waste repository in the state of Negeri Sembilan. There are several parameters should be considered related to the safety assessment in selecting the potential site. These parameters such as land-use, urban area, soil, rainfall, lithology, lineament, geomorphology, landslide potential, slope, elevation, hydrogeology and protected land need to be considered before choosing the site. In this phase, we only consider ten parameters for determining the potential suitable site. (author)

  16. Optimization of Allosteric With-No-Lysine (WNK) Kinase Inhibitors and Efficacy in Rodent Hypertension Models

    Energy Technology Data Exchange (ETDEWEB)

    Yamada, Ken; Levell, Julian; Yoon, Taeyong; Kohls, Darcy; Yowe, David; Rigel, Dean F.; Imase, Hidetomo; Yuan, Jun; Yasoshima, Kayo; DiPetrillo, Keith; Monovich, Lauren; Xu, Lingfei; Zhu, Meicheng; Kato, Mitsunori; Jain, Monish; Idamakanti, Neeraja; Taslimi, Paul; Kawanami, Toshio; Argikar, Upendra A.; Kunjathoor, Vidya; Xie, Xiaoling; Yagi, Yukiko I.; Iwaki, Yuki; Robinson, Zachary; Park, Hyi-Man (Novartis)

    2017-08-03

    The observed structure–activity relationship of three distinct ATP noncompetitive With-No-Lysine (WNK) kinase inhibitor series, together with a crystal structure of a previously disclosed allosteric inhibitor bound to WNK1, led to an overlay hypothesis defining core and side-chain relationships across the different series. This in turn enabled an efficient optimization through scaffold morphing, resulting in compounds with a good balance of selectivity, cellular potency, and pharmacokinetic profile, which were suitable for in vivo proof-of-concept studies. When dosed orally, the optimized compound reduced blood pressure in mice overexpressing human WNK1, and induced diuresis, natriuresis and kaliuresis in spontaneously hypertensive rats (SHR), confirming that this mechanism of inhibition of WNK kinase activity is effective at regulating cardiovascular homeostasis.

  17. Radio frequency selective addressing of localized atoms in a periodic potential

    International Nuclear Information System (INIS)

    Ott, H.; De Mirandes, E.; Ferlaino, F.; Roati, G.; Tuerck, V.; Modugno, G.; Inguscio, M.

    2004-01-01

    We study the localization and addressability of ultracold atoms in a combined parabolic and periodic potential. Such a potential supports the existence of localized stationary states and we show that applying a radio frequency field allows us to selectively address atoms in these states. This method is used to measure the energy and momentum distribution of the atoms in the localized states. We also discuss possible extensions of this scheme to address and manipulate atoms in single lattice sites

  18. Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL Kinase Function.

    Science.gov (United States)

    Grover, Prerna; Shi, Haibin; Baumgartner, Matthew; Camacho, Carlos J; Smithgall, Thomas E

    2015-01-01

    The ABL protein-tyrosine kinase regulates intracellular signaling pathways controlling diverse cellular processes and contributes to several forms of cancer. The kinase activity of ABL is repressed by intramolecular interactions involving its regulatory Ncap, SH3 and SH2 domains. Small molecules that allosterically regulate ABL kinase activity through its non-catalytic domains may represent selective probes of ABL function. Here we report a screening assay for chemical modulators of ABL kinase activity that target the regulatory interaction of the SH3 domain with the SH2-kinase linker. This fluorescence polarization (FP) assay is based on a purified recombinant ABL protein consisting of the N-cap, SH3 and SH2 domains plus the SH2-kinase linker (N32L protein) and a short fluorescein-labeled probe peptide that binds to the SH3 domain. In assay development experiments, we found that the probe peptide binds to the recombinant ABL N32L protein in vitro, producing a robust FP signal that can be competed with an excess of unlabeled peptide. The FP signal is not observed with control N32L proteins bearing either an inactivating mutation in the SH3 domain or enhanced SH3:linker interaction. A pilot screen of 1200 FDA-approved drugs identified four compounds that specifically reduced the FP signal by at least three standard deviations from the untreated controls. Secondary assays showed that one of these hit compounds, the antithrombotic drug dipyridamole, enhances ABL kinase activity in vitro to a greater extent than the previously described ABL agonist, DPH. Docking studies predicted that this compound binds to a pocket formed at the interface of the SH3 domain and the linker, suggesting that it activates ABL by disrupting this regulatory interaction. These results show that screening assays based on the non-catalytic domains of ABL can identify allosteric small molecule regulators of kinase function, providing a new approach to selective drug discovery for this important

  19. Active control of methanol carbonylation selectivity over Au/carbon anode by electrochemical potential.

    Science.gov (United States)

    Funakawa, Akiyasu; Yamanaka, Ichiro; Otsuka, Kiyoshi

    2005-05-12

    Electrochemical oxidative carbonylation of methanol was studied over Au supported carbon anode in CO. The major carbonylation products were dimethyl oxalate (DMO) and dimethyl carbonate (DMC). The minor oxidation products were dimethoxy methane (DMM) and methyl formate (MF) from methanol and CO(2). Influences of various reaction conditions were studied on carbonylation activities and selectivities. The selectivities to DMO and DMC can be controlled by the electrochemical potential. Electrocatalysis of Au/carbon anode was studied by cyclic voltammetry (CV), stoichiometric reactions among Au(3+), methanol, and CO, and UV-vis spectra. The Au/carbon anode was characterized by XRD, SEM, and BE images before and after the carbonylation. These experimental facts strongly suggest that transition of oxidation states of Au affects changing of the carbonylation selectivities to DMO and DMC. Au(0) is the active species for the selective DMO formation by direct electrochemical carbonylation at low potentials (selective DMC formation by indirect electrochemical carbonylation through Au(3+)/Au(+) redox at high potentials (>+1.3 V).

  20. Event-related potentials during visual selective attention in children of alcoholics.

    Science.gov (United States)

    van der Stelt, O; Gunning, W B; Snel, J; Kok, A

    1998-12-01

    Event-related potentials were recorded from 7- to 18-year-old children of alcoholics (COAs, n = 50) and age- and sex-matched control children (n = 50) while they performed a visual selective attention task. The task was to attend selectively to stimuli with a specified color (red or blue) in an attempt to detect the occurrence of target stimuli. COAs manifested a smaller P3b amplitude to attended-target stimuli over the parietal and occipital scalp than did the controls. A more specific analysis indicated that both the attentional relevance and the target properties of the eliciting stimulus determined the observed P3b amplitude differences between COAs and controls. In contrast, no significant group differences were observed in attention-related earlier occurring event-related potential components, referred to as frontal selection positivity, selection negativity, and N2b. These results represent neurophysiological evidence that COAs suffer from deficits at a late (semantic) level of visual selective information processing that are unlikely a consequence of deficits at earlier (sensory) levels of selective processing. The findings support the notion that a reduced visual P3b amplitude in COAs represents a high-level processing dysfunction indicating their increased vulnerability to alcoholism.

  1. Acoustic Noise Alters Selective Attention Processes as Indicated by Direct Current (DC) Brain Potential Changes

    OpenAIRE

    Trimmel, Karin; Schätzer, Julia; Trimmel, Michael

    2014-01-01

    Acoustic environmental noise, even of low to moderate intensity, is known to adversely affect information processing in animals and humans via attention mechanisms. In particular, facilitation and inhibition of information processing are basic functions of selective attention. Such mechanisms can be investigated by analyzing brain potentials under conditions of externally directed attention (intake of environmental information) versus internally directed attention (rejection of environmental ...

  2. Selective attention and the auditory vertex potential. 1: Effects of stimulus delivery rate

    Science.gov (United States)

    Schwent, V. L.; Hillyard, S. A.; Galambos, R.

    1975-01-01

    Enhancement of the auditory vertex potentials with selective attention to dichotically presented tone pips was found to be critically sensitive to the range of inter-stimulus intervals in use. Only at the shortest intervals was a clear-cut enhancement of the latency component to stimuli observed for the attended ear.

  3. Decarboxylative alkylation for site-selective bioconjugation of native proteins via oxidation potentials.

    Science.gov (United States)

    Bloom, Steven; Liu, Chun; Kölmel, Dominik K; Qiao, Jennifer X; Zhang, Yong; Poss, Michael A; Ewing, William R; MacMillan, David W C

    2018-02-01

    The advent of antibody-drug conjugates as pharmaceuticals has fuelled a need for reliable methods of site-selective protein modification that furnish homogeneous adducts. Although bioorthogonal methods that use engineered amino acids often provide an elegant solution to the question of selective functionalization, achieving homogeneity using native amino acids remains a challenge. Here, we explore visible-light-mediated single-electron transfer as a mechanism towards enabling site- and chemoselective bioconjugation. Specifically, we demonstrate the use of photoredox catalysis as a platform to selectivity wherein the discrepancy in oxidation potentials between internal versus C-terminal carboxylates can be exploited towards obtaining C-terminal functionalization exclusively. This oxidation potential-gated technology is amenable to endogenous peptides and has been successfully demonstrated on the protein insulin. As a fundamentally new approach to bioconjugation this methodology provides a blueprint toward the development of photoredox catalysis as a generic platform to target other redox-active side chains for native conjugation.

  4. Decarboxylative alkylation for site-selective bioconjugation of native proteins via oxidation potentials

    Science.gov (United States)

    Bloom, Steven; Liu, Chun; Kölmel, Dominik K.; Qiao, Jennifer X.; Zhang, Yong; Poss, Michael A.; Ewing, William R.; MacMillan, David W. C.

    2018-02-01

    The advent of antibody-drug conjugates as pharmaceuticals has fuelled a need for reliable methods of site-selective protein modification that furnish homogeneous adducts. Although bioorthogonal methods that use engineered amino acids often provide an elegant solution to the question of selective functionalization, achieving homogeneity using native amino acids remains a challenge. Here, we explore visible-light-mediated single-electron transfer as a mechanism towards enabling site- and chemoselective bioconjugation. Specifically, we demonstrate the use of photoredox catalysis as a platform to selectivity wherein the discrepancy in oxidation potentials between internal versus C-terminal carboxylates can be exploited towards obtaining C-terminal functionalization exclusively. This oxidation potential-gated technology is amenable to endogenous peptides and has been successfully demonstrated on the protein insulin. As a fundamentally new approach to bioconjugation this methodology provides a blueprint toward the development of photoredox catalysis as a generic platform to target other redox-active side chains for native conjugation.

  5. Conopeptide ρ-TIA Defines a New Allosteric Site on the Extracellular Surface of the α1B-Adrenoceptor*♦

    Science.gov (United States)

    Ragnarsson, Lotten; Wang, Ching-I Anderson; Andersson, Åsa; Fajarningsih, Dewi; Monks, Thea; Brust, Andreas; Rosengren, K. Johan; Lewis, Richard J.

    2013-01-01

    The G protein-coupled receptor (GPCR) superfamily is an important drug target that includes over 1000 membrane receptors that functionally couple extracellular stimuli to intracellular effectors. Despite the potential of extracellular surface (ECS) residues in GPCRs to interact with subtype-specific allosteric modulators, few ECS pharmacophores for class A receptors have been identified. Using the turkey β1-adrenergic receptor crystal structure, we modeled the α1B-adrenoceptor (α1B-AR) to help identify the allosteric site for ρ-conopeptide TIA, an inverse agonist at this receptor. Combining mutational radioligand binding and inositol 1-phosphate signaling studies, together with molecular docking simulations using a refined NMR structure of ρ-TIA, we identified 14 residues on the ECS of the α1B-AR that influenced ρ-TIA binding. Double mutant cycle analysis and docking confirmed that ρ-TIA binding was dominated by a salt bridge and cation-π between Arg-4-ρ-TIA and Asp-327 and Phe-330, respectively, and a T-stacking-π interaction between Trp-3-ρ-TIA and Phe-330. Water-bridging hydrogen bonds between Asn-2-ρ-TIA and Val-197, Trp-3-ρ-TIA and Ser-318, and the positively charged N terminus and Glu-186, were also identified. These interactions reveal that peptide binding to the ECS on transmembrane helix 6 (TMH6) and TMH7 at the base of extracellular loop 3 (ECL3) is sufficient to allosterically inhibit agonist signaling at a GPCR. The ligand-accessible ECS residues identified provide the first view of an allosteric inhibitor pharmacophore for α1-adrenoceptors and mechanistic insight and a new set of structural constraints for the design of allosteric antagonists at related GPCRs. PMID:23184947

  6. Non equivalence of the chains in the allosteric interaction of the hemoglobin

    International Nuclear Information System (INIS)

    Jacchieri, S.G.

    1983-01-01

    The importance, for the temperature dependence of the cooperative behaviour of hemoglobin, of the functional non equivalence of the polypeptide chains from which the hemoglobin molecule is built is studied. With such purpose thermodynamic allosteric parameters are introduced called 'mean allosteric parameters' which relate the last two oxygen bindings to the firsttwo ones. It is shown that the mean allosteric free energy is strongly correlated to the Hill parameter which is a classic measure of cooperativity; hence, the mean allosteric free energy measures the hemoglobin cooperativity. Recent experimental data show that the mean allosteric free energy decreasses with temperature; this is due to the mean allosteric enthalphy and entropy being positive quantities. To analise such behaviour in terms of thermodynamic's arguments equations are derived for the thermodynamic parameters of oxygen binding to hemoglobin in terms of those of its chains. Since the obtained equations have a great number of terms the same treatment is applied to a hypothetic dimer from which simpler relations are derived. From both cases it is concluded that the positive character of the mean allosteric enthalpy and entropy is due to the presence of cooperative and anticooperative terms. Since the last terms are absent in the equations of allosteric homoproteins, the characteristic temperature-dependence of hemoglobin's cooperativity depends on the presence of non-equivalent chains. (Author) [pt

  7. The second extracellular loop of the adenosine A1 receptor mediates activity of allosteric enhancers.

    Science.gov (United States)

    Kennedy, Dylan P; McRobb, Fiona M; Leonhardt, Susan A; Purdy, Michael; Figler, Heidi; Marshall, Melissa A; Chordia, Mahendra; Figler, Robert; Linden, Joel; Abagyan, Ruben; Yeager, Mark

    2014-02-01

    Allosteric enhancers of the adenosine A1 receptor amplify signaling by orthosteric agonists. Allosteric enhancers are appealing drug candidates because their activity requires that the orthosteric site be occupied by an agonist, thereby conferring specificity to stressed or injured tissues that produce adenosine. To explore the mechanism of allosteric enhancer activity, we examined their action on several A1 receptor constructs, including (1) species variants, (2) species chimeras, (3) alanine scanning mutants, and (4) site-specific mutants. These findings were combined with homology modeling of the A1 receptor and in silico screening of an allosteric enhancer library. The binding modes of known docked allosteric enhancers correlated with the known structure-activity relationship, suggesting that these allosteric enhancers bind to a pocket formed by the second extracellular loop, flanked by residues S150 and M162. We propose a model in which this vestibule controls the entry and efflux of agonists from the orthosteric site and agonist binding elicits a conformational change that enables allosteric enhancer binding. This model provides a mechanism for the observations that allosteric enhancers slow the dissociation of orthosteric agonists but not antagonists.

  8. Considering Future Potential Regarding Structural Diversity in Selection of Forest Reserves.

    Directory of Open Access Journals (Sweden)

    Johanna Lundström

    Full Text Available A rich structural diversity in forests promotes biodiversity. Forests are dynamic and therefore it is crucial to consider future structural potential when selecting reserves, to make robust conservation decisions. We analyzed forests in boreal Sweden based on 17,599 National Forest Inventory (NFI plots with the main aim to understand how effectiveness of reserves depends on the time dimension in the selection process, specifically by considering future structural diversity. In the study both the economic value and future values of 15 structural variables were simulated during a 100 year period. To get a net present structural value (NPSV, a single value covering both current and future values, we used four discounting alternatives: (1 only considering present values, (2 giving equal importance to values in each of the 100 years within the planning horizon, (3 applying an annual discount rate considering the risk that values could be lost, and (4 only considering the values in year 100. The four alternatives were evaluated in a reserve selection model under budget-constrained and area-constrained selections. When selecting young forests higher structural richness could be reached at a quarter of the cost over almost twice the area in a budget-constrained selection compared to an area-constrained selection. Our results point to the importance of considering future structural diversity in the selection of forest reserves and not as is done currently to base the selection on existing values. Targeting future values increases structural diversity and implies a relatively lower cost. Further, our results show that a re-orientation from old to young forests would imply savings while offering a more extensive reserve network with high structural qualities in the future. However, caution must be raised against a drastic reorientation of the current old-forest strategy since remnants of ancient forests will need to be prioritized due to their role for

  9. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.

    Science.gov (United States)

    Keedy, Daniel A; Hill, Zachary B; Biel, Justin T; Kang, Emily; Rettenmaier, T Justin; Brandao-Neto, Jose; Pearce, Nicholas M; von Delft, Frank; Wells, James A; Fraser, James S

    2018-06-07

    Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function. © 2018, Keedy et al.

  10. Orthosteric and Allosteric Regulation in Trypsin-Like Peptidases

    DEFF Research Database (Denmark)

    Kromann-Tofting, Tobias

    Trypsin-like serine peptidases play an important role in many physiological and pathophysiological processes, the latter including cardiovascular diseases and cancer. Binding of natural ligands to functional sites on the peptidase surface balances the level of activity and substrate specificity......-ray crystallography to determine crystal structures of active and inactive conformations of muPA, combined with biochemical analysis, elucidated an allosteric regulatory mechanism, which is now believed to be highly conserved in the trypsin-like serine peptidases. Targeting zymogen activation represents an attractive...

  11. A General Definition of the Heritable Variation that Determines the Potential of a Population to Respond to Selection

    NARCIS (Netherlands)

    Bijma, P.

    2011-01-01

    Genetic selection is a major force shaping life on earth. In classical genetic theory, response to selection is the product of the strength of selection and the additive genetic variance in a trait. The additive genetic variance reflects a population’s intrinsic potential to respond to selection.

  12. Maitotoxin Is a Potential Selective Activator of the Endogenous Transient Receptor Potential Canonical Type 1 Channel in Xenopus laevis Oocytes

    Directory of Open Access Journals (Sweden)

    Pedro L. Flores

    2017-06-01

    Full Text Available Maitotoxin (MTX is the most potent marine toxin known to date. It is responsible for a particular human intoxication syndrome called ciguatera fish poisoning (CFP. Several reports indicate that MTX is an activator of non-selective cation channels (NSCC in different cell types. The molecular identity of these channels is still an unresolved topic, and it has been proposed that the transient receptor potential (TRP channels are involved in this effect. In Xenopus laevis oocytes, MTX at picomolar (pM concentrations induces the activation of NSCC with functional and pharmacological properties that resemble the activity of TRP channels. The purpose of this study was to characterize the molecular identity of the TRP channel involved in the MTX response, using the small interference RNA (siRNA approach and the two-electrode voltage-clamp technique (TEVC. The injection of a specifically designed siRNA to silence the transient receptor potential canonical type 1 (TRPC1 protein expression abolished the MTX response. MTX had no effect on oocytes, even at doses 20-fold higher compared to cells without injection. Total mRNA and protein levels of TRPC1 were notably diminished. The TRPC4 siRNA did not change the MTX effect, even though it was important to note that the protein level was reduced by the silencing of TRPC4. Our results suggest that MTX could be a selective activator of TRPC1 channels in X. laevis oocytes and a useful pharmacological tool for further studies on these TRP channels.

  13. Crossmodal effects of Guqin and piano music on selective attention: an event-related potential study.

    Science.gov (United States)

    Zhu, Weina; Zhang, Junjun; Ding, Xiaojun; Zhou, Changle; Ma, Yuanye; Xu, Dan

    2009-11-27

    To compare the effects of music from different cultural environments (Guqin: Chinese music; piano: Western music) on crossmodal selective attention, behavioral and event-related potential (ERP) data in a standard two-stimulus visual oddball task were recorded from Chinese subjects in three conditions: silence, Guqin music or piano music background. Visual task data were then compared with auditory task data collected previously. In contrast with the results of the auditory task, the early (N1) and late (P300) stages exhibited no differences between Guqin and piano backgrounds during the visual task. Taking our previous study and this study together, we can conclude that: although the cultural-familiar music influenced selective attention both in the early and late stages, these effects appeared only within a sensory modality (auditory) but not in cross-sensory modalities (visual). Thus, the musical cultural factor is more obvious in intramodal than in crossmodal selective attention.

  14. College grade point average as a personnel selection device: ethnic group differences and potential adverse impact.

    Science.gov (United States)

    Roth, P L; Bobko, P

    2000-06-01

    College grade point average (GPA) is often used in a variety of ways in personnel selection. Unfortunately, there is little empirical research literature in human resource management that informs researchers or practitioners about the magnitude of ethnic group differences and any potential adverse impact implications when using cumulative GPA for selection. Data from a medium-sized university in the Southeast (N = 7,498) indicate that the standardized average Black-White difference for cumulative GPA in the senior year is d = 0.78. The authors also conducted analyses at 3 GPA screens (3.00, 3.25, and 3.50) to demonstrate that employers (or educators) might face adverse impact at all 3 levels if GPA continues to be implemented as part of a selection system. Implications and future research are discussed.

  15. A Potential Waste to be Selected as Media for Metal and Nutrient Removal

    Science.gov (United States)

    Zayadi, N.; Othman, N.; Hamdan, R.

    2016-07-01

    This study describes the potential of application of cassava peel, banana peel, coconut shell, and coconut coir to be selected as metal removal while limestone and steel slag for nutrient removal. The media were characterized by X-Ray Fluorescence (XRF), Fourier Transform Infrared (FTIR), Field Emission Scanning Electron Microscopy-Energy Dispersive X-Ray (FESEM-EDX), and X-Ray Powder Diffraction (XRD). The results of XRF analysis medias show the present of calcium oxide, CaO which confirm the high efficiency in adsorbing metal ions and nutrient which is in agreement with the result of XRD. The characteristics of medias by FTIR analysis also confirmed the involvement of alcohol, carboxylic, alkanes, amines and ethers which play important role to reduce ions while FESEM-EDX indicates the porous structures of study medias. The characterization analysis highlight that cassava peel and steel slag were selected as a potential media in this study.

  16. Diagnostic potentialities of pneumomediastinography and selective phlebography in the evaluation of thymus evolution in myasthenia

    Energy Technology Data Exchange (ETDEWEB)

    Vasil' ev, V.N.; Bel' chikova, N.S.; Kuksinskij, V.E. (Leningradskij Inst. Usovershenstvovaniya Vrachej (USSR))

    1983-01-01

    Based on an analysis of X-ray, intraoperative and histological findings in 124 operated on patients (thymectomy) with myasthenia the authors describe potentialities of pneumomediastinography (PMG) (pheumomediastinotomography-PMTG) in the determination of its main variants (hyperplasia, involution, tumor). Clear knowledge of the variants of x-ray image of the normal anatomical structures of the anterior mediastinum and age peculiarities of the thymus for correct interpretation of pneumomediastinograms is necessary. The importance of selective phlebography of the thymus for differential diagnosis of thymomas and nodular indurations of the fatty tissue in the anterior mediastinum, thymomas and fatty involution of the thymus, residual thymus and zones of fibrous-adipose tissue in the mediastinum is stressed. Selective phlebography is a simple and safe method that adds to PMG (PMTG) potentialities in the evaluation of thymus evolution in myasthenia.

  17. Diagnostic potentialities of pneumomediastinography and selective phlebography in the evaluation of thymus evolution in myasthenia

    International Nuclear Information System (INIS)

    Vasil'ev, V.N.; Bel'chikova, N.S.; Kuksinskij, V.E.

    1983-01-01

    Basing on an analysis of X-ray, intraoperative and histological findings in 124 operated on patients (thymectomy) with myasthenia the authors describe potentialities of pneumomediastinography (PMG) (pheumomediastinotomography-PMTG) in the determination of its main variants (hyperplasia, involUtion, tumor). Clear knowledge of the variants of x-ray image of the normal anatomical structures of the anterior mediastinum and age peculiarities of the thymus for correct interpretation of pneumomediastinograms is necessary. The importance of selective phlebography of the thymus for differential diagnosis of thymomas and nodular indurations of the fatty tissue in the anterior mediastinum, thymomas and fatty involution of the thymus, residual thymus and zones of fibrous-adipose tissue in the mediastinum is stressed. Selective phlebography is a simple and safe method that adds to PMG (PMTG) potentialities in the evaluation of thymus evolution in myasthenia

  18. Selecting for creativity and innovation potential: implications for practice in healthcare education.

    Science.gov (United States)

    Patterson, Fiona; Zibarras, Lara Dawn

    2017-05-01

    The ability to innovate is an important requirement in many organisations. Despite this pressing need, few selection systems in healthcare focus on identifying the potential for creativity and innovation and so this area has been vastly under-researched. As a first step towards understanding how we might select for creativity and innovation, this paper explores the use of a trait-based measure of creativity and innovation potential, and evaluates its efficacy for use in selection for healthcare education. This study uses a sample of 188 postgraduate physicians applying for education and training in UK General Practice. Participants completed two questionnaires (a trait-based measure of creativity and innovation, and a measure of the Big Five personality dimensions) and were also rated by assessors on creative problem solving measured during a selection centre. In exploring the construct validity of the trait-based measure of creativity and innovation, our research clarifies the associations between personality, and creativity and innovation. In particular, our study highlights the importance of motivation in the creativity and innovation process. Results also suggest that Openness to Experience is positively related to creativity and innovation whereas some aspects of Conscientiousness are negatively associated with creativity and innovation. Results broadly support the utility of using a trait-based measure of creativity and innovation in healthcare selection processes, although practically this may be best delivered as part of an interview process, rather than as a screening tool. Findings are discussed in relation to broader implications for placing more priority on creativity and innovation as selection criteria within healthcare education and training in future.

  19. Evoked potential correlates of selective attention with multi-channel auditory inputs

    Science.gov (United States)

    Schwent, V. L.; Hillyard, S. A.

    1975-01-01

    Ten subjects were presented with random, rapid sequences of four auditory tones which were separated in pitch and apparent spatial position. The N1 component of the auditory vertex evoked potential (EP) measured relative to a baseline was observed to increase with attention. It was concluded that the N1 enhancement reflects a finely tuned selective attention to one stimulus channel among several concurrent, competing channels. This EP enhancement probably increases with increased information load on the subject.

  20. Automatic selection of atomic fingerprints and reference configurations for machine-learning potentials

    Science.gov (United States)

    Imbalzano, Giulio; Anelli, Andrea; Giofré, Daniele; Klees, Sinja; Behler, Jörg; Ceriotti, Michele

    2018-06-01

    Machine learning of atomic-scale properties is revolutionizing molecular modeling, making it possible to evaluate inter-atomic potentials with first-principles accuracy, at a fraction of the costs. The accuracy, speed, and reliability of machine learning potentials, however, depend strongly on the way atomic configurations are represented, i.e., the choice of descriptors used as input for the machine learning method. The raw Cartesian coordinates are typically transformed in "fingerprints," or "symmetry functions," that are designed to encode, in addition to the structure, important properties of the potential energy surface like its invariances with respect to rotation, translation, and permutation of like atoms. Here we discuss automatic protocols to select a number of fingerprints out of a large pool of candidates, based on the correlations that are intrinsic to the training data. This procedure can greatly simplify the construction of neural network potentials that strike the best balance between accuracy and computational efficiency and has the potential to accelerate by orders of magnitude the evaluation of Gaussian approximation potentials based on the smooth overlap of atomic positions kernel. We present applications to the construction of neural network potentials for water and for an Al-Mg-Si alloy and to the prediction of the formation energies of small organic molecules using Gaussian process regression.

  1. The allosteric switching mechanism in bacteriophage MS2

    Energy Technology Data Exchange (ETDEWEB)

    Perkett, Matthew R.; Mirijanian, Dina T.; Hagan, Michael F., E-mail: hagan@brandeis.edu [Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474 (United States)

    2016-07-21

    We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.

  2. Allosteric substrate switching in a voltage-sensing lipid phosphatase.

    Science.gov (United States)

    Grimm, Sasha S; Isacoff, Ehud Y

    2016-04-01

    Allostery provides a critical control over enzyme activity, biasing the catalytic site between inactive and active states. We found that the Ciona intestinalis voltage-sensing phosphatase (Ci-VSP), which modifies phosphoinositide signaling lipids (PIPs), has not one but two sequential active states with distinct substrate specificities, whose occupancy is allosterically controlled by sequential conformations of the voltage-sensing domain (VSD). Using fast fluorescence resonance energy transfer (FRET) reporters of PIPs to monitor enzyme activity and voltage-clamp fluorometry to monitor conformational changes in the VSD, we found that Ci-VSP switches from inactive to a PIP3-preferring active state when the VSD undergoes an initial voltage-sensing motion and then into a second PIP2-preferring active state when the VSD activates fully. This two-step allosteric control over a dual-specificity enzyme enables voltage to shape PIP concentrations in time, and provides a mechanism for the complex modulation of PIP-regulated ion channels, transporters, cell motility, endocytosis and exocytosis.

  3. Allosteric substrate switching in a voltage sensing lipid phosphatase

    Science.gov (United States)

    Grimm, Sasha S.; Isacoff, Ehud Y.

    2016-01-01

    Allostery provides a critical control over enzyme activity, biasing the catalytic site between inactive and active states. We find the Ciona intestinalis voltage-sensing phosphatase (Ci-VSP), which modifies phosphoinositide signaling lipids (PIPs), to have not one but two sequential active states with distinct substrate specificities, whose occupancy is allosterically controlled by sequential conformations of the voltage sensing domain (VSD). Using fast FRET reporters of PIPs to monitor enzyme activity and voltage clamp fluorometry to monitor conformational changes in the VSD, we find that Ci-VSP switches from inactive to a PIP3-preferring active state when the VSD undergoes an initial voltage sensing motion and then into a second PIP2-preferring active state when the VSD activates fully. This novel 2-step allosteric control over a dual specificity enzyme enables voltage to shape PIP concentrations in time, and provides a mechanism for the complex modulation of PIP-regulated ion channels, transporters, cell motility and endo/exocytosis. PMID:26878552

  4. Studies on allosteric phenomena in glycogen phosphorylase b.

    Science.gov (United States)

    Madsen, N B; Avramovic-Zikic, O; Lue, P F; Honikel, K O

    1976-03-26

    This article attempts to trace, from a personal point of view, the history of discoveries of allosteric phenomena in phosphorylase b and the later development of systematic attempts to fit the data into comprehensive theoretical models. Work from our own laboratory is emphasized, but we try to integrate this into the results from other investigators and show their contributions to our ideas and experiments. Finally, some recent unpublished data is presented together with some conclusions and predictions from a new hypothesis. The discoveries by Carl and Gerty Cori of the activation of phosphorylase by AMP, the inhibition of glucose and the enzymatic interconversion of two forms fo the enzyme with different control properties helped lay the foundations of our present understanding of allosteric mechanisms. The later discovery of the oligomeric nature of phosphorylase and its relationship to AMP binding served as a basis for many years of research into the structure-function relationships of phosphorylase and other enzymes. Data showing that AMP lowers the entropy of activation is discussed with respect to the role of the nucleotide and its binding close to the active site. The discovery of the control of phosphorylase b by common metabolites and the impetus this gave to the intensive kinetic studies of the last ten years, wherein fitting to theoretical models has been a common feature, is reviewed.

  5. Allosteric behavior in the activation of transducin mediated by rhodopsin

    International Nuclear Information System (INIS)

    Wessling-Resnick, M.; Johnson, G.I.

    1986-01-01

    Transducin is a member of the family of regulatory GTP-binding proteins which provide a signal transduction mechanism for many cell surface receptors. These receptors act in a catalytic manner to displace GDP bound to the G protein in exchange for GTP during a process referred to as activation. The authors have studied the steady-state kinetics of the activation of transducin mediated by rhodopsin by employing the non-hydrolyzable GTP analog, [ 35 S]-GTPγS. The substrate-velocity curves display remarkable allosteric behavior with a Hill coefficient, n/sub H/ = 2. Lineweaver-Burke plots with respect to reciprocal [transducin] show curvilinearity indicative of positive cooperativity. However, a series of parallel lines are generated by plotting the linear transformation as [transducin] -2 . The double reciprocal plots with respect to [GTPγS] are a series of parallel lines. The initial rate analysis supports a double displacement catalytic mechanism for the molecular interactions between the photon receptor, G protein, and guanine nucleotides. It remains to be determined whether the positive cooperative behavior the authors observe can be assigned to the interaction of multiple transducins with rhodopsin, the presence of an allosteric effector, or hysteresis in the receptor's activity. These unique observations also provide insight into the molecular interactions of members of the family of G protein-coupled receptors

  6. Allosteric Inhibition of Macrophage Migration Inhibitory Factor Revealed by Ibudilast

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Y.; Crichlow, G; Vermeire, J; Leng, L; Du, X; Hodsdon, M; Bucala, R; Cappello, M; Gross, M; et al.

    2010-01-01

    AV411 (ibudilast; 3-isobutyryl-2-isopropylpyrazolo-[1,5-a]pyridine) is an antiinflammatory drug that was initially developed for the treatment of bronchial asthma but which also has been used for cerebrovascular and ocular indications. It is a nonselective inhibitor of various phosphodiesterases (PDEs) and has varied antiinflammatory activity. More recently, AV411 has been studied as a possible therapeutic for the treatment of neuropathic pain and opioid withdrawal through its actions on glial cells. As described herein, the PDE inhibitor AV411 and its PDE-inhibition-compromised analog AV1013 inhibit the catalytic and chemotactic functions of the proinflammatory protein, macrophage migration inhibitory factor (MIF). Enzymatic analysis indicates that these compounds are noncompetitive inhibitors of the p-hydroxyphenylpyruvate (HPP) tautomerase activity of MIF and an allosteric binding site of AV411 and AV1013 is detected by NMR. The allosteric inhibition mechanism is further elucidated by X-ray crystallography based on the MIF/AV1013 binary and MIF/AV1013/HPP ternary complexes. In addition, our antibody experiments directed against MIF receptors indicate that CXCR2 is the major receptor for MIF-mediated chemotaxis of peripheral blood mononuclear cells.

  7. Mining for diagnostic information in body surface potential maps: A comparison of feature selection techniques

    Directory of Open Access Journals (Sweden)

    McCullagh Paul J

    2005-09-01

    Full Text Available Abstract Background In body surface potential mapping, increased spatial sampling is used to allow more accurate detection of a cardiac abnormality. Although diagnostically superior to more conventional electrocardiographic techniques, the perceived complexity of the Body Surface Potential Map (BSPM acquisition process has prohibited its acceptance in clinical practice. For this reason there is an interest in striking a compromise between the minimum number of electrocardiographic recording sites required to sample the maximum electrocardiographic information. Methods In the current study, several techniques widely used in the domains of data mining and knowledge discovery have been employed to mine for diagnostic information in 192 lead BSPMs. In particular, the Single Variable Classifier (SVC based filter and Sequential Forward Selection (SFS based wrapper approaches to feature selection have been implemented and evaluated. Using a set of recordings from 116 subjects, the diagnostic ability of subsets of 3, 6, 9, 12, 24 and 32 electrocardiographic recording sites have been evaluated based on their ability to correctly asses the presence or absence of Myocardial Infarction (MI. Results It was observed that the wrapper approach, using sequential forward selection and a 5 nearest neighbour classifier, was capable of choosing a set of 24 recording sites that could correctly classify 82.8% of BSPMs. Although the filter method performed slightly less favourably, the performance was comparable with a classification accuracy of 79.3%. In addition, experiments were conducted to show how (a features chosen using the wrapper approach were specific to the classifier used in the selection model, and (b lead subsets chosen were not necessarily unique. Conclusion It was concluded that both the filter and wrapper approaches adopted were suitable for guiding the choice of recording sites useful for determining the presence of MI. It should be noted however

  8. Separate and combined effects of the GABAA positive allosteric modulator diazepam and Δ⁹-THC in humans discriminating Δ⁹-THC.

    Science.gov (United States)

    Lile, Joshua A; Kelly, Thomas H; Hays, Lon R

    2014-10-01

    Our previous research suggested the involvement of γ-aminobutyric acid (GABA), in particular the GABAB receptor subtype, in the interoceptive effects of Δ(9)-tetrahydrocannabinol (Δ(9)-THC). The aim of the present study was to determine the potential involvement of the GABAA receptor subtype by assessing the separate and combined effects of the GABAA positive allosteric modulator diazepam and Δ(9)-THC using pharmacologically selective drug-discrimination procedures. Ten cannabis users learned to discriminate 30 mg oral Δ(9)-THC from placebo and then received diazepam (5 and 10mg), Δ(9)-THC (5, 15 and 30 mg) and placebo, alone and in combination. Self-report, task performance and physiological measures were also collected. Δ(9)-THC functioned as a discriminative stimulus, produced subjective effects typically associated with cannabinoids (e.g., High, Stoned, Like Drug) and elevated heart rate. Diazepam alone impaired performance on psychomotor performance tasks and increased ratings on a limited number of self-report questionnaire items (e.g., Any Effect, Sedated), but did not substitute for the Δ(9)-THC discriminative stimulus or alter the Δ(9)-THC discrimination dose-response function. Similarly, diazepam had limited impact on the other behavioral effects of Δ(9)-THC. These results suggest that the GABAA receptor subtype has minimal involvement in the interoceptive effects of Δ(9)-THC, and by extension cannabis, in humans. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  9. Bacterial Membrane Depolarization-Linked Fuel Cell Potential Burst as Signal for Selective Detection of Alcohol.

    Science.gov (United States)

    Kaushik, Sharbani; Goswami, Pranab

    2018-06-06

    The biosensing application of microbial fuel cell (MFC) is hampered by its long response time, poor selectivity, and technical difficulty in developing portable devices. Herein, a novel signal form for rapid detection of ethanol was generated in a photosynthetic MFC (PMFC). First, a dual chambered (100 mL each) PMFC was fabricated by using cyanobacteria-based anode and abiotic cathode, and its performance was examined for detection of alcohols. A graphene-based nanobiocomposite matrix was layered over graphite anode to support cyanobacterial biofilm growth and to facilitate electron transfer. Injection of alcohols into the anodic chamber caused a transient potential burst of the PMFC within 60 s (load 1000 Ω), and the magnitude of potential could be correlated to the ethanol concentrations in the range 0.001-20% with a limit of detection (LOD) of 0.13% ( R 2 = 0.96). The device exhibited higher selectivity toward ethanol than methanol as discerned from the corresponding cell-alcohol interaction constant ( K i ) of 780 and 1250 mM. The concept was then translated to a paper-based PMFC (p-PMFC) (size ∼20 cm 2 ) wherein, the cells were merely immobilized over the anode. The device with a shelf life of ∼3 months detected ethanol within 10 s with a dynamic range of 0.005-10% and LOD of 0.02% ( R 2 = 0.99). The fast response time was attributed to the higher wettability of ethanol on the immobilized cell surface as validated by the contact angle data. Alcohols degraded the cell membrane on the order of ethanol > methanol, enhanced the redox current of the membrane-bound electron carrier proteins, and pushed the anodic band gap toward more negative value. The consequence was the potential burst, the magnitude of which was correlated to the ethanol concentrations. This novel approach has a great application potential for selective, sensitive, rapid, and portable detection of ethanol.

  10. Behind the curtain: cellular mechanisms for allosteric modulation of calcium-sensing receptors

    Science.gov (United States)

    Cavanaugh, Alice; Huang, Ying; Breitwieser, Gerda E

    2012-01-01

    Calcium-sensing receptors (CaSR) are integral to regulation of systemic Ca2+ homeostasis. Altered expression levels or mutations in CaSR cause Ca2+ handling diseases. CaSR is regulated by both endogenous allosteric modulators and allosteric drugs, including the first Food and Drug Administration-approved allosteric agonist, Cinacalcet HCl (Sensipar®). Recent studies suggest that allosteric modulators not only alter function of plasma membrane-localized CaSR, but regulate CaSR stability at the endoplasmic reticulum. This brief review summarizes our current understanding of the role of membrane-permeant allosteric agonists in cotranslational stabilization of CaSR, and highlights additional, indirect, signalling-dependent role(s) for membrane-impermeant allosteric drugs. Overall, these studies suggest that allosteric drugs act at multiple cellular organelles to control receptor abundance and hence function, and that drug hydrophobicity can bias the relative contributions of plasma membrane and intracellular organelles to CaSR abundance and signalling. LINKED ARTICLES This article is part of a themed section on the Molecular Pharmacology of G Protein-Coupled Receptors (GPCRs). To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2012.165.issue-6. To view the 2010 themed section on the same topic visit http://onlinelibrary.wiley.com/doi/10.1111/bph.2010.159.issue-5/issuetoc PMID:21470201

  11. Potential of organic Rankine cycle technology in India: Working fluid selection and feasibility study

    International Nuclear Information System (INIS)

    Sarkar, Jahar; Bhattacharyya, Souvik

    2015-01-01

    India has great potential to employ the ORC (organic Rankine cycle) technology for conversion of low temperature waste heat and renewable energy. In this study, available waste heat and relevant renewable heat sources in India are reviewed and suitable working fluids for ORC have been selected based on operational, environmental and safety criteria. A feasibility study and comparison of selected fluids for ORC is also presented for Indian climates along with discussions on component, operation and cost related aspects. A comprehensive review on available heat sources and sinks shows that India has plenty of waste heat and renewable energy sources for electricity generation by means of ORC; however, condenser operation may be challenging due to wide ambient temperature variation. Appropriate performance comparison among selected working fluids shows that ammonia is the best fluid in terms of net power generation and compactness of turbo-machineries, whereas n-Pentane is the best fluid in terms of thermal efficiency and heat exchanger compactness. Both are recommended as working fluids for ORC installations in India. The study reveals that there is a great opportunity to employ this technology in India provided we have to overcome some challenges related to component selection, finance and maintenance. - Highlights: • Available waste heat and renewable heat energies, and sinks in India are reviewed. • Suitable working fluids are selected by operational, environmental and safety criteria. • A feasibility study and comparison of selected fluids are presented for Indian climates. • Ammonia and n-Pentane are recommended for ORC installation in India. • Challenges related to plant component, operation and cost are discussed.

  12. Auditory selective attention in adolescents with major depression: An event-related potential study.

    Science.gov (United States)

    Greimel, E; Trinkl, M; Bartling, J; Bakos, S; Grossheinrich, N; Schulte-Körne, G

    2015-02-01

    Major depression (MD) is associated with deficits in selective attention. Previous studies in adults with MD using event-related potentials (ERPs) reported abnormalities in the neurophysiological correlates of auditory selective attention. However, it is yet unclear whether these findings can be generalized to MD in adolescence. Thus, the aim of the present ERP study was to explore the neural mechanisms of auditory selective attention in adolescents with MD. 24 male and female unmedicated adolescents with MD and 21 control subjects were included in the study. ERPs were collected during an auditory oddball paradigm. Depressive adolescents tended to show a longer N100 latency to target and non-target tones. Moreover, MD subjects showed a prolonged latency of the P200 component to targets. Across groups, longer P200 latency was associated with a decreased tendency of disinhibited behavior as assessed by a behavioral questionnaire. To be able to draw more precise conclusions about differences between the neural bases of selective attention in adolescents vs. adults with MD, future studies should include both age groups and apply the same experimental setting across all subjects. The study provides strong support for abnormalities in the neurophysiolgical bases of selective attention in adolecents with MD at early stages of auditory information processing. Absent group differences in later ERP components reflecting voluntary attentional processes stand in contrast to results reported in adults with MD and may suggest that adolescents with MD possess mechanisms to compensate for abnormalities in the early stages of selective attention. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. In search of allosteric modulators of a7-nAChR by solvent density guided virtual screening.

    Science.gov (United States)

    Dey, Raja; Chen, Lin

    2011-04-01

    Nicotinic acetylcholine receptors (nAChR) are pentameric ligand gated ion channels whose activity can be modulated by endogenous neurotransmitters as well as by synthetic ligands that bind the same or distinct sites from the natural ligand. The subtype of α7 nAChR has been considered as a potenial therapeutic target for Alzheimer's disease, schizophrenia and other neurological and psychiatric disorders. Here we have developed a homology model of α7 nAChR based on two high resolution crystal structures with Brookhaven Protein Data Bank (PDB) codes 2QC1 and 2WN9 for threading on one monomer and then for building a pentamer, respectively. A number of small molecule binding sites are identified using Pocket Finder (J. An, M. Tortov, and R. Abagyan, Molecular & Cellular Proteomics, 4.6, 752-761 (2005)) of Internal Coordinate Mechanics (ICM). Remarkably, these computer-identified sites match perfectly with ordered solvent densities found in the high-resolution crystal structure of α1 nAChR, suggesting that the surface cavities in the α7 nAChR model are likely binding sites of small molecules. A high throughput virtual screening by flexible ligand docking of 5008 small molecule compounds was performed at three potential allosteric modulator (AM) binding sites of α7 nAChR using Molsoft ICM software (R. Abagyan, M. Tortov and D. Kuznetsov, J Comput Chem 15, 488-506, (1994)). Some experimentally verified allosteric modulators of α7 like CCMI comp-6, LY 7082101, 5-HI, TQS, PNU-120596, genistein, and NS-1738 ranked among top 100 compounds, while the rest of the compounds in the list could guide further search for new allosteric modulators.

  14. The influence of caffeine on spatial-selective attention: an event-related potential study.

    Science.gov (United States)

    Ruijter, J; de Ruiter, M B; Snel, J; Lorist, M M

    2000-12-01

    Following the indications of previous studies that caffeine might have a specific effect on the processing of spatial information compared with other types of information, the present study investigated the influence of caffeine on an often used spatial-selective attention task. Event-related potentials (ERPs) were recorded from 11 participants under conditions of caffeine (250 mg) and placebo. Spatial-selective attention effects were reflected in the ERPs as more positive going occipital P1 and broadly distributed P2 components, and more negative going occipital-temporal N1 and broadly distributed N2 components. A treatment effect was found as a more positive going frontal P2 component in the caffeine condition, whereas interactions between treatment and attention were observed for P2 and N2 components, but not for P1 and N1 components. This pattern of results suggests that caffeine has no specific influence on spatial-selective attention, but rather, has a more general facilitating effect on perceptual processing, as well as a possible effect on the frontal control mechanisms, i.e. focusing attention and increasing selectivity.

  15. Direction-selective circuitry in rat retina develops independently of GABAergic, cholinergic and action potential activity.

    Directory of Open Access Journals (Sweden)

    Le Sun

    Full Text Available The ON-OFF direction selective ganglion cells (DSGCs in the mammalian retina code image motion by responding much more strongly to movement in one direction. They do so by receiving inhibitory inputs selectively from a particular sector of processes of the overlapping starburst amacrine cells, a type of retinal interneuron. The mechanisms of establishment and regulation of this selective connection are unknown. Here, we report that in the rat retina, the morphology, physiology of the ON-OFF DSGCs and the circuitry for coding motion directions develop normally with pharmacological blockade of GABAergic, cholinergic activity and/or action potentials for over two weeks from birth. With recent results demonstrating light independent formation of the retinal DS circuitry, our results strongly suggest the formation of the circuitry, i.e., the connections between the second and third order neurons in the visual system, can be genetically programmed, although emergence of direction selectivity in the visual cortex appears to require visual experience.

  16. Acoustic Noise Alters Selective Attention Processes as Indicated by Direct Current (DC Brain Potential Changes

    Directory of Open Access Journals (Sweden)

    Karin Trimmel

    2014-09-01

    Full Text Available Acoustic environmental noise, even of low to moderate intensity, is known to adversely affect information processing in animals and humans via attention mechanisms. In particular, facilitation and inhibition of information processing are basic functions of selective attention. Such mechanisms can be investigated by analyzing brain potentials under conditions of externally directed attention (intake of environmental information versus internally directed attention (rejection of environmental stimuli and focusing on memory/planning processes. This study investigated brain direct current (DC potential shifts—which are discussed to represent different states of cortical activation—of tasks that require intake and rejection of environmental information under noise. It was hypothesized that without background noise rejection tasks would show more positive DC potential changes compared to intake tasks and that under noise both kinds of tasks would show positive DC shifts as an expression of cortical inhibition caused by noise. DC potential shifts during intake and rejection tasks were analyzed at 16 standard locations in 45 persons during irrelevant speech or white noise vs. control condition. Without noise, rejection tasks were associated with more positive DC potential changes compared to intake tasks. During background noise, however, this difference disappeared and both kinds of tasks led to positive DC shifts. Results suggest—besides some limitations—that noise modulates selective attention mechanisms by switching to an environmental information processing and noise rejection mode, which could represent a suggested “attention shift”. Implications for fMRI studies as well as for public health in learning and performance environments including susceptible persons are discussed.

  17. Acoustic noise alters selective attention processes as indicated by direct current (DC) brain potential changes.

    Science.gov (United States)

    Trimmel, Karin; Schätzer, Julia; Trimmel, Michael

    2014-09-26

    Acoustic environmental noise, even of low to moderate intensity, is known to adversely affect information processing in animals and humans via attention mechanisms. In particular, facilitation and inhibition of information processing are basic functions of selective attention. Such mechanisms can be investigated by analyzing brain potentials under conditions of externally directed attention (intake of environmental information) versus internally directed attention (rejection of environmental stimuli and focusing on memory/planning processes). This study investigated brain direct current (DC) potential shifts-which are discussed to represent different states of cortical activation-of tasks that require intake and rejection of environmental information under noise. It was hypothesized that without background noise rejection tasks would show more positive DC potential changes compared to intake tasks and that under noise both kinds of tasks would show positive DC shifts as an expression of cortical inhibition caused by noise. DC potential shifts during intake and rejection tasks were analyzed at 16 standard locations in 45 persons during irrelevant speech or white noise vs. control condition. Without noise, rejection tasks were associated with more positive DC potential changes compared to intake tasks. During background noise, however, this difference disappeared and both kinds of tasks led to positive DC shifts. Results suggest-besides some limitations-that noise modulates selective attention mechanisms by switching to an environmental information processing and noise rejection mode, which could represent a suggested "attention shift". Implications for fMRI studies as well as for public health in learning and performance environments including susceptible persons are discussed.

  18. Allosteric and orthosteric sites in CC chemokine receptor (CCR5), a chimeric receptor approach

    DEFF Research Database (Denmark)

    Thiele, Stefanie; Steen, Anne; Jensen, Pia C

    2011-01-01

    -allosteric molecules. A chimera was successfully constructed between CCR5 and the closely related CCR2 by transferring all extracellular regions of CCR2 to CCR5, i.e. a Trojan horse that resembles CCR2 extracellularly but signals through a CCR5 transmembrane unit. The chimera bound CCR2 (CCL2 and CCL7), but not CCR5...... preserved, the allosteric enhancement of chemokine binding was disrupted. In summary, the Trojan horse chimera revealed that orthosteric and allosteric sites could be structurally separated and still act together with transmission of agonism and antagonism across the different receptor units....

  19. Facilitating the selection and creation of accurate interatomic potentials with robust tools and characterization

    Science.gov (United States)

    Trautt, Zachary T.; Tavazza, Francesca; Becker, Chandler A.

    2015-10-01

    The Materials Genome Initiative seeks to significantly decrease the cost and time of development and integration of new materials. Within the domain of atomistic simulations, several roadblocks stand in the way of reaching this goal. While the NIST Interatomic Potentials Repository hosts numerous interatomic potentials (force fields), researchers cannot immediately determine the best choice(s) for their use case. Researchers developing new potentials, specifically those in restricted environments, lack a comprehensive portfolio of efficient tools capable of calculating and archiving the properties of their potentials. This paper elucidates one solution to these problems, which uses Python-based scripts that are suitable for rapid property evaluation and human knowledge transfer. Calculation results are visible on the repository website, which reduces the time required to select an interatomic potential for a specific use case. Furthermore, property evaluation scripts are being integrated with modern platforms to improve discoverability and access of materials property data. To demonstrate these scripts and features, we will discuss the automation of stacking fault energy calculations and their application to additional elements. While the calculation methodology was developed previously, we are using it here as a case study in simulation automation and property calculations. We demonstrate how the use of Python scripts allows for rapid calculation in a more easily managed way where the calculations can be modified, and the results presented in user-friendly and concise ways. Additionally, the methods can be incorporated into other efforts, such as openKIM.

  20. Second generation bioethanol potential from selected Malaysia's biodiversity biomasses: A review.

    Science.gov (United States)

    Aditiya, H B; Chong, W T; Mahlia, T M I; Sebayang, A H; Berawi, M A; Nur, Hadi

    2016-01-01

    Rising global temperature, worsening air quality and drastic declining of fossil fuel reserve are the inevitable phenomena from the disorganized energy management. Bioethanol is believed to clear out the effects as being an energy-derivable product sourced from renewable organic sources. Second generation bioethanol interests many researches from its unique source of inedible biomass, and this paper presents the potential of several selected biomasses from Malaysia case. As one of countries with rich biodiversity, Malaysia holds enormous potential in second generation bioethanol production from its various agricultural and forestry biomasses, which are the source of lignocellulosic and starch compounds. This paper reviews potentials of biomasses and potential ethanol yield from oil palm, paddy (rice), pineapple, banana and durian, as the common agricultural waste in the country but uncommon to be served as bioethanol feedstock, by calculating the theoretical conversion of cellulose, hemicellulose and starch components of the biomasses into bioethanol. Moreover, the potential of the biomasses as feedstock are discussed based on several reported works. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Dynamics in the quantum/classical limit based on selective use of the quantum potential

    International Nuclear Information System (INIS)

    Garashchuk, Sophya; Dell’Angelo, David; Rassolov, Vitaly A.

    2014-01-01

    A classical limit of quantum dynamics can be defined by compensation of the quantum potential in the time-dependent Schrödinger equation. The quantum potential is a non-local quantity, defined in the trajectory-based form of the Schrödinger equation, due to Madelung, de Broglie, and Bohm, which formally generates the quantum-mechanical features in dynamics. Selective inclusion of the quantum potential for the degrees of freedom deemed “quantum,” defines a hybrid quantum/classical dynamics, appropriate for molecular systems comprised of light and heavy nuclei. The wavefunction is associated with all of the nuclei, and the Ehrenfest, or mean-field, averaging of the force acting on the classical degrees of freedom, typical of the mixed quantum/classical methods, is avoided. The hybrid approach is used to examine evolution of light/heavy systems in the harmonic and double-well potentials, using conventional grid-based and approximate quantum-trajectory time propagation. The approximate quantum force is defined on spatial domains, which removes unphysical coupling of the wavefunction fragments corresponding to distinct classical channels or configurations. The quantum potential, associated with the quantum particle, generates forces acting on both quantum and classical particles to describe the backreaction

  2. Dynamics in the quantum/classical limit based on selective use of the quantum potential

    Energy Technology Data Exchange (ETDEWEB)

    Garashchuk, Sophya, E-mail: garashchuk@sc.edu; Dell’Angelo, David; Rassolov, Vitaly A. [Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208 (United States)

    2014-12-21

    A classical limit of quantum dynamics can be defined by compensation of the quantum potential in the time-dependent Schrödinger equation. The quantum potential is a non-local quantity, defined in the trajectory-based form of the Schrödinger equation, due to Madelung, de Broglie, and Bohm, which formally generates the quantum-mechanical features in dynamics. Selective inclusion of the quantum potential for the degrees of freedom deemed “quantum,” defines a hybrid quantum/classical dynamics, appropriate for molecular systems comprised of light and heavy nuclei. The wavefunction is associated with all of the nuclei, and the Ehrenfest, or mean-field, averaging of the force acting on the classical degrees of freedom, typical of the mixed quantum/classical methods, is avoided. The hybrid approach is used to examine evolution of light/heavy systems in the harmonic and double-well potentials, using conventional grid-based and approximate quantum-trajectory time propagation. The approximate quantum force is defined on spatial domains, which removes unphysical coupling of the wavefunction fragments corresponding to distinct classical channels or configurations. The quantum potential, associated with the quantum particle, generates forces acting on both quantum and classical particles to describe the backreaction.

  3. Facilitating the selection and creation of accurate interatomic potentials with robust tools and characterization

    International Nuclear Information System (INIS)

    Trautt, Zachary T; Tavazza, Francesca; Becker, Chandler A

    2015-01-01

    The Materials Genome Initiative seeks to significantly decrease the cost and time of development and integration of new materials. Within the domain of atomistic simulations, several roadblocks stand in the way of reaching this goal. While the NIST Interatomic Potentials Repository hosts numerous interatomic potentials (force fields), researchers cannot immediately determine the best choice(s) for their use case. Researchers developing new potentials, specifically those in restricted environments, lack a comprehensive portfolio of efficient tools capable of calculating and archiving the properties of their potentials. This paper elucidates one solution to these problems, which uses Python-based scripts that are suitable for rapid property evaluation and human knowledge transfer. Calculation results are visible on the repository website, which reduces the time required to select an interatomic potential for a specific use case. Furthermore, property evaluation scripts are being integrated with modern platforms to improve discoverability and access of materials property data. To demonstrate these scripts and features, we will discuss the automation of stacking fault energy calculations and their application to additional elements. While the calculation methodology was developed previously, we are using it here as a case study in simulation automation and property calculations. We demonstrate how the use of Python scripts allows for rapid calculation in a more easily managed way where the calculations can be modified, and the results presented in user-friendly and concise ways. Additionally, the methods can be incorporated into other efforts, such as openKIM. (paper)

  4. Antimalarial activity of potential inhibitors of Plasmodium falciparum lactate dehydrogenase enzyme selected by docking studies.

    Directory of Open Access Journals (Sweden)

    Julia Penna-Coutinho

    Full Text Available The Plasmodium falciparum lactate dehydrogenase enzyme (PfLDH has been considered as a potential molecular target for antimalarials due to this parasite's dependence on glycolysis for energy production. Because the LDH enzymes found in P. vivax, P. malariae and P. ovale (pLDH all exhibit ∼90% identity to PfLDH, it would be desirable to have new anti-pLDH drugs, particularly ones that are effective against P. falciparum, the most virulent species of human malaria. Our present work used docking studies to select potential inhibitors of pLDH, which were then tested for antimalarial activity against P. falciparum in vitro and P. berghei malaria in mice. A virtual screening in DrugBank for analogs of NADH (an essential cofactor to pLDH and computational studies were undertaken, and the potential binding of the selected compounds to the PfLDH active site was analyzed using Molegro Virtual Docker software. Fifty compounds were selected based on their similarity to NADH. The compounds with the best binding energies (itraconazole, atorvastatin and posaconazole were tested against P. falciparum chloroquine-resistant blood parasites. All three compounds proved to be active in two immunoenzymatic assays performed in parallel using monoclonals specific to PfLDH or a histidine rich protein (HRP2. The IC(50 values for each drug in both tests were similar, were lowest for posaconazole (<5 µM and were 40- and 100-fold less active than chloroquine. The compounds reduced P. berghei parasitemia in treated mice, in comparison to untreated controls; itraconazole was the least active compound. The results of these activity trials confirmed that molecular docking studies are an important strategy for discovering new antimalarial drugs. This approach is more practical and less expensive than discovering novel compounds that require studies on human toxicology, since these compounds are already commercially available and thus approved for human use.

  5. Covalent Allosteric Inactivation of Protein Tyrosine Phosphatase 1B (PTP1B) by an Inhibitor-Electrophile Conjugate.

    Science.gov (United States)

    Punthasee, Puminan; Laciak, Adrian R; Cummings, Andrea H; Ruddraraju, Kasi Viswanatharaju; Lewis, Sarah M; Hillebrand, Roman; Singh, Harkewal; Tanner, John J; Gates, Kent S

    2017-04-11

    Protein tyrosine phosphatase 1B (PTP1B) is a validated drug target, but it has proven difficult to develop medicinally useful, reversible inhibitors of this enzyme. Here we explored covalent strategies for the inactivation of PTP1B using a conjugate composed of an active site-directed 5-aryl-1,2,5-thiadiazolidin-3-one 1,1-dioxide inhibitor connected via a short linker to an electrophilic α-bromoacetamide moiety. Inhibitor-electrophile conjugate 5a caused time-dependent loss of PTP1B activity consistent with a covalent inactivation mechanism. The inactivation occurred with a second-order rate constant of (1.7 ± 0.3) × 10 2 M -1 min -1 . Mass spectrometric analysis of the inactivated enzyme indicated that the primary site of modification was C121, a residue distant from the active site. Previous work provided evidence that covalent modification of the allosteric residue C121 can cause inactivation of PTP1B [Hansen, S. K., Cancilla, M. T., Shiau, T. P., Kung, J., Chen, T., and Erlanson, D. A. (2005) Biochemistry 44, 7704-7712]. Overall, our results are consistent with an unusual enzyme inactivation process in which noncovalent binding of the inhibitor-electrophile conjugate to the active site of PTP1B protects the nucleophilic catalytic C215 residue from covalent modification, thus allowing inactivation of the enzyme via selective modification of allosteric residue C121.

  6. Escitalopram, an antidepressant with an allosteric effect at the serotonin transporter--a review of current understanding of its mechanism of action.

    Science.gov (United States)

    Zhong, Huailing; Haddjeri, Nasser; Sánchez, Connie

    2012-01-01

    Escitalopram is a widely used antidepressant for the treatment of patients with major depression. It is the pure S-enantiomer of racemic citalopram. Several clinical trials and meta-analyses indicate that escitalopram is quantitatively more efficacious than many other antidepressants with a faster onset of action. This paper reviews current knowledge about the mechanism of action of escitalopram. The primary target for escitalopram is the serotonin transporter (SERT), which is responsible for serotonin (or 5-hydroxytryptamine [5-HT]) reuptake at the terminals and cell bodies of serotonergic neurons. Escitalopram and selective serotonin reuptake inhibitors bind with high affinity to the 5-HT binding site (orthosteric site) on the transporter. This leads to antidepressant effects by increasing extracellular 5-HT levels which enhance 5-HT neurotransmission. SERT also has one or more allosteric sites, binding to which modulates activity at the orthosteric binding site but does not directly affect 5-HT reuptake by the transporter. In vitro studies have shown that through allosteric binding, escitalopram decreases its own dissociation rate from the orthosteric site on the SERT. R-citalopram, the nontherapeutic enantiomer in citalopram, is also an allosteric modulator of SERT but can inhibit the actions of escitalopram by interfering negatively with its binding. Both nonclinical studies and some clinical investigations have demonstrated the cellular, neurochemical, neuroadaptive, and neuroplastic changes induced by escitalopram with acute and chronic administration. The findings from binding, neurochemical, and neurophysiological studies may provide a mechanistic rationale for the clinical difference observed with escitalopram compared to other antidepressant therapies.

  7. Ras activation by SOS: Allosteric regulation by altered fluctuation dynamics

    Science.gov (United States)

    Iversen, Lars; Tu, Hsiung-Lin; Lin, Wan-Chen; Christensen, Sune M.; Abel, Steven M.; Iwig, Jeff; Wu, Hung-Jen; Gureasko, Jodi; Rhodes, Christopher; Petit, Rebecca S.; Hansen, Scott D.; Thill, Peter; Yu, Cheng-Han; Stamou, Dimitrios; Chakraborty, Arup K.; Kuriyan, John; Groves, Jay T.

    2014-01-01

    Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras–guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average. PMID:24994643

  8. Selective effects of potassium elevations on glutamate signaling and action potential conduction in hippocampus.

    Science.gov (United States)

    Meeks, Julian P; Mennerick, Steven

    2004-01-07

    High-frequency synaptic transmission is depressed by moderate rises in the extracellular potassium concentration ([K+]o). Previous reports have indicated that depression of action potential signaling may underlie the synaptic depression. Here, we investigated the specific contribution of K+-induced action potential changes to synaptic depression. We found that glutamatergic transmission in the hippocampal area CA1 was significantly depressed by 8-10 mM [K+]o, but that GABAergic transmission remained intact. Riluzole, a drug that slows recovery from inactivation of voltage-gated sodium channels (NaChs), interacts with subthreshold [K+]o to depress afferent volleys and EPSCs strongly. Thus, elevated [K+]o likely depresses synapses by slowing NaCh recovery from inactivation. It is unclear from previous studies whether [K+]o-induced action potential depression is caused by changes in initiation, reliability, or waveform. We investigated these possibilities explicitly. [K+]o-induced afferent volley depression was independent of stimulus strength, suggesting that changes in action potential initiation do not explain [K+]o-induced depression. Measurements of action potentials from single axons revealed that 8 mM [K+]o increased conduction failures in a subpopulation of fibers and depressed action potential amplitude in all fibers. Together, these changes quantitatively account for the afferent volley depression. We estimate that conduction failure explains more than half of the synaptic depression observed at 8 mM [K+]o, with the remaining depression likely explained by waveform changes. These mechanisms of selective sensitivity of glutamate release to [K+]o accumulation represent a unique neuromodulatory mechanism and a brake on runaway excitation.

  9. Estrogenic activity, selected plasticizers and potential health risks associated with bottled water in South Africa.

    Science.gov (United States)

    Aneck-Hahn, Natalie H; Van Zijl, Magdalena C; Swart, Pieter; Truebody, Barry; Genthe, Bettina; Charmier, Jessica; Jager, Christiaan De

    2018-04-01

    Potential endocrine disrupting chemicals (EDCs) are present in bottled water from various countries. In South Africa (SA), increased bottled water consumption and concomitant increases in plastic packaging create important consequences for public health. This study aimed to screen SA bottled water for estrogenic activity, selected target chemicals and assessing potential health risks. Ten bottled water brands were exposed to 20 °C and 40 °C over 10 days. Estrogenic activity was assessed using the recombinant yeast estrogen screen (YES) and the T47D-KBluc reporter gene assay. Solid phase extracts of samples were analyzed for bis(2-ethylhexyl) adipate (DEHA), selected phthalates, bisphenol-A (BPA), 4-nonylphenol (4-NP), 17β-estradiol (E 2 ), estrone (E 1 ), and ethynylestradiol (EE 2 ) using gas chromatography-mass spectrophotometry. Using a scenario-based health risk assessment, human health risks associated with bottled water consumption were evaluated. Estrogenic activity was detected at 20 °C (n = 2) and at 40 °C (n = 8). Estradiol equivalent (EEq) values ranged from 0.001 to 0.003 ng/L. BPA concentrations ranged from 0.9 ng/L to 10.06 ng/L. Although EEqs and BPA concentrations were higher in bottled water stored at 40 °C compared to 20 °C, samples posed an acceptable risk for a lifetime of exposure. Irrespective of temperature, bottled water from SA contained chemicals with acceptable health risks.

  10. Copolymers enhance selective bacterial community colonization for potential root zone applications.

    Science.gov (United States)

    Pham, Vy T H; Murugaraj, Pandiyan; Mathes, Falko; Tan, Boon K; Truong, Vi Khanh; Murphy, Daniel V; Mainwaring, David E

    2017-11-21

    Managing the impact of anthropogenic and climate induced stress on plant growth remains a challenge. Here we show that polymeric hydrogels, which maintain their hydrous state, can be designed to exploit functional interactions with soil microorganisms. This microbial enhancement may mitigate biotic and abiotic stresses limiting productivity. The presence of mannan chains within synthetic polyacrylic acid (PAA) enhanced the dynamics and selectivity of bacterial ingress in model microbial systems and soil microcosms. Pseudomonas fluorescens exhibiting high mannan binding adhesins showed higher ingress and localised microcolonies throughout the polymeric network. In contrast, ingress of Bacillus subtilis, lacking adhesins, was unaltered by mannan showing motility comparable to bulk liquids. Incubation within microcosms of an agricultural soil yielded hydrogel populations significantly increased from the corresponding soil. Bacterial diversity was markedly higher in mannan containing hydrogels compared to both control polymer and soil, indicating enhanced selectivity towards microbial families that contain plant beneficial species. Here we propose functional polymers applied to the potential root zone which can positively influence rhizobacteria colonization and potentially plant growth as a new approach to stress tolerance.

  11. The analysis of the wind potential in selected locations in the southeastern Poland

    Directory of Open Access Journals (Sweden)

    Sornek Krzysztof

    2017-01-01

    Full Text Available This paper shows the results of analysis of the wind potential in selected locations in the southern Poland (placed in the Małopolskie, Świętokrzyskie and Podkarpackie Voivodships. The measurements and analysis of the wind resources in potential locations of the wind turbines are important part of the investment process. The statistical analysis involves the creation of histograms (e.g. histogram of the wind speed and direction and fitting those histograms to theoretical distributions (e.g. Weilbull distributions of wind speed. Such analysis has been described and conducted using measurement data for four selected locations. Basis on the conducted analysis, the economy efficiency and environmental impact of wind turbine operation has been estimated. Three market available wind turbines have been included to calculate NPV, IRR and SPBT indicators. Then, the avoided emissions of CO2, NOx, SO2 and dust have been calculated. There were also conducted some calculation using TRNSYS simulation software. The results of simulations have been compared with measurement data and the level of convergence have been found.

  12. Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL Kinase Function.

    Directory of Open Access Journals (Sweden)

    Prerna Grover

    Full Text Available The ABL protein-tyrosine kinase regulates intracellular signaling pathways controlling diverse cellular processes and contributes to several forms of cancer. The kinase activity of ABL is repressed by intramolecular interactions involving its regulatory Ncap, SH3 and SH2 domains. Small molecules that allosterically regulate ABL kinase activity through its non-catalytic domains may represent selective probes of ABL function. Here we report a screening assay for chemical modulators of ABL kinase activity that target the regulatory interaction of the SH3 domain with the SH2-kinase linker. This fluorescence polarization (FP assay is based on a purified recombinant ABL protein consisting of the N-cap, SH3 and SH2 domains plus the SH2-kinase linker (N32L protein and a short fluorescein-labeled probe peptide that binds to the SH3 domain. In assay development experiments, we found that the probe peptide binds to the recombinant ABL N32L protein in vitro, producing a robust FP signal that can be competed with an excess of unlabeled peptide. The FP signal is not observed with control N32L proteins bearing either an inactivating mutation in the SH3 domain or enhanced SH3:linker interaction. A pilot screen of 1200 FDA-approved drugs identified four compounds that specifically reduced the FP signal by at least three standard deviations from the untreated controls. Secondary assays showed that one of these hit compounds, the antithrombotic drug dipyridamole, enhances ABL kinase activity in vitro to a greater extent than the previously described ABL agonist, DPH. Docking studies predicted that this compound binds to a pocket formed at the interface of the SH3 domain and the linker, suggesting that it activates ABL by disrupting this regulatory interaction. These results show that screening assays based on the non-catalytic domains of ABL can identify allosteric small molecule regulators of kinase function, providing a new approach to selective drug discovery

  13. A potential approach for low flow selection in water resource supply and management

    Science.gov (United States)

    Ouyang, Ying

    2012-08-01

    SummaryLow flow selections are essential to water resource management, water supply planning, and watershed ecosystem restoration. In this study, a new approach, namely the frequent-low (FL) approach (or frequent-low index), was developed based on the minimum frequent-low flow or level used in minimum flows and/or levels program in northeast Florida, USA. This FL approach was then compared to the conventional 7Q10 approach for low flow selections prior to its applications, using the USGS flow data from the freshwater environment (Big Sunflower River, Mississippi) as well as from the estuarine environment (St. Johns River, Florida). Unlike the FL approach that is associated with the biological and ecological impacts, the 7Q10 approach could lead to the selections of extremely low flows (e.g., near-zero flows) that may hinder its use for establishing criteria to prevent streams from significant harm to biological and ecological communities. Additionally, the 7Q10 approach could not be used when the period of data records is less than 10 years by definition while this may not the case for the FL approach. Results from both approaches showed that the low flows from the Big Sunflower River and the St. Johns River decreased as time elapsed, demonstrating that these two rivers have become drier during the last several decades with a potential of salted water intrusion to the St. Johns River. Results from the FL approach further revealed that the recurrence probability of low flow increased while the recurrence interval of low flow decreased as time elapsed in both rivers, indicating that low flows occurred more frequent in these rivers as time elapsed. This report suggests that the FL approach, developed in this study, is a useful alternative for low flow selections in addition to the 7Q10 approach.

  14. Potential of Agricultural Biomass: Comparative Review of Selected EU Regions and Region of Vojvodina

    Directory of Open Access Journals (Sweden)

    Odavić Petrana

    2017-07-01

    Full Text Available Owing to the fact that the EU is committed to reducing greenhouse gas emissions by 20% below 1990 levels by 2020, and having in mind their high dependence on import of oil and oil derivatives, which, in turn, causes instability of power supply, increasing attention is being paid to renewable energy sources. Given the ongoing pre-accession process of the Republic of Serbia in relation to the EU, in order to determine the capacity of the country to increase the share of energy use from renewable sources, in this paper clustering of selected regions in the EU-28 has been carried out, after which a comparative analysis of regions was performed in terms of potential of agricultural biomass, for the purpose of generating energy. The aim of this study is to determine the level of the region of Vojvodina in relation to ten selected EU regions, based on parameters that affect the potential for using renewable energy sources, primarily residues from agriculture. By applying the K-means method, Borda count method and comparative analysis, and based on empirical data, results show that the region of Vojvodina takes a significant fifth place. Its share of agricultural land ranks it as the first, whereas production of cereals and the total number of farms larger than 100 ha rank it as the second. It could be concluded that Vojvodina is an agricultural region with large quantities of plant remains, primarily those left over from harvest, which represents a significant potential for energy generation from agricultural biomass.

  15. Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning

    Science.gov (United States)

    Gerek, Z. Nevin; Ozkan, S. Banu

    2011-01-01

    The allosteric mechanism plays a key role in cellular functions of several PDZ domain proteins (PDZs) and is directly linked to pharmaceutical applications; however, it is a challenge to elaborate the nature and extent of these allosteric interactions. One solution to this problem is to explore the dynamics of PDZs, which may provide insights about how intramolecular communication occurs within a single domain. Here, we develop an advancement of perturbation response scanning (PRS) that couples elastic network models with linear response theory (LRT) to predict key residues in allosteric transitions of the two most studied PDZs (PSD-95 PDZ3 domain and hPTP1E PDZ2 domain). With PRS, we first identify the residues that give the highest mean square fluctuation response upon perturbing the binding sites. Strikingly, we observe that the residues with the highest mean square fluctuation response agree with experimentally determined residues involved in allosteric transitions. Second, we construct the allosteric pathways by linking the residues giving the same directional response upon perturbation of the binding sites. The predicted intramolecular communication pathways reveal that PSD-95 and hPTP1E have different pathways through the dynamic coupling of different residue pairs. Moreover, our analysis provides a molecular understanding of experimentally observed hidden allostery of PSD-95. We show that removing the distal third alpha helix from the binding site alters the allosteric pathway and decreases the binding affinity. Overall, these results indicate that (i) dynamics plays a key role in allosteric regulations of PDZs, (ii) the local changes in the residue interactions can lead to significant changes in the dynamics of allosteric regulations, and (iii) this might be the mechanism that each PDZ uses to tailor their binding specificities regulation. PMID:21998559

  16. Mass, charge, and energy separation by selective acceleration with a traveling potential hill

    Science.gov (United States)

    Tung, L. Schwager; Barr, W. L.; Lowder, R. S.; Post, R. F.

    1996-10-01

    A traveling electric potential hill has been used to generate an ion beam with an energy distribution that is mass dependent from a monoenergetic ion beam of mixed masses. This effect can be utilized as a novel method for mass separation applied to identification or enrichment of ions (e.g., of elements, isotopes, or molecules). This theory for mass-selective acceleration is presented here and is shown to be confirmed by experiment and by a time-dependent particle-in-cell computer simulation. Results show that monoenergetic ions with the particular mass of choice are accelerated by controlling the hill potential and the hill velocity. The hill velocity is typically 20%-30% faster than the ions to be accelerated. The ability of the hill to pickup a particular mass uses the fact that small kinetic energy differences in the lab frame appear much larger in the moving hill frame. Ions will gain energy from the approaching hill if their relative energy in the moving hill frame is less than the peak potential of the hill. The final energy of these accelerated ions can be several times the source energy, which facilitates energy filtering for mass purification or identification. If the hill potential is chosen to accelerate multiple masses, the heaviest mass will have the greatest final energy. Hence, choosing the appropriate hill potential and collector retarding voltage will isolate ions with the lightest, heaviest, or intermediate mass. In the experimental device, called a Solitron, purified 20Ne and 22Ne are extracted from a ribbon beam of neon that is originally composed of 20Ne:22Ne in the natural ratio of 91:9. The isotopic content of the processed beam is determined by measuring the energy distribution of the detected current. These results agree with the theory. In addition to mass selectivity, our theory can also be applied to the filtration of an ion beam according to charge state or energy. Because of this variety of properties, the Solitron is envisioned to

  17. Phantom somatosensory evoked potentials following selective intraneural electrical stimulation in two amputees.

    Science.gov (United States)

    Granata, Giuseppe; Di Iorio, Riccardo; Romanello, Roberto; Iodice, Francesco; Raspopovic, Stanisa; Petrini, Francesco; Strauss, Ivo; Valle, Giacomo; Stieglitz, Thomas; Čvančara, Paul; Andreu, David; Divoux, Jean-Louis; Guiraud, David; Wauters, Loic; Hiairrassary, Arthur; Jensen, Winnie; Micera, Silvestro; Rossini, Paolo Maria

    2018-06-01

    The aim of the paper is to objectively demonstrate that amputees implanted with intraneural interfaces are truly able to feel a sensation in the phantom hand by recording "phantom" somatosensory evoked potentials from the corresponding brain areas. We implanted four transverse intrafascicular multichannel electrodes, available with percutaneous connections to a multichannel electrical stimulator, in the median and ulnar nerves of two left trans-radial amputees. Two channels of the implants that were able to elicit sensations during intraneural nerve stimulation were chosen, in both patients, for recording somatosensory evoked potentials. We recorded reproducible evoked responses by stimulating the median and the ulnar nerves in both cases. Latencies were in accordance with the arrival of somatosensory information to the primary somatosensory cortex. Our results provide evidence that sensations generated by intraneural stimulation are truly perceived by amputees and located in the phantom hand. Moreover, our results strongly suggest that sensations perceived in different parts of the phantom hand result in different evoked responses. Somatosensory evoked potentials obtained by selective intraneural electrical stimulation in amputee patients are a useful tool to provide an objective demonstration of somatosensory feedback in new generation bidirectional prostheses. Copyright © 2018. Published by Elsevier B.V.

  18. Allosteric inhibition enhances the efficacy of ABL kinase inhibitors to target unmutated BCR-ABL and BCR-ABL-T315I

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    Mian Afsar

    2012-09-01

    Full Text Available Abstract Background Chronic myelogenous leukemia (CML and Philadelphia chromosome-positive (Ph+ acute lymphatic leukemia (Ph + ALL are caused by the t(9;22, which fuses BCR to ABL resulting in deregulated ABL-tyrosine kinase activity. The constitutively activated BCR/ABL-kinase “escapes” the auto-inhibition mechanisms of c-ABL, such as allosteric inhibition. The ABL-kinase inhibitors (AKIs Imatinib, Nilotinib or Dasatinib, which target the ATP-binding site, are effective in Ph + leukemia. Another molecular therapy approach targeting BCR/ABL restores allosteric inhibition. Given the fact that all AKIs fail to inhibit BCR/ABL harboring the ‘gatekeeper’ mutation T315I, we investigated the effects of AKIs in combination with the allosteric inhibitor GNF2 in Ph + leukemia. Methods The efficacy of this approach on the leukemogenic potential of BCR/ABL was studied in Ba/F3 cells, primary murine bone marrow cells, and untransformed Rat-1 fibroblasts expressing BCR/ABL or BCR/ABL-T315I as well as in patient-derived long-term cultures (PDLTC from Ph + ALL-patients. Results Here, we show that GNF-2 increased the effects of AKIs on unmutated BCR/ABL. Interestingly, the combination of Dasatinib and GNF-2 overcame resistance of BCR/ABL-T315I in all models used in a synergistic manner. Conclusions Our observations establish a new approach for the molecular targeting of BCR/ABL and its resistant mutants using a combination of AKIs and allosteric inhibitors.

  19. An allosteric conduit facilitates dynamic multisite substrate recognition by the SCFCdc4 ubiquitin ligase

    Science.gov (United States)

    Csizmok, Veronika; Orlicky, Stephen; Cheng, Jing; Song, Jianhui; Bah, Alaji; Delgoshaie, Neda; Lin, Hong; Mittag, Tanja; Sicheri, Frank; Chan, Hue Sun; Tyers, Mike; Forman-Kay, Julie D.

    2017-01-01

    The ubiquitin ligase SCFCdc4 mediates phosphorylation-dependent elimination of numerous substrates by binding one or more Cdc4 phosphodegrons (CPDs). Methyl-based NMR analysis of the Cdc4 WD40 domain demonstrates that Cyclin E, Sic1 and Ash1 degrons have variable effects on the primary Cdc4WD40 binding pocket. Unexpectedly, a Sic1-derived multi-CPD substrate (pSic1) perturbs methyls around a previously documented allosteric binding site for the chemical inhibitor SCF-I2. NMR cross-saturation experiments confirm direct contact between pSic1 and the allosteric pocket. Phosphopeptide affinity measurements reveal negative allosteric communication between the primary CPD and allosteric pockets. Mathematical modelling indicates that the allosteric pocket may enhance ultrasensitivity by tethering pSic1 to Cdc4. These results suggest negative allosteric interaction between two distinct binding pockets on the Cdc4WD40 domain may facilitate dynamic exchange of multiple CPD sites to confer ultrasensitive dependence on substrate phosphorylation.

  20. 3β-Methyl-Neurosteroid Analogs are Preferential Positive Allosteric Modulators and Direct Activators of Extrasynaptic δGABA-A Receptors in the Hippocampus Dentate Gyrus Subfield.

    Science.gov (United States)

    Chuang, Shu-Hui; Reddy, Doodipala Samba

    2018-03-30

    Neurosteroids are powerful modulators of GABA-A receptors. Ganaxolone (3α-hydroxy-3β-methyl-5α-pregnan-20-one, GX) and synthetic analogs of the neurosteroid allopregnanolone (AP) are designed to treat epilepsy and related conditions. However, their precise mechanism of action in native neurons remains unclear. Here, we sought to determine the mode of action of GX and its analogs at GABA-A receptors in native hippocampal neurons by analyzing extrasynaptic receptor-mediated tonic currents and synaptic receptor-mediated phasic currents. Concentration-response profiles of GX were determined in two cell types: δ-containing dentate gyrus granule cells (DGGCs) and γ2-containing CA1 pyramidal cells (CA1PCs). GX produced significantly greater potentiation of the GABA-A receptor-activated chloride currents in DGGCs (500%) than CA1PCs (200%). In the absence of GABA, GX evoked 2-fold greater inward currents in DGGCs than CA1PCs, which were 2-fold greater than AP within DGGCs. In hippocampus slices, GX potentiated and directly activated tonic currents in DGGCs. These responses were significantly diminished in DGGCs from δ-subunit knockout (δKO) mice, confirming GX's selectivity for δGABA-A receptors. Like AP, GX potentiation of tonic currents was prevented by protein kinase C inhibition. Furthermore, GX's protection against hippocampus kindled seizures was significantly diminished in δKO mice. GX analogs exhibited greater potency and efficacy than GX on δGABA-A receptor-mediated tonic inhibition. In summary, these results provide strong evidence that GX and its analogs are preferential allosteric modulators and direct activators of extrasynaptic δGABA-A receptors regulating network inhibition and seizures in the dentate gyrus. Therefore, these findings provide a mechanistic rationale for the clinical use of synthetic neurosteroids in epilepsy and seizure disorders. The American Society for Pharmacology and Experimental Therapeutics.

  1. Selective attention and the auditory vertex potential. 2: Effects of signal intensity and masking noise

    Science.gov (United States)

    Schwent, V. L.; Hillyard, S. A.; Galambos, R.

    1975-01-01

    A randomized sequence of tone bursts was delivered to subjects at short inter-stimulus intervals with the tones originating from one of three spatially and frequency specific channels. The subject's task was to count the tones in one of the three channels at a time, ignoring the other two, and press a button after each tenth tone. In different conditions, tones were given at high and low intensities and with or without a background white noise to mask the tones. The N sub 1 component of the auditory vertex potential was found to be larger in response to attended channel tones in relation to unattended tones. This selective enhancement of N sub 1 was minimal for loud tones presented without noise and increased markedly for the lower tone intensity and in noise added conditions.

  2. Diffusion and Perfusion MR Imaging in Acute Stroke: Clinical Utility and Potential Limitations for Treatment Selection

    DEFF Research Database (Denmark)

    Bateman, Mathew; Slater, Lee-Anne; Leslie-Mazwi, Thabele M

    2017-01-01

    Magnetic resonance (MR) diffusion-weighted imaging (DWI) and perfusion-weighted imaging (PWI) offer unique insight into acute ischemic stroke pathophysiology. These techniques may offer the ability to apply pathophysiology to accurately individualize acute stroke reperfusion treatment, including ...... to be investigated in ongoing randomized controlled trials, and continued research into these techniques will help achieve the goal of tissue-based decision making and individualized acute stroke treatment....... extending the opportunity of reperfusion treatment to well beyond the current time-based treatment windows. This review examines the use of DWI and PWI in the major stroke trials, their current clinical utility, and potential limitations for reperfusion treatment selection. DWI and PWI continue...

  3. Acute stress alters auditory selective attention in humans independent of HPA: a study of evoked potentials.

    Directory of Open Access Journals (Sweden)

    Ludger Elling

    Full Text Available BACKGROUND: Acute stress is a stereotypical, but multimodal response to a present or imminent challenge overcharging an organism. Among the different branches of this multimodal response, the consequences of glucocorticoid secretion have been extensively investigated, mostly in connection with long-term memory (LTM. However, stress responses comprise other endocrine signaling and altered neuronal activity wholly independent of pituitary regulation. To date, knowledge of the impact of such "paracorticoidal" stress responses on higher cognitive functions is scarce. We investigated the impact of an ecological stressor on the ability to direct selective attention using event-related potentials in humans. Based on research in rodents, we assumed that a stress-induced imbalance of catecholaminergic transmission would impair this ability. METHODOLOGY/PRINCIPAL FINDINGS: The stressor consisted of a single cold pressor test. Auditory negative difference (Nd and mismatch negativity (MMN were recorded in a tonal dichotic listening task. A time series of such tasks confirmed an increased distractibility occurring 4-7 minutes after onset of the stressor as reflected by an attenuated Nd. Salivary cortisol began to rise 8-11 minutes after onset when no further modulations in the event-related potentials (ERP occurred, thus precluding a causal relationship. This effect may be attributed to a stress-induced activation of mesofrontal dopaminergic projections. It may also be attributed to an activation of noradrenergic projections. Known characteristics of the modulation of ERP by different stress-related ligands were used for further disambiguation of causality. The conjuncture of an attenuated Nd and an increased MMN might be interpreted as indicating a dopaminergic influence. The selective effect on the late portion of the Nd provides another tentative clue for this. CONCLUSIONS/SIGNIFICANCE: Prior studies have deliberately tracked the adrenocortical influence

  4. Potential of vetiver (vetiveria zizanioides l.) grass in removing selected pahs from diesel contaminated soil

    International Nuclear Information System (INIS)

    Nisa, W.U.; Rashid, A.

    2015-01-01

    Phytoremediation has been renowned as an encouraging technology for the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soils, little is known about how plant species behave during the process of PAH phytoremediation. Therefore, the aim of this study was to investigate the effectiveness of vetiver (Vetiveria zizanioides L.) plant in PAH phytoremediation and extraction potential of Vetiveria zizanioides for selected PAHs from the diesel contaminated soil. The field soil samples were spiked with varying concentrations (0.5% and 1%) of diesel and used for pot experiment which was conducted in greenhouse. Vetiver grass was used as experimental plant. Physico-chemical analysis of soil was performed before and after the experiment. Concentration of selected PAHs i.e. phenanthrene, pyrene and benzo(a)pyrene in soil was determined using HPLC. Plant parameters such as root/shoot length and dry mass were compared after harvest. Concentrations of PAHs were also determined in plant material and in soils after harvesting. Result showed that initial concentration of phenanthrene was significantly different from final concentration in treatments in which soil was spiked with diesel. Initial and final concentration of pyrene in soil was also significantly different from each other in two treatments in which soil was spiked with 1% diesel. Pyrene concentration was significantly different in roots and shoots of plants while benzo(a)pyrene concentration in treatments in which soil was spiked with diesel was also significantly different from roots and shoots. Phenanthrene was less extracted by the plant in all the treatments and it was present in higher concentration in soil as compared to plant. Our results indicate that vetiver grass has effectively removed PAHs from soil consequently a significantly higher root and shoot uptake of PAHs was observed than control treatments. Study concludes Vetiveria zizanioides as potentially promising plant specie for the removal

  5. Legionella Persistence in Manufactured Water Systems: Pasteurization Potentially Selecting for Thermal Tolerance

    Directory of Open Access Journals (Sweden)

    Harriet Whiley

    2017-07-01

    Full Text Available Legionella is an opportunistic waterborne pathogen of increasing public health significance. Pasteurization, otherwise known as super-heat and flush (increasing water temperature to above 70°C and flushing all outlets, has been identified as an important mechanism for the disinfection of Legionella in manufactured water systems. However, several studies have reported that this procedure was ineffective at remediating water distribution systems as Legionella was able to maintain long term persistent contamination. Up to 25% of L. pneumophila cells survived heat treatment of 70°C, but all of these were in a viable but non-culturable state. This demonstrates the limitations of the culture method of Legionella detection currently used to evaluate disinfection protocols. In addition, it has been demonstrated that pasteurization and nutrient starvation can select for thermal tolerant strains, where L. pneumophila was consistently identified as having greater thermal tolerance compared to other Legionella species. This review demonstrates that further research is needed to investigate the effectiveness of pasteurization as a disinfection method. In particular, it focuses on the potential for pasteurization to select for thermal tolerant L. pneumophila strains which, as the primary causative agent of Legionnaires disease, have greater public health significance compared to other Legionella species.

  6. Evaluation of functional potentiality of selected commonly consumed foods of Bangladesh

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    Nazma Shaheen

    2016-11-01

    Full Text Available Background: Rising tide of chronic nutrition related non-communicable diseases yoked with extant under nutrition problems makes it imperative to carry out scientific research towards the discovery of functional foods. Although the emergence of these diseases are believed to be related to a constellation of dietary, socio-economic and lifestyle related risk factors, central to the pathogenesis of these diseases (or disease states are free radicals, oxidative stress, and inflammatory processes typically accompanied by pain. Therefore, functional whole foods with physiologically active antioxidants, anti-inflammatory, and analgesic compounds seem to be the most promising option to deal with the pathogenesis of existing and emerging chronic diseases burden of Bangladesh. Methods: Edible portions of 70 commonly consumed Bangladeshi foods – including one cereal, five legumes, fourteen vegetables, four tea varieties, five oil seeds, twenty spices, and twenty one fruits – were evaluated for total phenol content (TPC by Folin-Ciocalteau assay. To evaluate functional potentiality, in vitro antioxidant capacity (AC of selected food items were evaluated by DPPH (2,2-diphenyl- 1-picrylhydrazyl radical scavenging assays, in vitro anti-inflammatory potential by observing the production of pro-inflammatory cytokine TNF-α using J774A.1 cells stimulated with lipopolysaccharide (LPS, in vivo anti-inflammatory potential by measuring carrageenan induced rat paw edema reduction, and in vivo analgesic potential by acetic acid induced writhing test in mice. Results: Spices, oilseeds, and teas showed high concentration of TPC among the analyzed foods, while spices and teas exhibited notable AC. Green tea showed highest concentrations of TPC (2349 mg Gallic Acid Equivalent / g and AC (2432 µmole Trolox Equivalent/g. Fourteen food items showed potential in vitro anti-inflammatory activity with confirmatory dose response effect shown by 8 items. In vivo, black sesame

  7. An event-related brain potential study of visual selective attention to conjunctions of color and shape.

    Science.gov (United States)

    Smid, H G; Jakob, A; Heinze, H J

    1999-03-01

    What cognitive processes underlie event-related brain potential (ERP) effects related to visual multidimensional selective attention and how are these processes organized? We recorded ERPs when participants attended to one conjunction of color, global shape and local shape and ignored other conjunctions of these attributes in three discriminability conditions. Attending to color and shape produced three ERP effects: frontal selection positivity (FSP), central negativity (N2b), and posterior selection negativity (SN). The results suggested that the processes underlying SN and N2b perform independent within-dimension selections, whereas the process underlying the FSP performs hierarchical between-dimension selections. At posterior electrodes, manipulation of discriminability changed the ERPs to the relevant but not to the irrelevant stimuli, suggesting that the SN does not concern the selection process itself but rather a cognitive process initiated after selection is finished. Other findings suggested that selection of multiple visual attributes occurs in parallel.

  8. Potential of Genomic Selection in Mass Selection Breeding of an Allogamous Crop: An Empirical Study to Increase Yield of Common Buckwheat

    Directory of Open Access Journals (Sweden)

    Shiori Yabe

    2018-03-01

    Full Text Available To evaluate the potential of genomic selection (GS, a selection experiment with GS and phenotypic selection (PS was performed in an allogamous crop, common buckwheat (Fagopyrum esculentum Moench. To indirectly select for seed yield per unit area, which cannot be measured on a single-plant basis, a selection index was constructed from seven agro-morphological traits measurable on a single plant basis. Over 3 years, we performed two GS and one PS cycles per year for improvement in the selection index. In GS, a prediction model was updated every year on the basis of genotypes of 14,598–50,000 markers and phenotypes. Plants grown from seeds derived from a series of generations of GS and PS populations were evaluated for the traits in the selection index and other yield-related traits. GS resulted in a 20.9% increase and PS in a 15.0% increase in the selection index in comparison with the initial population. Although the level of linkage disequilibrium in the breeding population was low, the target trait was improved with GS. Traits with higher weights in the selection index were improved more than those with lower weights, especially when prediction accuracy was high. No trait changed in an unintended direction in either GS or PS. The accuracy of genomic prediction models built in the first cycle decreased in the later cycles because the genetic bottleneck through the selection cycles changed linkage disequilibrium patterns in the breeding population. The present study emphasizes the importance of updating models in GS and demonstrates the potential of GS in mass selection of allogamous crop species, and provided a pilot example of successful application of GS to plant breeding.

  9. Potential of Genomic Selection in Mass Selection Breeding of an Allogamous Crop: An Empirical Study to Increase Yield of Common Buckwheat.

    Science.gov (United States)

    Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi

    2018-01-01

    To evaluate the potential of genomic selection (GS), a selection experiment with GS and phenotypic selection (PS) was performed in an allogamous crop, common buckwheat ( Fagopyrum esculentum Moench). To indirectly select for seed yield per unit area, which cannot be measured on a single-plant basis, a selection index was constructed from seven agro-morphological traits measurable on a single plant basis. Over 3 years, we performed two GS and one PS cycles per year for improvement in the selection index. In GS, a prediction model was updated every year on the basis of genotypes of 14,598-50,000 markers and phenotypes. Plants grown from seeds derived from a series of generations of GS and PS populations were evaluated for the traits in the selection index and other yield-related traits. GS resulted in a 20.9% increase and PS in a 15.0% increase in the selection index in comparison with the initial population. Although the level of linkage disequilibrium in the breeding population was low, the target trait was improved with GS. Traits with higher weights in the selection index were improved more than those with lower weights, especially when prediction accuracy was high. No trait changed in an unintended direction in either GS or PS. The accuracy of genomic prediction models built in the first cycle decreased in the later cycles because the genetic bottleneck through the selection cycles changed linkage disequilibrium patterns in the breeding population. The present study emphasizes the importance of updating models in GS and demonstrates the potential of GS in mass selection of allogamous crop species, and provided a pilot example of successful application of GS to plant breeding.

  10. Objective selection of EEG late potentials through residual dependence estimation of independent components

    International Nuclear Information System (INIS)

    Milanesi, M; James, C J; Martini, N; Menicucci, D; Gemignani, A; Ghelarducci, B; Landini, L

    2009-01-01

    This paper presents a novel method to objectively select electroencephalographic (EEG) cortical sources estimated by independent component analysis (ICA) in event-related potential (ERP) studies. A proximity measure based on mutual information is employed to estimate residual dependences of the components that are then hierarchically clustered based on these residual dependences. Next, the properties of each group of components are evaluated at each level of the hierarchical tree by two indices that aim to assess both cluster tightness and physiological reliability through a template matching process. These two indices are combined in three different approaches to bring to light the hierarchical structure of the cluster organizations. Our method is tested on a set of experiments with the purpose of enhancing late positive ERPs elicited by emotional picture stimuli. Results suggest that the best way to look for physiologically plausible late positive potential (LPP) sources is to explore in depth the tightness of those clusters that, taken together, best resemble the template. According to our results, after brain sources clustering, LPPs are always identified more accurately than from ensemble-averaged raw data. Since the late components of an ERP involve the same associative areas, regardless of the modality of stimulation or specific tasks administered, the proposed method can be simply adapted to other ERP studies, and extended from psychophysiological studies to pathological or sport training evaluation support

  11. Effects of potential partners' physical attractiveness and socioeconomic status on sexuality and partner selection.

    Science.gov (United States)

    Townsend, J M; Levy, G D

    1990-04-01

    Male (n = 170) and female (n = 212) college students viewed photographs, which had been prerated for physical attractiveness, of three opposite-sex individuals. These photographs were paired with three levels of occupational status and income. Subjects indicated their willingness to engage in relationships of varying levels of sexual intimacy and marital potential with the portrayed individuals. Analyses of variance, correlations, and trend analyses supported the hypotheses. Compared to men, women are more likely to prefer or insist that sexual intercourse occur in relationships that involve affection and marital potential, and women place more emphasis than men do on partners' SES in such relationships. Consequently, men's SES and their willingness and ability to invest affection and resources in relationships may often outweigh the effects of their physical attractiveness in women's actual selection of partners. These results and the literature reviewed are more consistent with parental investment theory than with the view that these sex differences are solely the result of differential access to resources and differential socialization.

  12. In vitro selection of bacteria with potential for use as probiotics in marine shrimp culture

    Directory of Open Access Journals (Sweden)

    Felipe do Nascimento Vieira

    2013-08-01

    Full Text Available The objective of this work was to isolate strains of lactic acid bacteria with probiotic potential from the digestive tract of marine shrimp (Litopenaeus vannamei, and to carry out in vitro selection based on multiple characters. The ideotype (ideal proposed strain was defined by the highest averages for the traits maximum growth velocity, final count of viable cells, and inhibition halo against nine freshwater and marine pathogens, and by the lowest averages for the traits duplication time and resistance of strains to NaCl (1.5 and 3%, pH (6, 8, and 9, and biliary salts (5%. Mahalanobis distance (D² was estimated among the evaluated strains, and the best ones were those with the shortest distances to the ideotype. Ten bacterial strains were isolated and biochemically identified as Lactobacillus plantarum (3, L. brevis (3, Weissella confusa (2, Lactococcus lactis (1, and L. delbrueckii (1. Lactobacillus plantarum strains showed a wide spectrum of action and the largest inhibition halos against pathogens, both Gram-positive and negative, high growth rate, and tolerance to all evaluated parameters. In relation to ideotype, L. plantarum showed the lowest Mahalanobis (D² distance, followed by the strains of W. confusa, L. brevis, L. lactis, and L. delbrueckii. Among the analyzed bacterial strains, those of Lactobacillus plantarum have the greatest potential for use as a probiotic for marine shrimp.

  13. Effects of 20 Selected Fruits on Ethanol Metabolism: Potential Health Benefits and Harmful Impacts.

    Science.gov (United States)

    Zhang, Yu-Jie; Wang, Fang; Zhou, Yue; Li, Ya; Zhou, Tong; Zheng, Jie; Zhang, Jiao-Jiao; Li, Sha; Xu, Dong-Ping; Li, Hua-Bin

    2016-04-01

    The consumption of alcohol is often accompanied by other foods, such as fruits and vegetables. This study is aimed to investigate the effects of 20 selected fruits on ethanol metabolism to find out their potential health benefits and harmful impacts. The effects of the fruits on ethanol metabolism were characterized by the concentrations of ethanol and acetaldehyde in blood, as well as activities of alcohol dehydrogenase and acetaldehyde dehydrogenase in liver of mice. Furthermore, potential health benefits and harmful impacts of the fruits were evaluated by biochemical parameters including aspartate transaminase (AST), alanine transferase (ALT), malondialdehyde, and superoxide dismutase. Generally, effects of these fruits on ethanol metabolism were very different. Some fruits (such as Citrus limon (yellow), Averrhoa carambola, Pyrus spp., and Syzygium samarangense) could decrease the concentration of ethanol in blood. In addition, several fruits (such as Cucumis melo) showed hepatoprotective effects by significantly decreasing AST or ALT level in blood, while some fruits (such as Averrhoa carambola) showed adverse effects. The results suggested that the consumption of alcohol should not be accompanied by some fruits, and several fruits could be developed as functional foods for the prevention and treatment of hangover and alcohol use disorder.

  14. Explore the Most Potential Supplier’s Selection Determinants in Modern Supply Chain Management

    Directory of Open Access Journals (Sweden)

    Ming-Yuan Hsieh

    2014-01-01

    Full Text Available To increment the research reliability, validity, and representativeness, this study creatively cross-employed the factor analysis (FA and the grey relational analysis (GRA methods. The results of the 144 fully completed questionnaires are analyzed by FA and then these results were utilized in second questionnaires design of 15 experts. Furthermore, the results of these second questionnaires were further analyzed by GRA in order to explore the most potential supplier’s selection determinants in the modern supply chain management (MSCM. Beyond a series of measurements, the measured results have induced three contributive findings: (1 the empirical interviewed industrialists reported concern that suppliers have to provide a higher material yield rate and material delivery on time rate for the qualitative increment as well as a higher supplier’s gross margin ROI for the financial stabilization in MSCM; (2 the 15 experts concluded that material insurance rate is an important attribute to estimate risky assessments and the supplier’s gross margin ROI and warehouse operations cost as a percentage of sales are critical elements in the financial evaluations of potential suppliers; and (3 Supplier’s gross margin ROI, outbound freight cost as a percentage of sales, and material insurance rate are the three most decisive determinants in MSCM.

  15. Regulation and regulatory role of WNT signaling in potentiating FSH action during bovine dominant follicle selection.

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    P S P Gupta

    Full Text Available Follicular development occurs in wave like patterns in monotocous species such as cattle and humans and is regulated by a complex interaction of gonadotropins with local intrafollicular regulatory molecules. To further elucidate potential mechanisms controlling dominant follicle selection, granulosa cell RNA harvested from F1 (largest and F2 (second largest follicles isolated at predeviation (PD and onset of diameter deviation (OD stages of the first follicular wave was subjected to preliminary RNA transcriptome analysis. Expression of numerous WNT system components was observed. Hence experiments were performed to test the hypothesis that WNT signaling modulates FSH action on granulosa cells during follicular waves. Abundance of mRNA for WNT pathway members was evaluated in granulosa cells harvested from follicles at emergence (EM, PD, OD and early dominance (ED stages of the first follicular wave. In F1 follicles, abundance of CTNNB1 and DVL1 mRNAs was higher and AXIN2 mRNA was lower at ED versus EM stages and DVL1 and FZD6 mRNAs were higher and AXIN2 mRNA was lower in F1 versus F2 follicle at the ED stage. Bovine granulosa cells were treated in vitro with increasing doses of the WNT inhibitor IWR-1+/- maximal stimulatory dose of FSH. IWR-1 treatment blocked the FSH-induced increase in granulosa cell numbers and reduced the FSH-induced increase in estradiol. Granulosa cells were also cultured in the presence or absence of FSH +/- IWR-1 and hormonal regulation of mRNA for WNT pathway members and known FSH targets determined. FSH treatment increased CYP19A1, CCND2, CTNNB1, AXIN2 and FZD6 mRNAs and the stimulatory effect on CYP19A1 mRNA was reduced by IWR-1. In contrast, FSH reduced CARTPT mRNA and IWR-1 partially reversed the inhibitory effect of FSH. Results support temporal and hormonal regulation and a potential role for WNT signaling in potentiating FSH action during dominant follicle selection.

  16. Conformational changes and allosteric communications in human serum albumin due to ligand binding.

    Science.gov (United States)

    Ahalawat, Navjeet; Murarka, Rajesh K

    2015-01-01

    It is well recognized that knowledge of structure alone is not sufficient to understand the fundamental mechanism of biomolecular recognition. Information of dynamics is necessary to describe motions involving relevant conformational states of functional importance. We carried out principal component analysis (PCA) of structural ensemble, derived from 84 crystal structures of human serum albumin (HSA) with different ligands and/or different conditions, to identify the functionally important collective motions, and compared with the motions along the low-frequency modes obtained from normal mode analysis of the elastic network model (ENM) of unliganded HSA. Significant overlap is observed in the collective motions derived from PCA and ENM. PCA and ENM analysis revealed that ligand selects the most favored conformation from accessible equilibrium structures of unliganded HSA. Further, we analyzed dynamic network obtained from molecular dynamics simulations of unliganded HSA and fatty acids- bound HSA. Our results show that fatty acids-bound HSA has more robust community network with several routes to communicate among different parts of the protein. Critical nodes (residues) identified from dynamic network analysis are in good agreement with allosteric residues obtained from sequence-based statistical coupling analysis method. This work underscores the importance of intrinsic structural dynamics of proteins in ligand recognition and can be utilized for the development of novel drugs with optimum activity.

  17. Intracellular calcium levels determine differential modulation of allosteric interactions within G protein-coupled receptor heteromers.

    Science.gov (United States)

    Navarro, Gemma; Aguinaga, David; Moreno, Estefania; Hradsky, Johannes; Reddy, Pasham P; Cortés, Antoni; Mallol, Josefa; Casadó, Vicent; Mikhaylova, Marina; Kreutz, Michael R; Lluís, Carme; Canela, Enric I; McCormick, Peter J; Ferré, Sergi

    2014-11-20

    The pharmacological significance of the adenosine A2A receptor (A2AR)-dopamine D2 receptor (D2R) heteromer is well established and it is being considered as an important target for the treatment of Parkinson’s disease and other neuropsychiatric disorders. However, the physiological factors that control its distinctive biochemical properties are still unknown. We demonstrate that different intracellular Ca2+ levels exert a differential modulation of A2AR-D2R heteromer-mediated adenylyl-cyclase and MAPK signaling in striatal cells. This depends on the ability of low and high Ca2+ levels to promote a selective interaction of the heteromer with the neuronal Ca2+-binding proteins NCS-1 and calneuron-1, respectively. These Ca2+-binding proteins differentially modulate allosteric interactions within the A2AR-D2R heteromer, which constitutes a unique cellular device that integrates extracellular (adenosine and dopamine) and intracellular (Ca+2) signals to produce a specific functional response.

  18. Wind Energy Potential and Power Law Indexes Assessment for Selected Near-Coastal Sites in Malaysia

    Directory of Open Access Journals (Sweden)

    Aliashim Albani

    2017-03-01

    Full Text Available This paper investigated the wind energy potential by analysing a certain amount of gathered 10-min measured data at four stations located at coastal sites in Malaysia, i.e., Kudat, Mersing, Kijal, and Langkawi. The wind data are collected from a total of four new wind measurement masts with sensors mounted at various heights on the tower. The measured data have enabled the establishment of wind resource maps and the power law indexes (PLIs analysis. In addition, the dependence of PLI upon surface temperature and terrain types is studied, as they are associated to the form of exponential fits. Moreover, the accuracy of exponential fits is assessed by comparing the results with the 1/7 law via the capacity factor (CF discrepancies. In order to do so, the wind turbine with a hub-height similar to the maximum height of the measured data at each site is selected to simulate energy production. Accordingly, the discrepancy of CF based on the extrapolated data by employing 1/7 laws and exponential fits, in spite of being computed using measured data, is determined as well. Furthermore, the large discrepancy of the wind data and the CF, which has been determined with the application of 1/7, is compared to the exponential fits. This is because; discrepancy in estimation of vertical wind speed could lead to inaccurate CF computation. Meanwhile, from the energy potential analysis based on the computed CF, only Kudat and Mersing display a promising potential to develop a medium capacity of wind turbine power, while the other sites may be suitable for wind turbines at a small scale.

  19. Selection of potential probiotic lactic acid bacteria from fermented olives by in vitro tests.

    Science.gov (United States)

    Argyri, Anthoula A; Zoumpopoulou, Georgia; Karatzas, Kimon-Andreas G; Tsakalidou, Effie; Nychas, George-John E; Panagou, Efstathios Z; Tassou, Chrysoula C

    2013-04-01

    The present study aims to evaluate the probiotic potential of lactic acid bacteria (LAB) isolated from naturally fermented olives and select candidates to be used as probiotic starters for the improvement of the traditional fermentation process and the production of newly added value functional foods. Seventy one (71) lactic acid bacterial strains (17 Leuconostoc mesenteroides, 1 Ln. pseudomesenteroides, 13 Lactobacillus plantarum, 37 Lb. pentosus, 1 Lb. paraplantarum, and 2 Lb. paracasei subsp. paracasei) isolated from table olives were screened for their probiotic potential. Lb. rhamnosus GG and Lb. casei Shirota were used as reference strains. The in vitro tests included survival in simulated gastrointestinal tract conditions, antimicrobial activity (against Listeria monocytogenes, Salmonella Enteritidis, Escherichia coli O157:H7), Caco-2 surface adhesion, resistance to 9 antibiotics and haemolytic activity. Three (3) Lb. pentosus, 4 Lb. plantarum and 2 Lb. paracasei subsp. paracasei strains demonstrated the highest final population (>8 log cfu/ml) after 3 h of exposure at low pH. The majority of the tested strains were resistant to bile salts even after 4 h of exposure, while 5 Lb. plantarum and 7 Lb. pentosus strains exhibited partial bile salt hydrolase activity. None of the strains inhibited the growth of the pathogens tested. Variable efficiency to adhere to Caco-2 cells was observed. This was the same regarding strains' susceptibility towards different antibiotics. None of the strains exhibited β-haemolytic activity. As a whole, 4 strains of Lb. pentosus, 3 strains of Lb. plantarum and 2 strains of Lb. paracasei subsp. paracasei were found to possess desirable in vitro probiotic properties similar to or even better than the reference probiotic strains Lb. casei Shirota and Lb. rhamnosus GG. These strains are good candidates for further investigation both with in vivo studies to elucidate their potential health benefits and in olive fermentation processes

  20. Screening of CHP Potential at Federal Sites in Select Regions of the U.S.

    Energy Technology Data Exchange (ETDEWEB)

    Energy Nexus Group, . .

    2002-02-25

    Combined Cooling Heat and Power (CHP) is a master term for onsite power generation technologies that sequentially produce electrical or mechanical energy and useful thermal energy. Some form of CHP has existed for more than 100 years and it is now achieving a greater level of acceptance due to an increasing need for reliable power service and energy cost management. Capturing and using the heat produced as a byproduct of generating electricity from fuel sources increases the usable energy that can be obtained from the original fuel source. CHP technologies have the potential to reduce energy consumption through increased efficiency--decreasing energy bills as well as pollution. The EPA recognizes CHP as a potent climate change mitigation measure. The U.S. Department of Energy (D.O.E.) Federal Energy Management Program (FEMP) is assisting Federal agencies to realize their energy efficiency goals. CHP is an efficiency measure that is receiving growing attention because of its sizable potential to provide efficiency, environmental, and reliability benefits. CHP therefore benefits the host facility, the electric infrastructure, and the U.S. society as a whole. This report and study seeks to make a preliminary inquiry into near term CHP opportunities for federal facilities in selected U.S. regions. It offers to help focus the attention of policy makers and energy facility managers on good candidate facilities for CHP. First, a ranked list of high potential individual sites is identified. Then, several classes of federal facilities are identified for the multiple opportunities they offer as a class. Recommendations are then offered for appropriate next steps for the evaluation and cost effective implementation of CHP. This study was designed to ultimately rank federal facilities in terms of their potential to take advantage of CHP economic and external savings in the near term. In order to best serve the purposes of this study, projections have been expressed in terms of

  1. Nanoporous spongy graphene: Potential applications for hydrogen adsorption and selective gas separation

    Energy Technology Data Exchange (ETDEWEB)

    Kostoglou, Nikolaos, E-mail: nikolaos.kostoglou@stud.unileoben.ac.at [Department of Mechanical and Manufacturing Engineering, University of Cyprus, 1678 Nicosia (Cyprus); Department of Physical Metallurgy and Materials Testing, Montanuniversität Leoben, 8700 Leoben (Austria); Constantinides, Georgios [Research Unit for Nanostructured Materials Systems, Department of Mechanical Engineering and Materials Science and Engineering, Cyprus University of Technology, 3036 Lemesos (Cyprus); Charalambopoulou, Georgia; Steriotis, Theodore [National Center for Scientific Research Demokritos, Agia Paraskevi Attikis, 15310 Athens (Greece); Polychronopoulou, Kyriaki [Department of Mechanical Engineering, Khalifa University of Science, Technology and Research, Abu Dhabi (United Arab Emirates); Li, Yuanqing; Liao, Kin [Department of Aerospace Engineering, Khalifa University of Science, Technology and Research, Abu Dhabi (United Arab Emirates); Ryzhkov, Vladislav [Nanotube Production Department, Fibrtec Incorporation, TX, 75551 Atlanta (United States); Mitterer, Christian [Department of Physical Metallurgy and Materials Testing, Montanuniversität Leoben, 8700 Leoben (Austria); Rebholz, Claus, E-mail: claus@ucy.ac.cy [Department of Mechanical and Manufacturing Engineering, University of Cyprus, 1678 Nicosia (Cyprus)

    2015-12-01

    In the present work, a nanoporous (pore width ~ 0.7 nm) graphene-based sponge-like material with large surface area (~ 350 m{sup 2}/g) was synthesized by wet chemical reduction of graphene oxide in combination with freeze-drying. Surface morphology and elemental composition were studied by scanning and transmission electron microscopy combined with energy dispersive X-ray spectroscopy. Surface chemistry was qualitatively examined by Fourier-transform infrared spectroscopy, while the respective structure was investigated by X-ray diffraction analysis. Textural properties, including Brunauer–Emmet–Teller (BET) surface area, micropore volume and surface area as well as pore size distribution, were deduced from nitrogen gas adsorption/desorption data obtained at 77 K and up to 1 bar. Potential use of the spongy graphene for gas storage and separation applications was preliminarily assessed by low-pressure (0–1 bar) H{sub 2}, CO{sub 2} and CH{sub 4} sorption measurements at different temperatures (77, 273 and 298 K). The adsorption capacities for each gas were evaluated up to ~ 1 bar, the isosteric enthalpies of adsorption for CO{sub 2} (28–33 kJ/mol) and CH{sub 4} (30–38 kJ/mol) were calculated using the Clausius–Clapeyron equation, while the CO{sub 2}/CH{sub 4} gas selectivity (up to 95:1) was estimated using the Ideal Adsorbed Solution Theory (IAST). - Highlights: • Nanoporous sponge produced by chemical reduction of graphene oxide and freeze-drying • Characterization performed using SEM, EDS, TEM, FT-IR, BET and XRD methods • Gas storage performance evaluated towards H{sub 2}, CO{sub 2} and CH{sub 4} adsorption up to 1 bar • CO{sub 2} over CH{sub 4} gas selectivity estimated between 45 and 95 at 273 K using the IAST model.

  2. In Vitro and in Vivo Selection of Potentially Probiotic Lactobacilli From Nocellara del Belice Table Olives

    Directory of Open Access Journals (Sweden)

    Barbara Guantario

    2018-03-01

    Full Text Available Table olives are increasingly recognized as a vehicle as well as a source of probiotic bacteria, especially those fermented with traditional procedures based on the activity of indigenous microbial consortia, originating from local environments. In the present study, we report characterization at the species level of 49 Lactic Acid Bacteria (LAB strains deriving from Nocellara del Belice table olives fermented with the Spanish or Castelvetrano methods, recently isolated in our previous work. Ribosomal 16S DNA analysis allowed identification of 4 Enterococcus gallinarum, 3 E. casseliflavus, 14 Leuconostoc mesenteroides, 19 Lactobacillus pentosus, 7 L. coryniformis, and 2 L. oligofermentans. The L. pentosus and L. coryniformis strains were subjected to further screening to evaluate their probiotic potential, using a combination of in vitro and in vivo approaches. The majority of them showed high survival rates under in vitro simulated gastro-intestinal conditions, and positive antimicrobial activity against Salmonella enterica serovar Typhimurium, Listeria monocytogenes and enterotoxigenic Escherichia coli (ETEC pathogens. Evaluation of antibiotic resistance to ampicillin, tetracycline, chloramphenicol, or erythromycin was also performed for all selected strains. Three L. coryniformis strains were selected as very good performers in the initial in vitro testing screens, they were antibiotic susceptible, as well as capable of inhibiting pathogen growth in vitro. Parallel screening employing the simplified model organism Caenorhabditis elegans, fed the Lactobacillus strains as a food source, revealed that one L. pentosus and one L. coryniformis strains significantly induced prolongevity effects and protection from pathogen-mediated infection. Moreover, both strains displayed adhesion to human intestinal epithelial Caco-2 cells and were able to outcompete foodborne pathogens for cell adhesion. Overall, these results are suggestive of beneficial

  3. Nanoporous spongy graphene: Potential applications for hydrogen adsorption and selective gas separation

    International Nuclear Information System (INIS)

    Kostoglou, Nikolaos; Constantinides, Georgios; Charalambopoulou, Georgia; Steriotis, Theodore; Polychronopoulou, Kyriaki; Li, Yuanqing; Liao, Kin; Ryzhkov, Vladislav; Mitterer, Christian; Rebholz, Claus

    2015-01-01

    In the present work, a nanoporous (pore width ~ 0.7 nm) graphene-based sponge-like material with large surface area (~ 350 m"2/g) was synthesized by wet chemical reduction of graphene oxide in combination with freeze-drying. Surface morphology and elemental composition were studied by scanning and transmission electron microscopy combined with energy dispersive X-ray spectroscopy. Surface chemistry was qualitatively examined by Fourier-transform infrared spectroscopy, while the respective structure was investigated by X-ray diffraction analysis. Textural properties, including Brunauer–Emmet–Teller (BET) surface area, micropore volume and surface area as well as pore size distribution, were deduced from nitrogen gas adsorption/desorption data obtained at 77 K and up to 1 bar. Potential use of the spongy graphene for gas storage and separation applications was preliminarily assessed by low-pressure (0–1 bar) H_2, CO_2 and CH_4 sorption measurements at different temperatures (77, 273 and 298 K). The adsorption capacities for each gas were evaluated up to ~ 1 bar, the isosteric enthalpies of adsorption for CO_2 (28–33 kJ/mol) and CH_4 (30–38 kJ/mol) were calculated using the Clausius–Clapeyron equation, while the CO_2/CH_4 gas selectivity (up to 95:1) was estimated using the Ideal Adsorbed Solution Theory (IAST). - Highlights: • Nanoporous sponge produced by chemical reduction of graphene oxide and freeze-drying • Characterization performed using SEM, EDS, TEM, FT-IR, BET and XRD methods • Gas storage performance evaluated towards H_2, CO_2 and CH_4 adsorption up to 1 bar • CO_2 over CH_4 gas selectivity estimated between 45 and 95 at 273 K using the IAST model

  4. The personal interview: assessing the potential for personality similarity to bias the selection of orthopaedic residents.

    Science.gov (United States)

    Quintero, Andres J; Segal, Lee S; King, Tonya S; Black, Kevin P

    2009-10-01

    The selection of medical students for training in orthopaedic surgery consists of an objective screening of cognitive skills to secure interviews for the brightest candidates, followed by subjective measures of candidates to confirm whether applicants are worthy of further consideration. The personal interview and its potential biased impact on the orthopaedic workforce were evaluated. During 2004-2006 at the Penn State College of Medicine, the authors performed a prospective cohort study in which 30 consenting interviewers and 135 interviewees completed the Myers-Briggs Type Indicator before the interviews. Completed surveys were evaluated after submitting the resident selection list to the National Residency Matching Program, and candidate rankings based solely on the personal interview were analyzed. Clinicians ranked candidates more favorably when they shared certain personality preferences (P = .044) and when they shared the preference groupings of the quadrant extrovert-sensing and either the function pair sensing-thinking (P = .007) or the temperament sensing-judging (P = .003), or the function pair sensing-feeling and the temperament sensing-judging (P = .029). No associations existed between personality preferences and interviewee rankings performed by basic scientists and resident interviewers. The results support the hypothesis that, within the department studied, there was a significant association between similarities in personality type and the rankings that individual faculty interviewers assigned to applicants at the completion of each interview session. The authors believe that it is important for the faculty member to recognize that this tendency exists. Finally, promoting diversity within the admission committee may foster a diverse resident body and orthopaedic workforce.

  5. Endogenous vs Exogenous Allosteric Modulators in GPCRs: A dispute for shuttling CB1 among different membrane microenvironments

    Science.gov (United States)

    Stornaiuolo, Mariano; Bruno, Agostino; Botta, Lorenzo; Regina, Giuseppe La; Cosconati, Sandro; Silvestri, Romano; Marinelli, Luciana; Novellino, Ettore

    2015-10-01

    A Cannabinoid Receptor 1 (CB1) binding site for the selective allosteric modulator ORG27569 is here identified through an integrate approach of consensus pocket prediction, mutagenesis studies and Mass Spectrometry. This unprecedented ORG27569 pocket presents the structural features of a Cholesterol Consensus Motif, a cholesterol interacting region already found in other GPCRs. ORG27569 and cholesterol affects oppositely CB1 affinity for orthosteric ligands. Moreover, the rise in cholesterol intracellular level results in CB1 trafficking to the axonal region of neuronal cells, while, on the contrary, ORG27568 binding induces CB1 enrichment at the soma. This control of receptor migration among functionally different membrane regions of the cell further contributes to downstream signalling and adds a previously unknown mechanism underpinning CB1 modulation by ORG27569 , that goes beyond a mere control of receptor affinity for orthosteric ligands.

  6. Selective oxidation of methionine residues in apolipoprotein A-I and its potential biological consequences

    International Nuclear Information System (INIS)

    Panzenboeck, U.; Waldeck, R.; Rye, K.A.; Sloane, T.; Kritharides, L.; Stocker, R.

    1998-01-01

    findings suggest that selective oxidation of Met residues of apo A-I may enhance rather than diminish known antiatherogenic activities of the apolipoprotein. Thus, our results are consistent with the overall hypothesis that detoxification of lipid hydroperoxides by Met residues of apo A-I is potentially antiatherogenic

  7. Development of an experimental activity for teaching cooperativity and allosterism

    Directory of Open Access Journals (Sweden)

    B. Manta

    2006-07-01

    Full Text Available Although  enzyme  control  and  regulation  is  an  important  topic  in  most  Biochemistry  and  Enzymology  courses, laboratory  activities  that  allow  an  experimental  approach  to  cooperativity  and  allosterism  are  difficult  to  implement. The objective of this work was to develop a simple and inexpensive experimental activity to teach this topic in basic courses.  We  decided  to  use  the  enzyme  glucosamine-6-phosphate  deaminase  (GNPD,  E.C.  3.5.99.6  from Escherichia coli,  that  is  both  kinetically  and  structurally  well-known.  GNPD  is  an  allosteric  enzyme,  activated  by  N-acetylglucosamine 6-phosphate, that catalyzes the conversion of glucosamine 6-phosphate into fructose 6-phosphate and  ammonia.  The  enzyme  is  a  typical  allosteric  K-system  and  can  be  well  described  by  the  Monod-Wyman-Changeux  (MWC  model.  GNPD  was  partially  purified  through  anionic-exchange  chromatography  from  a  mutant E.coli strain  which  expresses  constitutively  high  levels  of the  enzyme.  In  order  to  measure  activity  we  used  an end point  method  which  consists  in  stopping  the  reaction  at  a  certain  time  point  with  HCl  10  N,  and  quantifying  the fructose-6-phosphate  formed  with  resorcinol  (Selliwanoff  reaction  through  the  formation  of  a  red  color  that  is measured  spectrophotometrically.  We  developed  a  protocol  that  consisted  in  a  4-hour  experiment  in  which  the students  measured  the  activity  of  the  GNPD  with  increasing  concentrations  of  the  substrate,  in  the  presence  or absence  of  allosteric  modulator.  The  students  obtained  a  good  quality  data  set  that  they  analyzed  based  on  the equations  of  Hill,  MWC  and  Acerenza-Mirzaji

  8. Coarse-grained molecular simulations of allosteric cooperativity

    Energy Technology Data Exchange (ETDEWEB)

    Nandigrami, Prithviraj; Portman, John J. [Department of Physics, Kent State University, Kent, Ohio 44242 (United States)

    2016-03-14

    Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein’s functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two Ca{sup 2+} ions to each domain of Calmodulin (CaM) through simulations of a simple coarse-grained model. In this model, the protein’s conformational transitions between open and closed conformational ensembles are simulated explicitly and ligand binding and unbinding are treated implicitly within the grand canonical ensemble. Ligand binding is cooperative because the binding sites are coupled through a shift in the dominant conformational ensemble upon binding. The classic Monod-Wyman-Changeux model of allostery with appropriate binding free energies to the open and closed ensembles accurately describes the simulated binding thermodynamics. The simulations predict that the two domains of CaM have distinct binding affinity and cooperativity. In particular, the C-terminal domain binds Ca{sup 2+} with higher affinity and greater cooperativity than the N-terminal domain. From a structural point of view, the affinity of an individual binding loop depends sensitively on the loop’s structural compatibility with the ligand in the bound ensemble, as well as the conformational flexibility of the binding site in the unbound ensemble.

  9. Dipeptidyl peptidase IV as a potential target for selective prodrug activation and chemotherapeutic action in cancers.

    Science.gov (United States)

    Dahan, Arik; Wolk, Omri; Yang, Peihua; Mittal, Sachin; Wu, Zhiqian; Landowski, Christopher P; Amidon, Gordon L

    2014-12-01

    The efficacy of chemotherapeutic drugs is often offset by severe side effects attributable to poor selectivity and toxicity to normal cells. Recently, the enzyme dipeptidyl peptidase IV (DPPIV) was considered as a potential target for the delivery of chemotherapeutic drugs. The purpose of this study was to investigate the feasibility of targeting chemotherapeutic drugs to DPPIV as a strategy to enhance their specificity. The expression profile of DPPIV was obtained for seven cancer cell lines using DNA microarray data from the DTP database, and was validated by RT-PCR. A prodrug was then synthesized by linking the cytotoxic drug melphalan to a proline-glycine dipeptide moiety, followed by hydrolysis studies in the seven cell lines with a standard substrate, as well as the glycyl-prolyl-melphalan (GP-Mel). Lastly, cell proliferation studies were carried out to demonstrate enzyme-dependent activation of the candidate prodrug. The relative RT-PCR expression levels of DPPIV in the cancer cell lines exhibited linear correlation with U95Av2 Affymetrix data (r(2) = 0.94), and with specific activity of a standard substrate, glycine-proline-p-nitroanilide (r(2) = 0.96). The significantly higher antiproliferative activity of GP-Mel in Caco-2 cells (GI₅₀ = 261 μM) compared to that in SK-MEL-5 cells (GI₅₀ = 807 μM) was consistent with the 9-fold higher specific activity of the prodrug in Caco-2 cells (5.14 pmol/min/μg protein) compared to SK-MEL-5 cells (0.68 pmol/min/μg protein) and with DPPIV expression levels in these cells. Our results demonstrate the great potential to exploit DPPIV as a prodrug activating enzyme for efficient chemotherapeutic drug targeting.

  10. The Role of Protein-Ligand Contacts in Allosteric Regulation of the Escherichia coli Catabolite Activator Protein*

    Science.gov (United States)

    Townsend, Philip D.; Rodgers, Thomas L.; Glover, Laura C.; Korhonen, Heidi J.; Richards, Shane A.; Colwell, Lucy J.; Pohl, Ehmke; Wilson, Mark R.; Hodgson, David R. W.; McLeish, Tom C. B.; Cann, Martin J.

    2015-01-01

    Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distant site. Both experimental and theoretical evidence demonstrate that allostery can be communicated through altered slow relaxation protein dynamics without conformational change. The catabolite activator protein (CAP) of Escherichia coli is an exemplar for the analysis of such entropically driven allostery. Negative allostery in CAP occurs between identical cAMP binding sites. Changes to the cAMP-binding pocket can therefore impact the allosteric properties of CAP. Here we demonstrate, through a combination of coarse-grained modeling, isothermal calorimetry, and structural analysis, that decreasing the affinity of CAP for cAMP enhances negative cooperativity through an entropic penalty for ligand binding. The use of variant cAMP ligands indicates the data are not explained by structural heterogeneity between protein mutants. We observe computationally that altered interaction strength between CAP and cAMP variously modifies the change in allosteric cooperativity due to second site CAP mutations. As the degree of correlated motion between the cAMP-contacting site and a second site on CAP increases, there is a tendency for computed double mutations at these sites to drive CAP toward noncooperativity. Naturally occurring pairs of covarying residues in CAP do not display this tendency, suggesting a selection pressure to fine tune allostery on changes to the CAP ligand-binding pocket without a drive to a noncooperative state. In general, we hypothesize an evolutionary selection pressure to retain slow relaxation dynamics-induced allostery in proteins in which evolution of the ligand-binding site is occurring. PMID:26187469

  11. The Role of Protein-Ligand Contacts in Allosteric Regulation of the Escherichia coli Catabolite Activator Protein.

    Science.gov (United States)

    Townsend, Philip D; Rodgers, Thomas L; Glover, Laura C; Korhonen, Heidi J; Richards, Shane A; Colwell, Lucy J; Pohl, Ehmke; Wilson, Mark R; Hodgson, David R W; McLeish, Tom C B; Cann, Martin J

    2015-09-04

    Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distant site. Both experimental and theoretical evidence demonstrate that allostery can be communicated through altered slow relaxation protein dynamics without conformational change. The catabolite activator protein (CAP) of Escherichia coli is an exemplar for the analysis of such entropically driven allostery. Negative allostery in CAP occurs between identical cAMP binding sites. Changes to the cAMP-binding pocket can therefore impact the allosteric properties of CAP. Here we demonstrate, through a combination of coarse-grained modeling, isothermal calorimetry, and structural analysis, that decreasing the affinity of CAP for cAMP enhances negative cooperativity through an entropic penalty for ligand binding. The use of variant cAMP ligands indicates the data are not explained by structural heterogeneity between protein mutants. We observe computationally that altered interaction strength between CAP and cAMP variously modifies the change in allosteric cooperativity due to second site CAP mutations. As the degree of correlated motion between the cAMP-contacting site and a second site on CAP increases, there is a tendency for computed double mutations at these sites to drive CAP toward noncooperativity. Naturally occurring pairs of covarying residues in CAP do not display this tendency, suggesting a selection pressure to fine tune allostery on changes to the CAP ligand-binding pocket without a drive to a noncooperative state. In general, we hypothesize an evolutionary selection pressure to retain slow relaxation dynamics-induced allostery in proteins in which evolution of the ligand-binding site is occurring. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Jun; Byrne, Noel; Wang, John; Bricogne, Gerard; Brown, Frank K.; Chobanian, Harry R.; Colletti, Steven L.; Di Salvo, Jerry; Thomas-Fowlkes, Brande; Guo, Yan; Hall, Dawn L.; Hadix, Jennifer; Hastings, Nicholas B.; Hermes, Jeffrey D.; Ho, Thu; Howard, Andrew D.; Josien, Hubert; Kornienko, Maria; Lumb, Kevin J.; Miller, Michael W.; Patel, Sangita B.; Pio, Barbara; Plummer, Christopher W.; Sherborne, Bradley S.; Sheth, Payal; Souza, Sarah; Tummala, Srivanya; Vonrhein, Clemens; Webb, Maria; Allen, Samantha J.; Johnston, Jennifer M.; Weinglass, Adam B.; Sharma, Sujata; Soisson, Stephen M. (Merck); (Globel Phasing)

    2017-06-05

    Clinical studies indicate that partial agonists of the G-protein-coupled, free fatty acid receptor 1 GPR40 enhance glucose-dependent insulin secretion and represent a potential mechanism for the treatment of type 2 diabetes mellitus. Full allosteric agonists (AgoPAMs) of GPR40 bind to a site distinct from partial agonists and can provide additional efficacy. We report the 3.2-Å crystal structure of human GPR40 (hGPR40) in complex with both the partial agonist MK-8666 and an AgoPAM, which exposes a novel lipid-facing AgoPAM-binding pocket outside the transmembrane helical bundle. Comparison with an additional 2.2-Å structure of the hGPR40–MK-8666 binary complex reveals an induced-fit conformational coupling between the partial agonist and AgoPAM binding sites, involving rearrangements of the transmembrane helices 4 and 5 (TM4 and TM5) and transition of the intracellular loop 2 (ICL2) into a short helix. These conformational changes likely prime GPR40 to a more active-like state and explain the binding cooperativity between these ligands.

  13. Selective formation of biphasic thin films of metal–organic frameworks by potential-controlled cathodic electrodeposition

    OpenAIRE

    Li, Minyuan Miller; Dinca, Mircea

    2013-01-01

    Cathodic electrodeposition lends itself to the formation of biphasic metal–organic framework thin films at room temperature from single deposition baths using potential bias as the main user input. Depending on the applied potential, we selectively deposit two different phases as either bulk mixtures or bilayer films.

  14. Effects of selective activation of M1 and M4 muscarinic receptors on object recognition memory performance in rats.

    Science.gov (United States)

    Galloway, Claire R; Lebois, Evan P; Shagarabi, Shezza L; Hernandez, Norma A; Manns, Joseph R

    2014-01-01

    Acetylcholine signaling through muscarinic receptors has been shown to benefit memory performance in some conditions, but pan-muscarinic activation also frequently leads to peripheral side effects. Drug therapies that selectively target M1 or M4 muscarinic receptors could potentially improve memory while minimizing side effects mediated by the other muscarinic receptor subtypes. The ability of three recently developed drugs that selectively activate M1 or M4 receptors to improve recognition memory was tested by giving Long-Evans rats subcutaneous injections of three different doses of the M1 agonist VU0364572, the M1 positive allosteric modulator BQCA or the M4 positive allosteric modulator VU0152100 before performing an object recognition memory task. VU0364572 at 0.1 mg/kg, BQCA at 1.0 mg/kg and VU0152100 at 3.0 and 30.0 mg/kg improved the memory performance of rats that performed poorly at baseline, yet the improvements in memory performance were the most statistically robust for VU0152100 at 3.0 mg/kg. The results suggested that selective M1 and M4 receptor activation each improved memory but that the likelihood of obtaining behavioral efficacy at a given dose might vary between subjects even in healthy groups depending on baseline performance. These results also highlighted the potential of drug therapies that selectively target M1 or M4 receptors to improve memory performance in individuals with impaired memory.

  15. A general definition of the heritable variation that determines the potential of a population to respond to selection.

    Science.gov (United States)

    Bijma, Piter

    2011-12-01

    Genetic selection is a major force shaping life on earth. In classical genetic theory, response to selection is the product of the strength of selection and the additive genetic variance in a trait. The additive genetic variance reflects a population's intrinsic potential to respond to selection. The ordinary additive genetic variance, however, ignores the social organization of life. With social interactions among individuals, individual trait values may depend on genes in others, a phenomenon known as indirect genetic effects. Models accounting for indirect genetic effects, however, lack a general definition of heritable variation. Here I propose a general definition of the heritable variation that determines the potential of a population to respond to selection. This generalizes the concept of heritable variance to any inheritance model and level of organization. The result shows that heritable variance determining potential response to selection is the variance among individuals in the heritable quantity that determines the population mean trait value, rather than the usual additive genetic component of phenotypic variance. It follows, therefore, that heritable variance may exceed phenotypic variance among individuals, which is impossible in classical theory. This work also provides a measure of the utilization of heritable variation for response to selection and integrates two well-known models of maternal genetic effects. The result shows that relatedness between the focal individual and the individuals affecting its fitness is a key determinant of the utilization of heritable variance for response to selection.

  16. Newly-formed emotional memories guide selective attention processes: Evidence from event-related potentials

    Science.gov (United States)

    Schupp, Harald T.; Kirmse, Ursula; Schmälzle, Ralf; Flaisch, Tobias; Renner, Britta

    2016-01-01

    Emotional cues can guide selective attention processes. However, emotional stimuli can both activate long-term memory representations reflecting general world knowledge and engage newly formed memory representations representing specific knowledge from the immediate past. Here, the self-completion feature of associative memory was utilized to assess the regulation of attention processes by newly-formed emotional memory. First, new memory representations were formed by presenting pictures depicting a person either in an erotic pose or as a portrait. Afterwards, to activate newly-built memory traces, edited pictures were presented showing only the head region of the person. ERP recordings revealed the emotional regulation of attention by newly-formed memories. Specifically, edited pictures from the erotic compared to the portrait category elicited an early posterior negativity and late positive potential, similar to the findings observed for the original pictures. A control condition showed that the effect was dependent on newly-formed memory traces. Given the large number of new memories formed each day, they presumably make an important contribution to the regulation of attention in everyday life. PMID:27321471

  17. Improvement of selected strains through gamma irradiation for enhanced lipolytic potential

    International Nuclear Information System (INIS)

    Iftikhar, T.; Mubashir, N.; Hussain, Y.; Abbas, S.Q.; Ashraf, I.

    2010-01-01

    The purpose of the present investigation was to enhance the production of industrially important enzyme lipase by subjecting the wild lipase producing fungal strains i.e. Aspergillus niger, Rhizopus microsporus and Penicillium atrovenetum to various doses of gamma irradiation (20, 40, 60, 80, 100, 120, 140 and 160 Gy). The isolation and lipolytic activity of selected mutant derived strains is described in this paper. Among all the mutants tested, MBL-5 obtained at 140Gy of Aspergillus niger strain showed highest extracellular lipase activity (13.75 +- 0.15 U mL/sup -1/) while MBL-1 Rhizopus microsporus at the rate 20Gy showed the lowest activity i.e., 1.06 +- 0.11 U mL/sup -1/. A range of pH 3, 5, 7, 9 and 11 was used to check the lipolytic potential of various mutants along with their wild type. It was observed that MBL-5 (Aspergillus niger) and MBL-2 (Rhizopus microsporus) showed enhanced extracellular lipase activity at pH 11 while MBL-3 (Penicillium atrovenetum) showed the highest extracellular lipase activity 22.53 +- 0.21 U mL/sup -1/ at pH 9. It indicates a possible role for the MBL-2, MBL-3 and MBL-5 mutant strains in the detergent industry for the development of eco-friendly technologies. (author)

  18. Newly-formed emotional memories guide selective attention processes: Evidence from event-related potentials.

    Science.gov (United States)

    Schupp, Harald T; Kirmse, Ursula; Schmälzle, Ralf; Flaisch, Tobias; Renner, Britta

    2016-06-20

    Emotional cues can guide selective attention processes. However, emotional stimuli can both activate long-term memory representations reflecting general world knowledge and engage newly formed memory representations representing specific knowledge from the immediate past. Here, the self-completion feature of associative memory was utilized to assess the regulation of attention processes by newly-formed emotional memory. First, new memory representations were formed by presenting pictures depicting a person either in an erotic pose or as a portrait. Afterwards, to activate newly-built memory traces, edited pictures were presented showing only the head region of the person. ERP recordings revealed the emotional regulation of attention by newly-formed memories. Specifically, edited pictures from the erotic compared to the portrait category elicited an early posterior negativity and late positive potential, similar to the findings observed for the original pictures. A control condition showed that the effect was dependent on newly-formed memory traces. Given the large number of new memories formed each day, they presumably make an important contribution to the regulation of attention in everyday life.

  19. Transport and selective chaining of bidisperse particles in a travelling wave potential.

    Science.gov (United States)

    Tierno, Pietro; Straube, Arthur V

    2016-05-01

    We combine experiments, theory and numerical simulation to investigate the dynamics of a binary suspension of paramagnetic colloidal particles dispersed in water and transported above a stripe-patterned magnetic garnet film. The substrate generates a one-dimensional periodic energy landscape above its surface. The application of an elliptically polarized rotating magnetic field causes the landscape to translate, inducing direct transport of paramagnetic particles placed above the film. The ellipticity of the applied field can be used to control and tune the interparticle interactions, from net repulsive to net attractive. When considering particles of two distinct sizes, we find that, depending on their elevation above the surface of the magnetic substrate, the particles feel effectively different potentials, resulting in different mobilities. We exploit this feature to induce selective chaining for certain values of the applied field parameters. In particular, when driving two types of particles, we force only one type to condense into travelling parallel chains. These chains confine the movement of the other non-chaining particles within narrow colloidal channels. This phenomenon is explained by considering the balance of pairwise magnetic forces between the particles and their individual coupling with the travelling landscape.

  20. Selection of a mineral binder with potentialities for the stabilization/solidification of aluminum metal

    Energy Technology Data Exchange (ETDEWEB)

    Cau Dit Coumes, C., E-mail: celine.cau-dit-coumes@cea.fr [Commissariat à l’Energie Atomique et aux Energies Alternatives, CEA/DEN/MAR/DTCD/SPDE, BP17171, 30207 Bagnols-sur-Cèze cedex (France); Lambertin, D.; Lahalle, H.; Antonucci, P. [Commissariat à l’Energie Atomique et aux Energies Alternatives, CEA/DEN/MAR/DTCD/SPDE, BP17171, 30207 Bagnols-sur-Cèze cedex (France); Cannes, C.; Delpech, S. [Institut de Physique Nucléaire, CNRS, Univ. Paris-Sud 11, 91406 Orsay Cedex (France)

    2014-10-15

    Highlights: • Binders capable of reducing the pore solution pH compared with Portland cements are reviewed. • The binders are then tested against aluminum corrosion. • Corrosion of aluminum metal is minimal with magnesium phosphate cement. • The H{sub 2} release can be reduced still further by adding LiNO{sub 3} to the mixing solution. • Electrochemical characterizations show that aluminum tends to a passive state. - Abstract: In a strongly alkaline medium, such as that encountered in conventional cementitious materials based on Portland cement, aluminum metal is corroded, with continued production of hydrogen. In order to develop a mineral matrix having enhanced compatibility with aluminum, a literature review was first undertaken to identify binders capable of reducing the pore solution pH compared with Portland cement. An experimental study was then carried out to measure the hydrogen production resulting from corrosion of aluminum metal rods encapsulated in the different selected cement pastes. The best results were achieved with magnesium phosphate cement, which released very little hydrogen over the duration of the study. This production could be reduced still further by adding a corrosion inhibitor (lithium nitrate) to the mixing solution. Open circuit potential measurement and Electrochemical Impedance Spectroscopy of aluminum electrode encapsulated in two pastes based on Portland cement and magnesium phosphate cement showed different redox behaviors. In the Portland cement paste, the electrochemical data confirmed the corrosion of aluminum whereas this latter tended to a passive state in the magnesium phosphate binder.

  1. The selective Aurora B kinase inhibitor AZD1152 is a potential new treatment for multiple myeloma.

    Science.gov (United States)

    Evans, Robert P; Naber, Claudia; Steffler, Tara; Checkland, Tamara; Maxwell, Christopher A; Keats, Jonathan J; Belch, Andrew R; Pilarski, Linda M; Lai, Raymond; Reiman, Tony

    2008-02-01

    Aurora kinases are potential targets for cancer therapy. Previous studies have validated Aurora kinase A as a therapeutic target in multiple myeloma (MM), and have demonstrated in vitro anti-myeloma effects of small molecule Aurora kinase inhibitors that inhibit both Aurora A and B. This study demonstrated that Aurora B kinase was strongly expressed in myeloma cell lines and primary plasma cells. The selective Aurora B inhibitor AZD1152-induced apoptotic death in myeloma cell lines at nanomolar concentrations, with a cell cycle phenotype consistent with that reported previously for Aurora B inhibition. In some cases, AZD1152 in combination with dexamethasone showed increased anti-myeloma activity compared with the use of either agent alone. AZD1152 was active against sorted CD138(+) BM plasma cells from myeloma patients but also, as expected, was toxic to CD138(-) marrow cells from the same patients. In a murine myeloma xenograft model, AZD1152-inhibited tumour growth at well-tolerated doses and induced cell death in established tumours, with associated mild, transient leucopenia. AZD1152 shows promise in these preclinical studies as a novel treatment for MM.

  2. Nutritional Potential of Selected Insect Species Reared on the Island of Sumatra.

    Science.gov (United States)

    Adámková, Anna; Mlček, Jiří; Kouřimská, Lenka; Borkovcová, Marie; Bušina, Tomáš; Adámek, Martin; Bednářová, Martina; Krajsa, Jan

    2017-05-12

    Inhabitants of the Indonesian island of Sumatra are faced with the problem of insufficient food supplies and the consequent risk of undernourishment and health issues. Edible insects as a traditional and readily available food source could be part of the solution. The nutritional value of insects depends on many factors, e.g., species, developmental stage, sex, diet, and climatic conditions. However, edible insects bred in Sumatra for human consumption have never before been assessed with regard to their nutritional value. Our study involved analyses of crude protein, chitin, fat and selected fatty acid contents of giant mealworm larvae ( Zophobas morio ), larvae of the common mealworm ( Tenebrio molitor) and nymphs of the field cricket ( Gryllus assimilis ). Crude protein content in the samples ranged from 46% to 56%. Highest (35%) and lowest (31%) amounts of fat were recorded in giant mealworm larvae and larvae of the common mealworm, respectively. Chitin amounts ranged from 6% to 13%. Based on these values, which are comparable to those known from other food insects reared in different regions of the world, the edible species bred in Sumatra could become food sources with a potential to help stave off hunger and undernourishment.

  3. EEG Channel Selection Using Particle Swarm Optimization for the Classification of Auditory Event-Related Potentials

    Directory of Open Access Journals (Sweden)

    Alejandro Gonzalez

    2014-01-01

    Full Text Available Brain-machine interfaces (BMI rely on the accurate classification of event-related potentials (ERPs and their performance greatly depends on the appropriate selection of classifier parameters and features from dense-array electroencephalography (EEG signals. Moreover, in order to achieve a portable and more compact BMI for practical applications, it is also desirable to use a system capable of accurate classification using information from as few EEG channels as possible. In the present work, we propose a method for classifying P300 ERPs using a combination of Fisher Discriminant Analysis (FDA and a multiobjective hybrid real-binary Particle Swarm Optimization (MHPSO algorithm. Specifically, the algorithm searches for the set of EEG channels and classifier parameters that simultaneously maximize the classification accuracy and minimize the number of used channels. The performance of the method is assessed through offline analyses on datasets of auditory ERPs from sound discrimination experiments. The proposed method achieved a higher classification accuracy than that achieved by traditional methods while also using fewer channels. It was also found that the number of channels used for classification can be significantly reduced without greatly compromising the classification accuracy.

  4. Intrinsic Immunomodulatory Effects of Low-Digestible Carbohydrates Selectively Extend Their Anti-Inflammatory Prebiotic Potentials

    Directory of Open Access Journals (Sweden)

    Jérôme Breton

    2015-01-01

    Full Text Available The beneficial effects of carbohydrate-derived fibers are mainly attributed to modulation of the microbiota, increased colonic fermentation, and the production of short-chain fatty acids. We studied the direct immune responses to alimentary fibers in in vitro and in vivo models. Firstly, we evaluated the immunomodulation induced by nine different types of low-digestible fibers on human peripheral blood mononuclear cells. None of the fibers tested induced cytokine production in baseline conditions. However, only one from all fibers almost completely inhibited the production of anti- and proinflammatory cytokines induced by bacteria. Secondly, the impact of short- (five days and long-term (three weeks oral treatments with selected fibers was assessed in the trinitrobenzene-sulfonic acid colitis model in mice. The immunosuppressive fiber significantly reduced levels of inflammatory markers over both treatment periods, whereas a nonimmunomodulatory fiber had no effect. The two fibers did not differ in terms of the observed fermentation products and colonic microbiota after three weeks of treatment, suggesting that the anti-inflammatory action was not related to prebiotic properties. Hence, we observed a direct effect of a specific fiber on the murine immune system. This intrinsic, fiber-dependent immunomodulatory potential may extend prebiotic-mediated protection in inflammatory bowel disease.

  5. Automated tube potential selection for standard chest and abdominal CT in follow-up patients with testicular cancer: comparison with fixed tube potential

    Energy Technology Data Exchange (ETDEWEB)

    Gnannt, Ralph; Winklehner, Anna; Frauenfelder, Thomas; Alkadhi, Hatem [University Hospital Zurich, Institute of Diagnostic and Interventional Radiology, Zurich (Switzerland); Eberli, Daniel [University Hospital Zurich, Clinic for Urology, Zurich (Switzerland); Knuth, Alexander [University Hospital Zurich, Clinic for Oncology, Zurich (Switzerland)

    2012-09-15

    To evaluate prospectively, in patients with testicular cancer, the radiation dose-saving potential and image quality of contrast-enhanced chest and abdominal CT with automated tube potential selection. Forty consecutive patients with testicular cancer underwent contrast-enhanced arterio-venous chest and portal-venous abdominal CT with automated tube potential selection (protocol B; tube potential 80-140 kVp), which is based on the attenuation of the CT topogram. All had a first CT at 120 kVp (protocol A) using the same 64-section CT machine and similar settings. Image quality was assessed; dose information (CTDI{sub vol}) was noted. Image noise and attenuation in the liver and spleen were significantly higher for protocol B (P < 0.05 each), whereas attenuation in the deltoid and erector spinae muscles was similar. In protocol B, tube potential was reduced to 100 kVp in 18 chest and 33 abdominal examinations, and to 80 kVp in 5 abdominal CT examinations; it increased to 140 kVp in one patient. Image quality of examinations using both CT protocols was rated as diagnostic. CTDI{sub vol} was significantly lower for protocol B compared to protocol A (reduction by 12%, P < 0.01). In patients with testicular cancer, radiation dose of chest and abdominal CT can be reduced with automated tube potential selection, while image quality is preserved. (orig.)

  6. Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions.

    Science.gov (United States)

    Hacisuleyman, Aysima; Erman, Burak

    2017-06-01

    A fast and approximate method of generating allosteric communication landscapes in proteins is presented by using Schreiber's entropy transfer concept in combination with the Gaussian Network Model of proteins. Predictions of the model and the allosteric communication landscapes generated show that information transfer in proteins does not necessarily take place along a single path, but an ensemble of pathways is possible. The model emphasizes that knowledge of entropy only is not sufficient for determining allosteric communication and additional information based on time delayed correlations should be introduced, which leads to the presence of causality in proteins. The model provides a simple tool for mapping entropy sink-source relations into pairs of residues. By this approach, residues that should be manipulated to control protein activity may be determined. This should be of great importance for allosteric drug design and for understanding the effects of mutations on function. The model is applied to determine allosteric communication in three proteins, Ubiquitin, Pyruvate Kinase, and the PDZ domain. Predictions are in agreement with molecular dynamics simulations and experimental evidence. Proteins 2017; 85:1056-1064. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  7. Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure.

    Science.gov (United States)

    Takayanagi, Masayoshi; Kurisaki, Ikuo; Nagaoka, Masataka

    2014-04-08

    Protein allostery is essential for vital activities. Allosteric regulation of human hemoglobin (HbA) with two quaternary states T and R has been a paradigm of allosteric structural regulation of proteins. It is widely accepted that oxygen molecules (O2) act as a "site-specific" homotropic effector, or the successive O2 binding to the heme brings about the quaternary regulation. However, here we show that the site-specific allosteric effect is not necessarily only a unique mechanism of O2 allostery. Our simulation results revealed that the solution environment of high O2 partial pressure enhances the quaternary change from T to R without binding to the heme, suggesting an additional "non-site-specific" allosteric effect of O2. The latter effect should play a complementary role in the quaternary change by affecting the intersubunit contacts. This analysis must become a milestone in comprehensive understanding of the allosteric regulation of HbA from the molecular point of view.

  8. Understanding the Functional Plasticity in Neural Networks of the Basal Ganglia in Cocaine Use Disorder: A Role for Allosteric Receptor-Receptor Interactions in A2A-D2 Heteroreceptor Complexes

    Directory of Open Access Journals (Sweden)

    Dasiel O. Borroto-Escuela

    2016-01-01

    Full Text Available Our hypothesis is that allosteric receptor-receptor interactions in homo- and heteroreceptor complexes may form the molecular basis of learning and memory. This principle is illustrated by showing how cocaine abuse can alter the adenosine A2AR-dopamine D2R heterocomplexes and their receptor-receptor interactions and hereby induce neural plasticity in the basal ganglia. Studies with A2AR ligands using cocaine self-administration procedures indicate that antagonistic allosteric A2AR-D2R heterocomplexes of the ventral striatopallidal GABA antireward pathway play a significant role in reducing cocaine induced reward, motivation, and cocaine seeking. Anticocaine actions of A2AR agonists can also be produced at A2AR homocomplexes in these antireward neurons, actions in which are independent of D2R signaling. At the A2AR-D2R heterocomplex, they are dependent on the strength of the antagonistic allosteric A2AR-D2R interaction and the number of A2AR-D2R and A2AR-D2R-sigma1R heterocomplexes present in the ventral striatopallidal GABA neurons. It involves a differential cocaine-induced increase in sigma1Rs in the ventral versus the dorsal striatum. In contrast, the allosteric brake on the D2R protomer signaling in the A2AR-D2R heterocomplex of the dorsal striatopallidal GABA neurons is lost upon cocaine self-administration. This is potentially due to differences in composition and allosteric plasticity of these complexes versus those in the ventral striatopallidal neurons.

  9. Orthosteric and Allosteric Ligands of Nicotinic Acetylcholine Receptors for Smoking Cessation

    Directory of Open Access Journals (Sweden)

    Tasnim S. Mohamed

    2015-11-01

    Full Text Available Nicotine addiction, the result of tobacco use, leads to over six million premature deaths world-wide, a number that is expected to increase by a third within the next two decades. While more than half of smokers want and attempt to quit, only a small percentage of smokers are able to quit without pharmacological interventions. Therefore, over the past decades, researchers in academia and the pharmaceutical industry have focused their attention on the development of more effective smoking cessation therapies, which is now a growing 1.9 billion dollar market. Because the role of neuronal nicotinic acetylcholine receptors (nAChR in nicotine addiction is well established, nAChR based therapeutics remain the leading strategy for smoking cessation. However, the development of neuronal nAChR drugs that are selective for a nAChR subpopulation is challenging, and only few neuronal nAChR drugs are clinically available. Among the many neuronal nAChR subtypes that have been identified in the brain, the α4β2 subtype is the most abundant and plays a critical role in nicotine addiction. Here, we review the role of neuronal nAChRs, especially the α4β2 subtype, in the development and treatment of nicotine addiction. We also compare available smoking cessation medications and other nAChR orthosteric and allosteric ligands that have been developed with emphasis on the difficulties faced in the development of clinically useful compounds with high nAChR subtype selectivity.

  10. Shift in the Equilibrium between On and Off States of the Allosteric Switch in Ras-GppNHp Affected by Small Molecules and Bulk Solvent Composition

    Energy Technology Data Exchange (ETDEWEB)

    Holzapfel, Genevieve; Buhrman, Greg; Mattos, Carla (NCSU)

    2012-08-31

    Ras GTPase cycles between its active GTP-bound form promoted by GEFs and its inactive GDP-bound form promoted by GAPs to affect the control of various cellular functions. It is becoming increasingly apparent that subtle regulation of the GTP-bound active state may occur through promotion of substates mediated by an allosteric switch mechanism that induces a disorder to order transition in switch II upon ligand binding at an allosteric site. We show with high-resolution structures that calcium acetate and either dithioerythritol (DTE) or dithiothreitol (DTT) soaked into H-Ras-GppNHp crystals in the presence of a moderate amount of poly(ethylene glycol) (PEG) can selectively shift the equilibrium to the 'on' state, where the active site appears to be poised for catalysis (calcium acetate), or to what we call the 'ordered off' state, which is associated with an anticatalytic conformation (DTE or DTT). We also show that the equilibrium is reversible in our crystals and dependent on the nature of the small molecule present. Calcium acetate binding in the allosteric site stabilizes the conformation observed in the H-Ras-GppNHp/NOR1A complex, and PEG, DTE, and DTT stabilize the anticatalytic conformation observed in the complex between the Ras homologue Ran and Importin-{beta}. The small molecules are therefore selecting biologically relevant conformations in the crystal that are sampled by the disordered switch II in the uncomplexed GTP-bound form of H-Ras. In the presence of a large amount of PEG, the ordered off conformation predominates, whereas in solution, in the absence of PEG, switch regions appear to remain disordered in what we call the off state, unable to bind DTE.

  11. Phenolic content, antioxidant potential and Aedes aegyptii ecological friend larvicidal activity of some selected Egyptian plants.

    Science.gov (United States)

    El-Hela, Atef A; Abdel-Hady, Nevein M; Dawoud, Gouda T M; Hamed, Abdo M; Morsy, Tosson A

    2013-04-01

    Polyphenols constitute a distinct group of natural compounds of medicinal importance exhibiting wide range of physiological activities as antioxidant, immunestimulant, antitumor and antiparasitic. Yellow fever and dengue fever are mosquito-borne infectious diseases transmitted by Aedes aegyptii, the presence of yellow fever in Sudan and dengue fever in Saudi Arabia are threats to Egypt with the reemerging of Ae. aegyptii in Southern Egypt, larvae control is feasible than flying adults. This work was conducted targeting estimation of the relative levels of total phenolic content, antioxidant potential and larvicidal activity of 110 selected Egyptian plants. The highest total phenolic contents were estimated in aqueous extracts of Coronilla scorpioides L., Forsskaolea tenacissima L., Crataegus sinaica Boiss., Pistacia khinjuk Boiss. and Loranthus acacia Benth.; they were 916.70 +/- 4.80, 813.70 +/- 4.16, 744.90 +/- 4.93, 549.00 +/- 3.93& 460.80 +/- 4.02 mg% while those of methanol extracts were estimated in Coronilla scorpioides, Forsskaolea tenacissima, Crataegus sinaica, Loranthus acacia and Pistacia khinjuk, they were 915.60-4.86, 664.60 +/- 4.16, 659.30 +/- 4.80, 590.80 +/- 4.49 & 588.00 +/- 3.85 mg% respectively. Investigation of the antioxidant potentials revealed that the most potent plants were Co-ronilla scorpioides, Forsskaolea tenacissima, Crataegus sinaica, Pistacia khinjuk and Loranthus acacia with calculated values of 454.80 +/- 4.83, 418.4 +/- 4.16, 399.10 +/- 4.90, 342.5 +/- 2.72 & 239.7 +/- 2.91% for aqueous extracts and 452.9 +/- 4.94, 389.6 +/- 4.6, 378.48 +/- 3.84, 352.3 +/- 3.06 & 346.5 +/- 2.98% for methanol extracts respectively while screening of larvicidal activity proved that Coronilla scorpioides, Forsskaolea tenacissima, Crataegus sinaica, Pistacia khinjuk and Loranthus acacia exhibited highest potency calculated as 22.53 +/- 2.01, 23.85 +/- 2.07, 28.17 +/- 2.06, 31.60 +/- 2.93 & 39.73 +/- 4.58 mg% aqueous extracts and 18.53 +/- 1.95, 18

  12. Atrial-selective K+ channel blockers: potential antiarrhythmic drugs in atrial fibrillation?

    Science.gov (United States)

    Ravens, Ursula

    2017-11-01

    In the wake of demographic change in Western countries, atrial fibrillation has reached an epidemiological scale, yet current strategies for drug treatment of the arrhythmia lack sufficient efficacy and safety. In search of novel medications, atrial-selective drugs that specifically target atrial over other cardiac functions have been developed. Here, I will address drugs acting on potassium (K + ) channels that are either predominantly expressed in atria or possess electrophysiological properties distinct in atria from ventricles. These channels include the ultra-rapidly activating, delayed outward-rectifying Kv1.5 channel conducting I Kur , the acetylcholine-activated inward-rectifying Kir3.1/Kir3.4 channel conducting I K,ACh , the Ca 2+ -activated K + channels of small conductance (SK) conducting I SK , and the two-pore domain K + (K2P) channels (tandem of P domains, weak inward-rectifying K + channels (TWIK-1), TWIK-related acid-sensitive K + channels (TASK-1 and TASK-3)) that are responsible for voltage-independent background currents I TWIK-1 , I TASK-1 , and I TASK-3 . Direct drug effects on these channels are described and their putative value in treatment of atrial fibrillation is discussed. Although many potential drug targets have emerged in the process of unravelling details of the pathophysiological mechanisms responsible for atrial fibrillation, we do not know whether novel antiarrhythmic drugs will be more successful when modulating many targets or a single specific one. The answer to this riddle can only be solved in a clinical context.

  13. Mutation of I696 and W697 in the TRP box of vanilloid receptor subtype I modulates allosteric channel activation.

    Science.gov (United States)

    Gregorio-Teruel, Lucia; Valente, Pierluigi; González-Ros, José Manuel; Fernández-Ballester, Gregorio; Ferrer-Montiel, Antonio

    2014-03-01

    The transient receptor potential vanilloid receptor subtype I (TRPV1) channel acts as a polymodal sensory receptor gated by chemical and physical stimuli. Like other TRP channels, TRPV1 contains in its C terminus a short, conserved domain called the TRP box, which is necessary for channel gating. Substitution of two TRP box residues-I696 and W697-with Ala markedly affects TRPV1's response to all activating stimuli, which indicates that these two residues play a crucial role in channel gating. We systematically replaced I696 and W697 with 18 native l-amino acids (excluding cysteine) and evaluated the effect on voltage- and capsaicin-dependent gating. Mutation of I696 decreased channel activation by either voltage or capsaicin; furthermore, gating was only observed with substitution of hydrophobic amino acids. Substitution of W697 with any of the 18 amino acids abolished gating in response to depolarization alone, shifting the threshold to unreachable voltages, but not capsaicin-mediated gating. Moreover, vanilloid-activated responses of W697X mutants showed voltage-dependent gating along with a strong voltage-independent component. Analysis of the data using an allosteric model of activation indicates that mutation of I696 and W697 primarily affects the allosteric coupling constants of the ligand and voltage sensors to the channel pore. Together, our findings substantiate the notion that inter- and/or intrasubunit interactions at the level of the TRP box are critical for efficient coupling of stimulus sensing and gate opening. Perturbation of these interactions markedly reduces the efficacy and potency of the activating stimuli. Furthermore, our results identify these interactions as potential sites for pharmacological intervention.

  14. Pharmacology of basimglurant (RO4917523, RG7090), a unique metabotropic glutamate receptor 5 negative allosteric modulator in clinical development for depression.

    Science.gov (United States)

    Lindemann, Lothar; Porter, Richard H; Scharf, Sebastian H; Kuennecke, Basil; Bruns, Andreas; von Kienlin, Markus; Harrison, Anthony C; Paehler, Axel; Funk, Christoph; Gloge, Andreas; Schneider, Manfred; Parrott, Neil J; Polonchuk, Liudmila; Niederhauser, Urs; Morairty, Stephen R; Kilduff, Thomas S; Vieira, Eric; Kolczewski, Sabine; Wichmann, Juergen; Hartung, Thomas; Honer, Michael; Borroni, Edilio; Moreau, Jean-Luc; Prinssen, Eric; Spooren, Will; Wettstein, Joseph G; Jaeschke, Georg

    2015-04-01

    Major depressive disorder (MDD) is a serious public health burden and a leading cause of disability. Its pharmacotherapy is currently limited to modulators of monoamine neurotransmitters and second-generation antipsychotics. Recently, glutamatergic approaches for the treatment of MDD have increasingly received attention, and preclinical research suggests that metabotropic glutamate receptor 5 (mGlu5) inhibitors have antidepressant-like properties. Basimglurant (2-chloro-4-[1-(4-fluoro-phenyl)-2,5-dimethyl-1H-imidazol-4-ylethynyl]-pyridine) is a novel mGlu5 negative allosteric modulator currently in phase 2 clinical development for MDD and fragile X syndrome. Here, the comprehensive preclinical pharmacological profile of basimglurant is presented with a focus on its therapeutic potential for MDD and drug-like properties. Basimglurant is a potent, selective, and safe mGlu5 inhibitor with good oral bioavailability and long half-life supportive of once-daily administration, good brain penetration, and high in vivo potency. It has antidepressant properties that are corroborated by its functional magnetic imaging profile as well as anxiolytic-like and antinociceptive features. In electroencephalography recordings, basimglurant shows wake-promoting effects followed by increased delta power during subsequent non-rapid eye movement sleep. In microdialysis studies, basimglurant had no effect on monoamine transmitter levels in the frontal cortex or nucleus accumbens except for a moderate increase of accumbal dopamine, which is in line with its lack of pharmacological activity on monoamine reuptake transporters. These data taken together, basimglurant has favorable drug-like properties, a differentiated molecular mechanism of action, and antidepressant-like features that suggest the possibility of also addressing important comorbidities of MDD including anxiety and pain as well as daytime sleepiness and apathy or lethargy. Copyright © 2015 by The American Society for

  15. Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases

    Science.gov (United States)

    Buey, Rubén M.; Ledesma-Amaro, Rodrigo; Velázquez-Campoy, Adrián; Balsera, Mónica; Chagoyen, Mónica; de Pereda, José M.; Revuelta, José L.

    2015-11-01

    Inosine-5'-monophosphate dehydrogenase (IMPDH) plays key roles in purine nucleotide metabolism and cell proliferation. Although IMPDH is a widely studied therapeutic target, there is limited information about its physiological regulation. Using Ashbya gossypii as a model, we describe the molecular mechanism and the structural basis for the allosteric regulation of IMPDH by guanine nucleotides. We report that GTP and GDP bind to the regulatory Bateman domain, inducing octamers with compromised catalytic activity. Our data suggest that eukaryotic and prokaryotic IMPDHs might have developed different regulatory mechanisms, with GTP/GDP inhibiting only eukaryotic IMPDHs. Interestingly, mutations associated with human retinopathies map into the guanine nucleotide-binding sites including a previously undescribed non-canonical site and disrupt allosteric inhibition. Together, our results shed light on the mechanisms of the allosteric regulation of enzymes mediated by Bateman domains and provide a molecular basis for certain retinopathies, opening the door to new therapeutic approaches.

  16. Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins.

    Science.gov (United States)

    Yao, Xin-Qiu; Malik, Rabia U; Griggs, Nicholas W; Skjærven, Lars; Traynor, John R; Sivaramakrishnan, Sivaraj; Grant, Barry J

    2016-02-26

    G protein α subunits cycle between active and inactive conformations to regulate a multitude of intracellular signaling cascades. Important structural transitions occurring during this cycle have been characterized from extensive crystallographic studies. However, the link between observed conformations and the allosteric regulation of binding events at distal sites critical for signaling through G proteins remain unclear. Here we describe molecular dynamics simulations, bioinformatics analysis, and experimental mutagenesis that identifies residues involved in mediating the allosteric coupling of receptor, nucleotide, and helical domain interfaces of Gαi. Most notably, we predict and characterize novel allosteric decoupling mutants, which display enhanced helical domain opening, increased rates of nucleotide exchange, and constitutive activity in the absence of receptor activation. Collectively, our results provide a framework for explaining how binding events and mutations can alter internal dynamic couplings critical for G protein function. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Penalized regression procedures for variable selection in the potential outcomes framework.

    Science.gov (United States)

    Ghosh, Debashis; Zhu, Yeying; Coffman, Donna L

    2015-05-10

    A recent topic of much interest in causal inference is model selection. In this article, we describe a framework in which to consider penalized regression approaches to variable selection for causal effects. The framework leads to a simple 'impute, then select' class of procedures that is agnostic to the type of imputation algorithm as well as penalized regression used. It also clarifies how model selection involves a multivariate regression model for causal inference problems and that these methods can be applied for identifying subgroups in which treatment effects are homogeneous. Analogies and links with the literature on machine learning methods, missing data, and imputation are drawn. A difference least absolute shrinkage and selection operator algorithm is defined, along with its multiple imputation analogs. The procedures are illustrated using a well-known right-heart catheterization dataset. Copyright © 2015 John Wiley & Sons, Ltd.

  18. Biased signaling of lipids and allosteric actions of synthetic molecules for GPR119

    DEFF Research Database (Denmark)

    Hassing, Helle A; Fares, Suzan; Larsen, Olav

    2016-01-01

    for 2h with the 2-MAG-lipase inhibitor JZL84 doubled the constitutive activity, indicating that endogenous lipids contribute to the apparent constitutive activity. Finally, besides being an agonist, AR231453 acted as a positive allosteric modulator of OEA and increased its potency by 54-fold at 100nM AR......231453. Our studies uncovering broad and biased signaling, masked constitutive activity by endogenous MAGs, and ago-allosteric properties of synthetic ligands may explain why many GPR119 drug-discovery programs have failed so far....

  19. Allosteric regulation and communication between subunits in uracil phosphoribosyltransferase from Sulfolobus solfataricus

    DEFF Research Database (Denmark)

    Arent, Susan; Harris, Pernille; Jensen, Kaj Frank

    2005-01-01

    organisms. To understand the allosteric regulation, crystal structures were determined for S. solfataricus UPRTase in complex with UMP and with UMP and the allosteric inhibitor CTP. Also, a structure with UMP bound in half of the active sites was determined. All three complexes form tetramers but reveal...... to rearrangements in the quaternary structure imply that this residue plays a major role in regulation of the enzyme and in communication between subunits. The ribose ring of UMP adopts alternative conformations in the cis and trans subunits of the UPRTase-UMP tetramer with associated differences...

  20. Studies on the matched potential method for determining the selectivity coefficients of ion-selective electrodes based on neutral ionophores: experimental and theoretical verification.

    Science.gov (United States)

    Tohda, K; Dragoe, D; Shibata, M; Umezawa, Y

    2001-06-01

    A theory is presented that describes the matched potential method (MPM) for the determination of the potentiometric selectivity coefficients (KA,Bpot) of ion-selective electrodes for two ions with any charge. This MPM theory is based on electrical diffuse layers on both the membrane and the aqueous side of the interface, and is therefore independent of the Nicolsky-Eisenman equation. Instead, the Poisson equation is used and a Boltzmann distribution is assumed with respect to all charged species, including primary, interfering and background electrolyte ions located at the diffuse double layers. In this model, the MPM-selectivity coefficients of ions with equal charge (ZA = ZB) are expressed as the ratio of the concentrations of the primary and interfering ions in aqueous solutions at which the same amounts of the primary and interfering ions permselectively extracted into the membrane surface. For ions with unequal charge (ZA not equal to ZB), the selectivity coefficients are expressed as a function not only of the amounts of the primary and interfering ions permeated into the membrane surface, but also of the primary ion concentration in the initial reference solution and the delta EMF value. Using the measured complexation stability constants and single ion distribution coefficients for the relevant systems, the corresponding MPM selectivity coefficients can be calculated from the developed MPM theory. It was found that this MPM theory is capable of accurately and precisely predicting the MPM selectivity coefficients for a series of ion-selective electrodes (ISEs) with representative ionophore systems, which are generally in complete agreement with independently determined MPM selectivity values from the potentiometric measurements. These results also conclude that the assumption for the Boltzmann distribution was in fact valid in the theory. The recent critical papers on MPM have pointed out that because the MPM selectivity coefficients are highly concentration

  1. Determination of heavy metal pollution in soils from selected potentially contaminated sites in Tema

    International Nuclear Information System (INIS)

    Nyaaba, A.K.L.

    2011-01-01

    The objective of the study was to assess the concentration and determine the level of pollution by harmful heavy metals in soils from selected potentially contaminated sites in Tema. The metals of interest include; mercury, lead, cadmium, cobalt zinc, arsenic, nickel, copper and chromium. A total of forty seven (47) samples comprising thirty eight sub-samples (38) and nine (9) composite samples were collected from nine (9) different locations. These included playgrounds, steel processing factories, used Lead Acid Battery (ULAB) recycling plant, mechanic workshops and the municipal waste disposal site. The samples were prepared after which the elemental concentrations were determined using energy dispersive X-ray fluorescence (EDXRF) with a secondary target excitation arrangement (5.9 keV). The analysis of the samples yielded the following mean heavy metal concentrations in mg/kg: 424.38 (Cr); 408.68 (Ni); 14427 (Cu); 4129.87 (Zn); 1580.68 (As); 647.48 (Hg); 73361.51 (Pb) and 1176.16 (Co). The mean concentrations of heavy metals in the soils were in the following order Pb>Zn>As>Co>Cu>Hg>Cr>Ni. Mercury was detected at only two of the sites. The average heavy metals in the soils from the sites were generally high since most of them exceeded the optimum and action values of the New Dutch List. The Enrichment Factor (EF) ratios show that the enrichment of the elements in the soils ranged from deficiently to extremely highly enriched. The contamination factor show that the contamination by the heavy metals were low at some of the sites and very high at others. The geoaccumulation indices indicated that the playground (PG) has not been contaminated by any of the metals, C8 is contaminated strongly by mercury only and the contamination at the remaining sites varied from moderately contaminated to extremely contaminated by the metals. The Igeo also indicated that the elements accounting for extreme contamination are lead, arsenic, copper, zinc mercury and chromium. Lead

  2. Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions.

    Science.gov (United States)

    Belinky, Frida; Rogozin, Igor B; Koonin, Eugene V

    2017-09-29

    Reconstruction of the evolution of start codons in 36 groups of closely related bacterial and archaeal genomes reveals purifying selection affecting AUG codons. The AUG starts are replaced by GUG and especially UUG significantly less frequently than expected under the neutral expectation derived from the frequencies of the respective nucleotide triplet substitutions in non-coding regions and in 4-fold degenerate sites. Thus, AUG is the optimal start codon that is actively maintained by purifying selection. However, purifying selection on start codons is significantly weaker than the selection on the same codons in coding sequences, although the switches between the codons result in conservative amino acid substitutions. The only exception is the AUG to UUG switch that is strongly selected against among start codons. Selection on start codons is most pronounced in evolutionarily conserved, highly expressed genes. Mutation of the start codon to a sub-optimal form (GUG or UUG) tends to be compensated by mutations in the Shine-Dalgarno sequence towards a stronger translation initiation signal. Together, all these findings indicate that in prokaryotes, translation start signals are subject to weak but significant selection for maximization of initiation rate and, consequently, protein production.

  3. Potential sources of analytical bias and error in selected trace element data-quality analyses

    Science.gov (United States)

    Paul, Angela P.; Garbarino, John R.; Olsen, Lisa D.; Rosen, Michael R.; Mebane, Christopher A.; Struzeski, Tedmund M.

    2016-09-28

    Potential sources of analytical bias and error associated with laboratory analyses for selected trace elements where concentrations were greater in filtered samples than in paired unfiltered samples were evaluated by U.S. Geological Survey (USGS) Water Quality Specialists in collaboration with the USGS National Water Quality Laboratory (NWQL) and the Branch of Quality Systems (BQS).Causes for trace-element concentrations in filtered samples to exceed those in associated unfiltered samples have been attributed to variability in analytical measurements, analytical bias, sample contamination either in the field or laboratory, and (or) sample-matrix chemistry. These issues have not only been attributed to data generated by the USGS NWQL but have been observed in data generated by other laboratories. This study continues the evaluation of potential analytical bias and error resulting from matrix chemistry and instrument variability by evaluating the performance of seven selected trace elements in paired filtered and unfiltered surface-water and groundwater samples collected from 23 sampling sites of varying chemistries from six States, matrix spike recoveries, and standard reference materials.Filtered and unfiltered samples have been routinely analyzed on separate inductively coupled plasma-mass spectrometry instruments. Unfiltered samples are treated with hydrochloric acid (HCl) during an in-bottle digestion procedure; filtered samples are not routinely treated with HCl as part of the laboratory analytical procedure. To evaluate the influence of HCl on different sample matrices, an aliquot of the filtered samples was treated with HCl. The addition of HCl did little to differentiate the analytical results between filtered samples treated with HCl from those samples left untreated; however, there was a small, but noticeable, decrease in the number of instances where a particular trace-element concentration was greater in a filtered sample than in the associated

  4. Therapeutic potential of functional selectivity in the treatment of heart failure

    DEFF Research Database (Denmark)

    Christensen, Gitte Lund; Aplin, Mark; Hansen, Jakob Lerche

    2010-01-01

    Adrenergic and angiotensin receptors are prominent targets in pharmacological alleviation of cardiac remodeling and heart failure, but their use is associated with cardiodepressant side effects. Recent advances in our understanding of seven transmembrane receptor signaling show that it is possible...... to design ligands with "functional selectivity," acting as agonists on certain signaling pathways while antagonizing others. This represents a major pharmaceutical opportunity to separate desired from adverse effects governed by the same receptor. Accordingly, functionally selective ligands are currently...

  5. Rational Design and Tuning of Functional RNA Switch to Control an Allosteric Intermolecular Interaction.

    Science.gov (United States)

    Endoh, Tamaki; Sugimoto, Naoki

    2015-08-04

    Conformational transitions of biomolecules in response to specific stimuli control many biological processes. In natural functional RNA switches, often called riboswitches, a particular RNA structure that has a suppressive or facilitative effect on gene expression transitions to an alternative structure with the opposite effect upon binding of a specific metabolite to the aptamer region. Stability of RNA secondary structure (-ΔG°) can be predicted based on thermodynamic parameters and is easily tuned by changes in nucleobases. We envisioned that tuning of a functional RNA switch that causes an allosteric interaction between an RNA and a peptide would be possible based on a predicted switching energy (ΔΔG°) that corresponds to the energy difference between the RNA secondary structure before (-ΔG°before) and after (-ΔG°after) the RNA conformational transition. We first selected functional RNA switches responsive to neomycin with predicted ΔΔG° values ranging from 5.6 to 12.2 kcal mol(-1). We then demonstrated a simple strategy to rationally convert the functional RNA switch to switches responsive to natural metabolites thiamine pyrophosphate, S-adenosyl methionine, and adenine based on the predicted ΔΔG° values. The ΔΔG° values of the designed RNA switches proportionally correlated with interaction energy (ΔG°interaction) between the RNA and peptide, and we were able to tune the sensitivity of the RNA switches for the trigger molecule. The strategy demonstrated here will be generally applicable for construction of functional RNA switches and biosensors in which mechanisms are based on conformational transition of nucleic acids.

  6. Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications.

    Directory of Open Access Journals (Sweden)

    Kristin Blacklock

    2014-06-01

    Full Text Available A fundamental role of the Hsp90 chaperone in regulating functional activity of diverse protein clients is essential for the integrity of signaling networks. In this work we have combined biophysical simulations of the Hsp90 crystal structures with the protein structure network analysis to characterize the statistical ensemble of allosteric interaction networks and communication pathways in the Hsp90 chaperones. We have found that principal structurally stable communities could be preserved during dynamic changes in the conformational ensemble. The dominant contribution of the inter-domain rigidity to the interaction networks has emerged as a common factor responsible for the thermodynamic stability of the active chaperone form during the ATPase cycle. Structural stability analysis using force constant profiling of the inter-residue fluctuation distances has identified a network of conserved structurally rigid residues that could serve as global mediating sites of allosteric communication. Mapping of the conformational landscape with the network centrality parameters has demonstrated that stable communities and mediating residues may act concertedly with the shifts in the conformational equilibrium and could describe the majority of functionally significant chaperone residues. The network analysis has revealed a relationship between structural stability, global centrality and functional significance of hotspot residues involved in chaperone regulation. We have found that allosteric interactions in the Hsp90 chaperone may be mediated by modules of structurally stable residues that display high betweenness in the global interaction network. The results of this study have suggested that allosteric interactions in the Hsp90 chaperone may operate via a mechanism that combines rapid and efficient communication by a single optimal pathway of structurally rigid residues and more robust signal transmission using an ensemble of suboptimal multiple

  7. Activation of Extracellular Signal-Regulated Kinase but Not of p38 Mitogen-Activated Protein Kinase Pathways in Lymphocytes Requires Allosteric Activation of SOS

    Science.gov (United States)

    Jun, Jesse E.; Yang, Ming; Chen, Hang; Chakraborty, Arup K.

    2013-01-01

    Thymocytes convert graded T cell receptor (TCR) signals into positive selection or deletion, and activation of extracellular signal-related kinase (ERK), p38, and Jun N-terminal protein kinase (JNK) mitogen-activated protein kinases (MAPKs) has been postulated to play a discriminatory role. Two families of Ras guanine nucleotide exchange factors (RasGEFs), SOS and RasGRP, activate Ras and the downstream RAF-MEK-ERK pathway. The pathways leading to lymphocyte p38 and JNK activation are less well defined. We previously described how RasGRP alone induces analog Ras-ERK activation while SOS and RasGRP cooperate to establish bimodal ERK activation. Here we employed computational modeling and biochemical experiments with model cell lines and thymocytes to show that TCR-induced ERK activation grows exponentially in thymocytes and that a W729E allosteric pocket mutant, SOS1, can only reconstitute analog ERK signaling. In agreement with RasGRP allosterically priming SOS, exponential ERK activation is severely decreased by pharmacological or genetic perturbation of the phospholipase Cγ (PLCγ)-diacylglycerol-RasGRP1 pathway. In contrast, p38 activation is not sharply thresholded and requires high-level TCR signal input. Rac and p38 activation depends on SOS1 expression but not allosteric activation. Based on computational predictions and experiments exploring whether SOS functions as a RacGEF or adaptor in Rac-p38 activation, we established that the presence of SOS1, but not its enzymatic activity, is critical for p38 activation. PMID:23589333

  8. The potential of selected macroalgal species for treatment of AMD at different pH ranges in temperate regions

    CSIR Research Space (South Africa)

    Oberholster, Paul J

    2014-09-01

    Full Text Available The metal bioaccumulation potential of selected macroalgae species at different pH ranges was study for usage as part of a possible secondary passive acid mine drainage (AMD) treatment technology in algae ponds. Two separate studies were conducted...

  9. Selectivity control of carbonylation of methanol to dimethyl oxalate and dimethyl carbonate over gold anode by electrochemical potential.

    Science.gov (United States)

    Funakawa, Akiyasu; Yamanaka, Ichiro; Takenaka, Sakae; Otsuka, Kiyoshi

    2004-05-05

    New and unique electrocatalysis of gold for the carbonylation of methanol to dimethyl oxalate (DMO) and dimethyl carbonate (DMC) was found. The selectivity to DMO and DMC could be controlled over gold anode by electrochemical potential, as you like. Drastic changes of gold electrocatalysis was due to changes of the oxidation state of gold, Au0 or Au3+.

  10. Potential Science and Technology Game Changers for the Ground Warfare of 2050: Selected Projections Made in 2017

    Science.gov (United States)

    2018-02-01

    ARL-TR-8283 ● FEB 2018 US Army Research Laboratory Potential Science and Technology Game Changers for the Ground Warfare of 2050...Science and Technology Game Changers for the Ground Warfare of 2050: Selected Projections Made in 2017 by Alexander Kott Office of the Director...Brian Sadler Vehicle Technology Directorate, ARL Ananthram Swami Computational and Information Sciences Directorate, ARL Approved for

  11. Refrigeration Playbook: Natural Refrigerants; Selecting and Designing Energy-Efficient Commercial Refrigeration Systems That Use Low Global Warming Potential Refrigerants

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, Caleb [CTA Architects Engineers, Boise, ID (United States); Reis, Chuck [CTA Architects Engineers, Boise, ID (United States); Nelson, Eric [CTA Architects Engineers, Boise, ID (United States); Armer, James [CTA Architects Engineers, Boise, ID (United States); Arthur, Rob [CTA Architects Engineers, Boise, ID (United States); Heath, Richard [CTA Architects Engineers, Boise, ID (United States); Rono, James [CTA Architects Engineers, Boise, ID (United States); Hirsch, Adam [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Doebber, Ian [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2015-03-01

    This report provides guidance for selecting and designing energy efficient commercial refrigeration systems using low global warming potential refrigerants. Refrigeration systems are generally the largest energy end use in a supermarket type building, often accounting for more than half of a building's energy consumption.

  12. An event-related brain potential study of visual selective attention to conjunctions of color and shape

    NARCIS (Netherlands)

    Smid, HGOM; Jakob, A; Heinze, HJ

    What cognitive processes underlie event-related brain potential (ERP) effects related to visual multidimensional selective attention and how are these processes organized? We recorded ERPs when participants attended to one conjunction of color, global shape and local shape and ignored other

  13. Plant operator selection system for evaluating employment candidates' potential for success in electric power plant operations positions

    International Nuclear Information System (INIS)

    Dunnette, M.D.

    1982-01-01

    The Plant Operator Selection System is a battery of tests and questionnaires that can be administered to job candidates in less than three hours. Various components of the battery measure what a job candidate has accomplished in previous educational and work situations, how well a candidate compares with others on a number of important aptitudes or abilities, and whether or not a candidate possesses the kind of personal stability required in power plant operations positions. A job candidate's answers to the tests and questionnaires of the Plant Operator Selection System are scored and converted to an OVERALL POTENTIAL INDEX. Values of the OVERALL POTENTIAL INDEX [OPI] range between 0 and 15. Candidates with high OPI values are much more likely to become effective and successful plant operators than candidates with low OPI values. It is possible to estimate the financial advantages to a company of using the Plant Operator Selection System in evaluating candidates for plant operations jobs

  14. Butt rot defect and potential hazard in lodgepole pine on selected California recreational areas

    Science.gov (United States)

    Lee A. Paine

    1966-01-01

    Within the area sampled, potentially hazardous lodgepole pine were common on recreational sites. The incidence of decayed and mechanically weak trees was correlated with fire damage. Two-thirds of fire-scarred trees were decayed; one-third were rated potentially hazardous. Fire scars occurred roughly in proportion to level of plot recreational use.

  15. Selective mixed potential based ammonia exhaust gas sensor; Selektiver Ammoniakabgassensor auf Mischpotentialbasis

    Energy Technology Data Exchange (ETDEWEB)

    Schoenauer, D.; Moos, R. [Bayreuth Univ. (Germany). Lehrstuhl fuer Funktionsmaterialien; Wiesner, K.; Fleischer, M. [Siemens AG, CT PS 6, Muenchen (Germany)

    2007-07-01

    Mixed potential sensors with additional catalytic deposits on one of two electrodes show a high potential for NH{sub 3} detection. With defined reactions at the covered electrode it is possible to derive a temperature dependent correlation between the gas concentration/composition and the sensor signal which is characteristic for the used electrode material and the catalyst.

  16. Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.

    Directory of Open Access Journals (Sweden)

    Aysima Hacisuleyman

    2017-01-01

    Full Text Available It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.

  17. Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.

    Science.gov (United States)

    Hacisuleyman, Aysima; Erman, Burak

    2017-01-01

    It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.

  18. A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase

    Energy Technology Data Exchange (ETDEWEB)

    Wellington, Samantha; Nag, Partha P.; Michalska, Karolina; Johnston, Stephen E.; Jedrzejczak, Robert P.; Kaushik, Virendar K.; Clatworthy, Anne E.; Siddiqi, Noman; McCarren, Patrick; Bajrami, Besnik; Maltseva, Natalia I.; Combs, Senya; Fisher, Stewart L.; Joachimiak, Andrzej; Schreiber, Stuart L.; Hung, Deborah T.

    2017-07-03

    New antibiotics with novel targets are greatly needed. Bacteria have numerous essential functions, but only a small fraction of such processes—primarily those involved in macromolecular synthesis—are inhibited by current drugs. Targeting metabolic enzymes has been the focus of recent interest, but effective inhibitors have been difficult to identify. We describe a synthetic azetidine derivative, BRD4592, that kills Mycobacterium tuberculosis (Mtb) through allosteric inhibition of tryptophan synthase (TrpAB), a previously untargeted, highly allosterically regulated enzyme. BRD4592 binds at the TrpAB a–b-subunit interface and affects multiple steps in the enzyme’s overall reaction, resulting in inhibition not easily overcome by changes in metabolic environment. We show that TrpAB is required for the survival of Mtb and Mycobacterium marinum in vivo and that this requirement may be independent of an adaptive immune response. This work highlights the effectiveness of allosteric inhibition for targeting proteins that are naturally highly dynamic and that are essential in vivo, despite their apparent dispensability under in vitro conditions, and suggests a framework for the discovery of a next generation of allosteric inhibitors.

  19. A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase

    Energy Technology Data Exchange (ETDEWEB)

    Wellington, Samantha; Nag, Partha P.; Michalska, Karolina; Johnston, Stephen E.; Jedrzejczak, Robert P.; Kaushik, Virendar K.; Clatworthy, Anne E.; Siddiqi, Noman; McCarren, Patrick; Bajrami, Besnik; Maltseva, Natalia I.; Combs, Senya; Fisher, Stewart L.; Joachimiak, Andrzej; Schreiber, Stuart L.; Hung, Deborah T.

    2017-07-03

    New antibiotics with novel targets are greatly needed. Bacteria have numerous essential functions, but only a small fraction of such processes—primarily those involved in macromolecular synthesis—are inhibited by current drugs. Targeting metabolic enzymes has been the focus of recent interest, but effective inhibitors have been difficult to identify. We describe a synthetic azetidine derivative, BRD4592, that kills Mycobacterium tuberculosis (Mtb) through allosteric inhibition of tryptophan synthase (TrpAB), a previously untargeted, highly allosterically regulated enzyme. BRD4592 binds at the TrpAB α–β-subunit interface and affects multiple steps in the enzyme's overall reaction, resulting in inhibition not easily overcome by changes in metabolic environment. We show that TrpAB is required for the survival of Mtb and Mycobacterium marinum in vivo and that this requirement may be independent of an adaptive immune response. This work highlights the effectiveness of allosteric inhibition for targeting proteins that are naturally highly dynamic and that are essential in vivo, despite their apparent dispensability under in vitro conditions, and suggests a framework for the discovery of a next generation of allosteric inhibitors.

  20. Divergence of allosteric effects of rapacuronium on binding and function of muscarinic receptors

    Czech Academy of Sciences Publication Activity Database

    Jakubík, Jan; Randáková, Alena; El-Fakahany, E. E.; Doležal, Vladimír

    2009-01-01

    Roč. 9, č. 15 (2009), s. 1-20 ISSN 1471-2210 R&D Projects: GA ČR GA305/09/0681; GA MŠk(CZ) LC554; GA AV ČR(CZ) IAA500110703 Institutional research plan: CEZ:AV0Z50110509 Keywords : muscarinic receptors * allosteric modulation * rapacuronium Subject RIV: ED - Physiology

  1. Identification of an allosteric binding site for RORγt inhibition

    NARCIS (Netherlands)

    Scheepstra, M.; Leysen, S.; van Almen, G.; Miller, J.R.; Piesvaux, J.; Kutilek, V.; van Eenennaam, H.; Zhang, H.; Barr, K.; Nagpal, S.; Soisson, S.M.; Kornienko, M.; Wiley, K.; Elsen, N.; Sharma, S.; Correll, C.C.; Trotter, B.W.; Stelt, van der M.; Oubrie, A.; Ottmann, C.; Parthasarathy, G.; Brunsveld, L.

    2015-01-01

    RORγt is critical for the differentiation and proliferation of Th17 cells associated with several chronic autoimmune diseases. We report the discovery of a novel allosteric binding site on the nuclear receptor RORγt. Co-crystallization of the ligand binding domain (LBD) of RORγt with a series of

  2. Molecular Basis for Allosteric Inhibition of Acid-Sensing Ion Channel 1a by Ibuprofen

    DEFF Research Database (Denmark)

    Lynagh, Timothy; Romero-Rojo, José Luis; Lund, Camilla

    2017-01-01

    -clamp fluorometry. Our results show that ibuprofen is an allosteric inhibitor of ASIC1a, which binds to a crucial site in the agonist transduction pathway and causes conformational changes that oppose channel activation. Ibuprofen inhibits several ASIC subtypes, but certain ibuprofen derivatives show some...

  3. A generalized allosteric mechanism for cis-regulated cyclic nucleotide binding domains.

    Directory of Open Access Journals (Sweden)

    Alexandr P Kornev

    2008-04-01

    Full Text Available Cyclic nucleotides (cAMP and cGMP regulate multiple intracellular processes and are thus of a great general interest for molecular and structural biologists. To study the allosteric mechanism of different cyclic nucleotide binding (CNB domains, we compared cAMP-bound and cAMP-free structures (PKA, Epac, and two ionic channels using a new bioinformatics method: local spatial pattern alignment. Our analysis highlights four major conserved structural motifs: 1 the phosphate binding cassette (PBC, which binds the cAMP ribose-phosphate, 2 the "hinge," a flexible helix, which contacts the PBC, 3 the beta(2,3 loop, which provides precise positioning of an invariant arginine from the PBC, and 4 a conserved structural element consisting of an N-terminal helix, an eight residue loop and the A-helix (N3A-motif. The PBC and the hinge were included in the previously reported allosteric model, whereas the definition of the beta(2,3 loop and the N3A-motif as conserved elements is novel. The N3A-motif is found in all cis-regulated CNB domains, and we present a model for an allosteric mechanism in these domains. Catabolite gene activator protein (CAP represents a trans-regulated CNB domain family: it does not contain the N3A-motif, and its long range allosteric interactions are substantially different from the cis-regulated CNB domains.

  4. Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Federica Chiappori

    Full Text Available Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD modulate substrate recognition at the Substrate Binding Domain (SBD. Herein, a comparative analysis of an allosteric (Hsp70-DnaK and a non-allosteric structural homolog (Hsp110-Sse1 of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.

  5. A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein.

    Directory of Open Access Journals (Sweden)

    Anurag Sethi

    Full Text Available The HIV-1 envelope (Env spike, which consists of a compact, heterodimeric trimer of the glycoproteins gp120 and gp41, is the target of neutralizing antibodies. However, the high mutation rate of HIV-1 and plasticity of Env facilitates viral evasion from neutralizing antibodies through various mechanisms. Mutations that are distant from the antibody binding site can lead to escape, probably by changing the conformation or dynamics of Env; however, these changes are difficult to identify and define mechanistically. Here we describe a network analysis-based approach to identify potential allosteric immune evasion mechanisms using three known HIV-1 Env gp120 protein structures from two different clades, B and C. First, correlation and principal component analyses of molecular dynamics (MD simulations identified a high degree of long-distance coupled motions that exist between functionally distant regions within the intrinsic dynamics of the gp120 core, supporting the presence of long-distance communication in the protein. Then, by integrating MD simulations with network theory, we identified the optimal and suboptimal communication pathways and modules within the gp120 core. The results unveil both strain-dependent and -independent characteristics of the communication pathways in gp120. We show that within the context of three structurally homologous gp120 cores, the optimal pathway for communication is sequence sensitive, i.e. a suboptimal pathway in one strain becomes the optimal pathway in another strain. Yet the identification of conserved elements within these communication pathways, termed inter-modular hotspots, could present a new opportunity for immunogen design, as this could be an additional mechanism that HIV-1 uses to shield vulnerable antibody targets in Env that induce neutralizing antibody breadth.

  6. An antibody that prevents serpin polymerisation acts by inducing a novel allosteric behaviour.

    Science.gov (United States)

    Motamedi-Shad, Neda; Jagger, Alistair M; Liedtke, Maximilian; Faull, Sarah V; Nanda, Arjun Scott; Salvadori, Enrico; Wort, Joshua L; Kay, Christopher W M; Heyer-Chauhan, Narinder; Miranda, Elena; Perez, Juan; Ordóñez, Adriana; Haq, Imran; Irving, James A; Lomas, David A

    2016-10-01

    Serpins are important regulators of proteolytic pathways with an antiprotease activity that involves a conformational transition from a metastable to a hyperstable state. Certain mutations permit the transition to occur in the absence of a protease; when associated with an intermolecular interaction, this yields linear polymers of hyperstable serpin molecules, which accumulate at the site of synthesis. This is the basis of many pathologies termed the serpinopathies. We have previously identified a monoclonal antibody (mAb4B12) that, in single-chain form, blocks α1-antitrypsin (α1-AT) polymerisation in cells. Here, we describe the structural basis for this activity. The mAb4B12 epitope was found to encompass residues Glu32, Glu39 and His43 on helix A and Leu306 on helix I. This is not a region typically associated with the serpin mechanism of conformational change, and correspondingly the epitope was present in all tested structural forms of the protein. Antibody binding rendered β-sheet A - on the opposite face of the molecule - more liable to adopt an 'open' state, mediated by changes distal to the breach region and proximal to helix F. The allosteric propagation of induced changes through the molecule was evidenced by an increased rate of peptide incorporation and destabilisation of a preformed serpin-enzyme complex following mAb4B12 binding. These data suggest that prematurely shifting the β-sheet A equilibrium towards the 'open' state out of sequence with other changes suppresses polymer formation. This work identifies a region potentially exploitable for a rational design of ligands that is able to dynamically influence α1-AT polymerisation. © 2016 The Author(s).

  7. Negative Allosteric Modulators of Metabotropic Glutamate Receptors Subtype 5 in Addiction: a Therapeutic Window

    Science.gov (United States)

    2016-01-01

    Background: Abundant evidence at the anatomical, electrophysiological, and molecular levels implicates metabotropic glutamate receptor subtype 5 (mGluR5) in addiction. Consistently, the effects of a wide range of doses of different mGluR5 negative allosteric modulators (NAMs) have been tested in various animal models of addiction. Here, these studies were subjected to a systematic review to find out if mGluR5 NAMs have a therapeutic potential that can be translated to the clinic. Methods: Literature on consumption/self-administration and reinstatement of drug seeking as outcomes of interest published up to April 2015 was retrieved via PubMed. The review focused on the effects of systemic (i.p., i.v., s.c.) administration of the mGluR5 NAMs 3-((2-Methyl-4-thiazolyl)ethynyl)pyridine (MTEP) and 2-Methyl-6-(phenylethynyl)pyridine (MPEP) on paradigms with cocaine, ethanol, nicotine, and food in rats. Results: MTEP and MPEP were found to reduce self-administration of cocaine, ethanol, and nicotine at doses ≥1mg/kg and 2.5mg/kg, respectively. Dose-response relationship resembled a sigmoidal curve, with low doses not reaching statistical significance and high doses reliably inhibiting self-administration of drugs of abuse. Importantly, self-administration of cocaine, ethanol, and nicotine, but not food, was reduced by MTEP and MPEP in the dose range of 1 to 2mg/kg and 2.5 to 3.2mg/kg, respectively. This dose range corresponds to approximately 50% to 80% mGluR5 occupancy. Interestingly, the limited data found in mice and monkeys showed a similar therapeutic window. Conclusion: Altogether, this review suggests a therapeutic window for mGluR5 NAMs that can be translated to the treatment of substance-related and addictive disorders. PMID:26802568

  8. Substrate specificity changes for human reticulocyte and epithelial 15-lipoxygenases reveal allosteric product regulation.

    Science.gov (United States)

    Wecksler, Aaron T; Kenyon, Victor; Deschamps, Joshua D; Holman, Theodore R

    2008-07-15

    Human reticulocyte 15-lipoxygenase (15-hLO-1) and epithelial 15-lipoxygenase (15-hLO-2) have been implicated in a number of human diseases, with differences in their substrate specificity potentially playing a central role. In this paper, we present a novel method for accurately measuring the substrate specificity of the two 15-hLO isozymes and demonstrate that both cholate and specific LO products affect substrate specificity. The linoleic acid (LA) product, 13-hydroperoxyoctadienoic acid (13-HPODE), changes the ( k cat/ K m) (AA)/( k cat/ K m) (LA) ratio more than 5-fold for 15-hLO-1 and 3-fold for 15-hLO-2, while the arachidonic acid (AA) product, 12-( S)-hydroperoxyeicosatetraenoic acid (12-HPETE), affects only the ratio of 15-hLO-1 (more than 5-fold). In addition, the reduced products, 13-( S)-hydroxyoctadecadienoic acid (13-HODE) and 12-( S)-hydroxyeicosatetraenoic acid (12-HETE), also affect substrate specificity, indicating that iron oxidation is not responsible for the change in the ( k cat/ K m) (AA)/( k cat/ K m) (LA) ratio. These results, coupled with the dependence of the 15-hLO-1 k cat/ K m kinetic isotope effect ( (D) k cat/ K m) on the presence of 12-HPETE and 12-HETE, indicate that the allosteric site, previously identified in 15-hLO-1 [Mogul, R., Johansen, E., and Holman, T. R. (1999) Biochemistry 39, 4801-4807], is responsible for the change in substrate specificity. The ability of LO products to regulate substrate specificity may be relevant with respect to cancer progression and warrants further investigation into the role of this product-feedback loop in the cell.

  9. Selective activation of heteromeric SK channels contributes to action potential repolarization in mouse atrial myocytes.

    Science.gov (United States)

    Hancock, Jane M; Weatherall, Kate L; Choisy, Stéphanie C; James, Andrew F; Hancox, Jules C; Marrion, Neil V

    2015-05-01

    Activation of small conductance calcium-activated potassium (SK) channels is proposed to contribute to repolarization of the action potential in atrial myocytes. This role is controversial, as these cardiac SK channels appear to exhibit an uncharacteristic pharmacology. The objectives of this study were to resolve whether activation of SK channels contributes to atrial action potential repolarization and to determine the likely subunit composition of the channel. The effect of 2 SK channel inhibitors was assessed on outward current evoked in voltage clamp and on action potential duration in perforated patch and whole-cell current clamp recording from acutely isolated mouse atrial myocytes. The presence of SK channel subunits was assessed using immunocytochemistry. A significant component of outward current was reduced by the SK channel blockers apamin and UCL1684. Block by apamin displayed a sensitivity indicating that this current was carried by homomeric SK2 channels. Action potential duration was significantly prolonged by UCL1684, but not by apamin. This effect was accompanied by an increase in beat-to-beat variability and action potential triangulation. This pharmacology was matched by that of expressed heteromeric SK2-SK3 channels in HEK293 cells. Immunocytochemistry showed that atrial myocytes express both SK2 and SK3 channels with an overlapping expression pattern. Only proposed heteromeric SK2-SK3 channels are physiologically activated to contribute to action potential repolarization, which is indicated by the difference in pharmacology of evoked outward current and prolongation of atrial action potential duration. The effect of blocking this channel on the action potential suggests that SK channel inhibition during cardiac function has the potential to be proarrhythmic. Copyright © 2015 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

  10. Selective Attention, Working Memory, and Executive Function as Potential Independent Sources of Cognitive Dysfunction in Schizophrenia.

    Science.gov (United States)

    Gold, James M; Robinson, Benjamin; Leonard, Carly J; Hahn, Britta; Chen, Shuo; McMahon, Robert P; Luck, Steven J

    2017-11-11

    People with schizophrenia demonstrate impairments in selective attention, working memory, and executive function. Given the overlap in these constructs, it is unclear if these represent distinct impairments or different manifestations of one higher-order impairment. To examine this question, we administered tasks from the basic cognitive neuroscience literature to measure visual selective attention, working memory capacity, and executive function in 126 people with schizophrenia and 122 healthy volunteers. Patients demonstrated deficits on all tasks with the exception of selective attention guided by strong bottom-up inputs. Although the measures of top-down control of selective attention, working memory, and executive function were all intercorrelated, several sources of evidence indicate that working memory and executive function are separate sources of variance. Specifically, both working memory and executive function independently contributed to the discrimination of group status and independently accounted for variance in overall general cognitive ability as assessed by the MATRICS battery. These two cognitive functions appear to be separable features of the cognitive impairments observed in schizophrenia. © The Author 2017. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  11. The influence of caffeine on spatial-selective attention : an event-related potential study

    NARCIS (Netherlands)

    de Ruiter, MB; Snel, J; Lorist, MM; Ruijter, J

    2000-01-01

    Objectives: Following the indications of previous studies that caffeine might have a specific effect on the processing of spatial information compared with other types of information, the present study investigated the influence of caffeine on an often used spatial-selective attention task. Methods:

  12. Evaluation of oenological potential on clonal selections of cv. Cabernet Sauvignon from Chile

    Directory of Open Access Journals (Sweden)

    Ceppi de Lecco C.

    2014-01-01

    Full Text Available 13 clonal selections of cv Cabernet Sauvignon, established in Nancagua VI Region, Chile (34.39 °S 71.17 °W. The genetic identity of the vines was confirmed by ampelography and microsatellite markers (SSR. Evaluations in the 2012–2013 season include: performance, analytical and sensorial parameters on the wines made by microvinification. The results were statistically analyzed with the Statgraphics Plus program and multiple comparison test of Tukey at 95% confidence level. Sensorially, the wines were evaluated by a panel of 12 experts. The results were likewise analyzed by testing principal components (PCA with covariance matrix without rotation. In the season studied the selection 108 highlighted with a high yield (kg/plant, in the composition of the wine selections generally highlighted for contents of total polyphenols and anthocyanins over average. The results show typical sensory characteristics of wines from that grape variety, and it was possible to group the selections by their attributes (PCA with cherry red wines at different intensities, but without significant differences, with fruity and vegetal aromas, interesting complex flavors and with structured tannins.

  13. A Potential Approach for Low Flow Selection in Water Resource Supply and Management

    Science.gov (United States)

    Ying Ouyang

    2012-01-01

    Low flow selections are essential to water resource management, water supply planning, and watershed ecosystem restoration. In this study, a new approach, namely the frequent-low (FL) approach (or frequent-low index), was developed based on the minimum frequent-low flow or level used in minimum flows and/or levels program in northeast Florida, USA. This FL approach was...

  14. Selection of phosphorus solubilizing bacteria with biocontrol potential for growth in phosphorus rich animal bone charcoal

    NARCIS (Netherlands)

    Postma, J.; Nijhuis, E.H.; Sommeus, E.

    2010-01-01

    Bacteria with the ability to solubilize phosphorus (P) and to improve plant health were selected and tested for growth and survival in P-rich animal bone charcoal (ABC). ABC is suggested to be suitable as a carrier for biocontrol agents, offering them a protected niche as well as delivering

  15. Potential exposure to endocrine disrupting chemicals and selected adverse pregnancy outcomes

    DEFF Research Database (Denmark)

    Bengtsson, Jessica; Thygesen, Pernille Søgaard; Kaerlev, Linda

    2017-01-01

    potential occupational exposure to endocrine disrupting chemicals (EDC) of the mother during pregnancy is associated with preterm birth and low birth weight. Methods: Pregnant women referred to an Occupational Health Clinic (OHC) in two Danish regions (Copenhagen or Aarhus) between 1984 and 2010, suspected...... on the suspicion of other exposures than EDC (n = 620), and to a sample of births by all occupationally active women in the same geographical regions (n = 346,544), including 1,077 births of the referred women’s non-referred pregnancies. Results: No indications of reduced birth weight or increased risk of preterm...... birth were found among women potentially exposed to EDC. Women potentially exposed to EDC had children with a higher birth weight compared to the sample of occupationally active women but not compared to other women referred to an OHC. Conclusions: Potential maternal exposure to EDC at Danish workplaces...

  16. Greenhouse gases reduction potential through consumer’s behavioral changes in terms of food-related product selection

    International Nuclear Information System (INIS)

    Yoshikawa, Naoki; Fujiwara, Natsumi; Nagata, Junko; Amano, Koji

    2016-01-01

    Highlights: • Greenhouse gases (GHG) reduction potential by shopping behavior change is analyzed. • Four scenarios related to food consumption is evaluated using life cycle assessment. • Total GHG reduction potential by four scenarios in Japan is 1367 kt-CO_2/year. • Potential reduces to 45% when considering feasible ratio of taking behavior change. • Contribution of seasonal production/consumption scenario is highest among scenarios. - Abstract: Sustainable consumption plays an important role in the mitigation of global warming and the conservation of energy. Promoting more environmentally responsible consumer behavior, especially through open communication between stakeholders, is one way to achieve low-carbon consumption. This study evaluates the potential for reducing greenhouse gas (GHG) emissions through behavioral transformation of consumers in terms of their daily shopping habits. In this context, the behavioral transformative actions pertain to certain foods and daily necessities, and are analyzed from a life cycle assessment perspective. We developed multiple product-selection scenarios to evaluate GHG emissions related to the daily purchase of commodities. Based on the life cycle assessment, we estimated the GHG emissions that result from the production and distribution of these commodities, pertaining to both the current product selection and to a possibly improved selection. The results of our study show that because of seasonal consumption patterns and energy conversion, there is a substantial potential to reduce GHG emissions resulting from out-of-season produce cultivation. The GHG reduction potential is not high for each individual commodity because diverse commodities are needed on a daily basis. However, various actions in combination could have substantial potential for reducing emissions.

  17. Heat Capacity Changes and Disorder-to-Order Transitions in Allosteric Activation.

    Science.gov (United States)

    Cressman, William J; Beckett, Dorothy

    2016-01-19

    Allosteric coupling in proteins is ubiquitous but incompletely understood, particularly in systems characterized by coupling over large distances. Binding of the allosteric effector, bio-5'-AMP, to the Escherichia coli biotin protein ligase, BirA, enhances the protein's dimerization free energy by -4 kcal/mol. Previous studies revealed that disorder-to-order transitions at the effector binding and dimerization sites, which are separated by 33 Å, are integral to functional coupling. Perturbations to the transition at the ligand binding site alter both ligand binding and coupled dimerization. Alanine substitutions in four loops on the dimerization surface yield a range of energetic effects on dimerization. A glycine to alanine substitution at position 142 in one of these loops results in a complete loss of allosteric coupling, disruption of the disorder-to-order transitions at both functional sites, and a decreased affinity for the effector. In this work, allosteric communication between the effector binding and dimerization surfaces in BirA was further investigated by performing isothermal titration calorimetry measurements on nine proteins with alanine substitutions in three dimerization surface loops. In contrast to BirAG142A, at 20 °C all variants bind to bio-5'-AMP with free energies indistinguishable from that measured for wild-type BirA. However, the majority of the variants exhibit altered heat capacity changes for effector binding. Moreover, the ΔCp values correlate with the dimerization free energies of the effector-bound proteins. These thermodynamic results, combined with structural information, indicate that allosteric activation of the BirA monomer involves formation of a network of intramolecular interactions on the dimerization surface in response to bio-5'-AMP binding at the distant effector binding site.

  18. Geotechnology and landscape ecology applied to the selection of potential forest fragments for seed harvesting.

    Science.gov (United States)

    Santos, Alexandre Rosa Dos; Antonio Alvares Soares Ribeiro, Carlos; de Oliveira Peluzio, Telma Machado; Esteves Peluzio, João Batista; de Queiroz, Vagner Tebaldi; Figueira Branco, Elvis Ricardo; Lorenzon, Alexandre Simões; Domingues, Getulio Fonseca; Marcatti, Gustavo Eduardo; de Castro, Nero Lemos Martins; Teixeira, Thaisa Ribeiro; Dos Santos, Gleissy Mary Amaral Dino Alves; Santos Mota, Pedro Henrique; Ferreira da Silva, Samuel; Vargas, Rozimelia; de Carvalho, José Romário; Macedo, Leandro Levate; da Silva Araújo, Cintia; de Almeida, Samira Luns Hatum

    2016-12-01

    The Atlantic Forest biome is recognized for its biodiversity and is one of the most threatened biomes on the planet, with forest fragmentation increasing due to uncontrolled land use, land occupation, and population growth. The most serious aspect of the forest fragmentation process is the edge effect and the loss of biodiversity. In this context, the aim of this study was to evaluate the dynamics of forest fragmentation and select potential forest fragments with a higher degree of conservation for seed harvesting in the Itapemirim river basin, Espírito Santo State, Brazil. Image classification techniques, forest landscape ecology, and multi-criteria analysis were used to evaluate the evolution of forest fragmentation to develop the landscape metric indexes, and to select potential forest fragments for seed harvesting for the years 1985 and 2013. According to the results, there was a reduction of 2.55% of the occupancy of the fragments in the basin between the years 1985 and 2013. For the years 1985 and 2013, forest fragment units 2 and 3 were spatialized with a high potential for seed harvesting, representing 6.99% and 16.01% of the total fragments, respectively. The methodology used in this study has the potential to be used to support decisions for the selection of potential fragments for seed harvesting because selecting fragments in different environments by their spatial attributes provides a greater degree of conservation, contributing to the protection and conscious management of the forests. The proposed methodology can be adapted to other areas and different biomes of the world. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Newly-formed emotional memories guide selective attention processes: Evidence from event-related potentials

    OpenAIRE

    Harald T. Schupp; Ursula Kirmse; Ralf Schmälzle; Tobias Flaisch; Britta Renner

    2016-01-01

    Emotional cues can guide selective attention processes. However, emotional stimuli can both activate long-term memory representations reflecting general world knowledge and engage newly formed memory representations representing specific knowledge from the immediate past. Here, the self-completion feature of associative memory was utilized to assess the regulation of attention processes by newly-formed emotional memory. First, new memory representations were formed by presenting pictures depi...

  20. Selection and Characterization of Potential Baker’s Yeast from Indigenous Resources of Nepal

    OpenAIRE

    Tika B. Karki; Parash Mani Timilsina; Archana Yadav; Gyanu Raj Pandey; Yogesh Joshi; Sahansila Bhujel; Rojina Adhikari; Katyayanee Neupane

    2017-01-01

    The study aims to isolate the yeast strains that could be used effectively as baker’s yeast and compare them with the commercial baker’s yeast available in the market of Nepal. A total of 10 samples including locally available sources like fruits, Murcha, and a local tree “Dar” were collected from different localities of Bhaktapur, Kavre, and Syangja districts of Nepal, respectively. Following enrichment and fermentation of the samples, 26 yeast strains were isolated using selective medium Wa...

  1. Literature Review: Validity and Potential Usefulness of Psychomotor Ability Tests for Personnel Selection and Classification

    Science.gov (United States)

    1988-04-01

    processing capabilities. Craik and Lockhart (1972), for example, investigated limitations In the ability to store Information In short-term storage...F. I. M., & Lockhart , R. S. (1972). Levels of processing : A framework for memory research. Journal of Verbal Learning and Verbal Behavior, 11, 671...preferable to an information processing taxonomy for purposes of the current selection and classification research. i-irst, on a theoretical level

  2. Potential evapotranspiration and its impact on autumn phenological phases of selected plants

    International Nuclear Information System (INIS)

    Palesova, I.

    2011-01-01

    The work deals with the assessment of the impact of water balance on the timing of phenological phases at two locations (Hips and Bukovina), on the selected tree species (hazel (Corylus avellana L.), hornbeam (Carpinus betulus L.), sessile oak (Quercus petraea, Liebl.)). Phenological observations have been held since 2007, and together with measurements of meteorological parameters allow us to evaluate the microclimate in the stands in detail. (authors)

  3. Selection and Characterization of Potential Baker's Yeast from Indigenous Resources of Nepal.

    Science.gov (United States)

    Karki, Tika B; Timilsina, Parash Mani; Yadav, Archana; Pandey, Gyanu Raj; Joshi, Yogesh; Bhujel, Sahansila; Adhikari, Rojina; Neupane, Katyayanee

    2017-01-01

    The study aims to isolate the yeast strains that could be used effectively as baker's yeast and compare them with the commercial baker's yeast available in the market of Nepal. A total of 10 samples including locally available sources like fruits, Murcha, and a local tree "Dar" were collected from different localities of Bhaktapur, Kavre, and Syangja districts of Nepal, respectively. Following enrichment and fermentation of the samples, 26 yeast strains were isolated using selective medium Wallerstein Laboratory Nutrient Agar. From the differential tests which included morphological and microscopic observation and physiological and biochemical characterization such as nitrate reduction and lactose utilization tests, 8 strains were selected as possible Saccharomyces strain. The selected strains were further assessed for their efficient leavening ability by tests such as ethanol tolerance, osmotolerance, invertase test, and stress exclusion test. The three most potent strains ENG, MUR3B, and SUG1 isolated from grape, Murcha, and sugarcane, respectively, were used in the fermentation and baking of dough. These strains also carried a possibility of being used as industrial baker's yeast.

  4. Patagonian red wines: selection of Lactobacillus plantarum isolates as potential starter cultures for malolactic fermentation.

    Science.gov (United States)

    Bravo-Ferrada, Bárbara Mercedes; Hollmann, Axel; Delfederico, Lucrecia; Valdés La Hens, Danay; Caballero, Adriana; Semorile, Liliana

    2013-09-01

    The aim of this study was to evaluate fifty-three Lactobacillus plantarum isolates obtained from a Patagonian red wine, molecularly identified and typified using RAPD analysis, in order to select starter cultures for malolactic fermentation (MLF). The results obtained suggest a considerable genetic diversity, taking into account that all L. plantarum isolates were obtained from one cellar and one vintage. Based on the capacity to tolerate a concentration of 14 % ethanol in MRS broth for 2 days, eight isolates were selected for the subsequent analysis. The incidence of various wine stress factors (ethanol, acid pH, lysozyme and sulfur dioxide) on isolates growth was studied. Besides, glucosidase and tannase activities were evaluated, and the presence of genes involved in the synthesis of biogenic amines was examined by PCR. A previously characterized indigenous Oenococcus oeni strain was included with comparative purposes. Differences in technologically relevant characteristics were observed among the eight L. plantarum selected isolates, revealing an isolate-dependent behavior. Detectable glucosidase and tannase activities were found in all isolates. The presence of genes encoding histidine and tyrosine descarboxylases and putrescine carbamoyltransferase was not detected. The ability of L. plantarum isolates to grow and consume L-malic acid in simulated laboratory-scale vinifications revealed that two of them could be considered as possible MLF starter cultures for Patagonian red wines. These isolates will be subjected to further analysis, for a final winery technological characterization.

  5. The Immunomodulatory Potential of Selected Bioactive Plant-Based Compounds in Breast Cancer: A Review.

    Science.gov (United States)

    Baraya, Yushau Shuaibu; Wong, Kah Keng; Yaacob, Nik Soriani

    2017-01-01

    Breast cancer has continued to cause high cancer death rates among women worldwide. The use of plants' natural products in breast cancer treatment has received more attention in recent years due to their potentially wider safety margin and the potential to complement conventional chemotherapeutic drugs. Plantbased products have demonstrated anticancer potential through different biological pathways including modulation of the immune system. Immunomodulatory properties of medicinal plants have been shown to mitigate breast cancer cell growth. Different immune cell types participate in this process especially cytotoxic T cells and natural killer cells, and cytokines including chemokines and tumor necrosis factor-α. Medicinal plants such as Glycyrrhiza glabra, Uncaria tomentosa, Camellia sinensis, Panax ginseng, Prunus armenaica (apricot), Allium sativum, Arctium lappa and Curcuma longa were reported to hold strong potential in breast cancer treatment in various parts of the world. Interestingly, research findings have shown that these plants possess bioactive immunomodulators as their main constituents producing the anticancer effects. These immunomodulatory compounds include ajoene, arctigenin, β-carotene, curcumin, epigallocatechin-3-gallate, ginsan, glabridin and quinic acid. In this review, we discussed the ability of these eight immunomodulators in regulating the immune system potentially applicable in breast cancer treatment via anti-inflammatory (curcumin, arctigenin, glabridin and ajoene) and lymphocytes activation (β-carotene, epigallocatechin-3-gallate, quinic acid and ginsan) properties, as well as future research direction in their use for breast cancer treatment. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  6. Effects of intraperitoneal administration of the GABAB receptor positive allosteric modulator 2,6-di tert-butyl-4-(2-hydroxy-2,2-dimethyl-propyl)-phenol (CGP7930) on food intake in non-deprived rats.

    Science.gov (United States)

    Ebenezer, Ivor S

    2012-09-05

    γ-Aminobutyric acid-(B) (GABA(B)) receptor positive allosteric modulators (PAMs) act on an allosteric site on the GABA(B) receptor to potentiate the effects of GABA and GABA(B) receptor agonists. It has previously been demonstrated that the GABA(B) receptor agonist baclofen increases food intake in non-deprived rats. The aim of this study was to investigate whether the GABA(B) receptor PAM 2,6-di tert-butyl-4-(2-hydroxy-2,2-dimethyl-propyl)-phenol (CGP7930) would (i) increase food intake, and (ii) potentiate the hyperphagic effects of baclofen in rats. In Experiment 1, the effects of intraperitoneal (i.p.) administration of CGP7930 (1, 6 and 12 mg/kg) was investigated on food intake in non-deprived male Wistar rats. The 12 mg/kg dose of CGP7930 significantly increased cumulative food intake 30, 60 and 120 min (PGABA and GABA(B) receptor agonists by allosteric modulation of the GABA(B) receptor. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Active prey selection in two pelagic copepods feeding on potentially toxic and non-toxic dinoflagellates

    DEFF Research Database (Denmark)

    Schultz, Mette; Kiørboe, Thomas

    2009-01-01

    Grazing on two red tide dinoflagellates, the potentially toxic Karenia mikimotoi and the non-toxic Gyrodinium instriatum, was examined in two species of marine copepods, Pseudocalanus elongatus and Temora longicornis. Both copepods cleared K. mikimotoi at rates that were a little lower but compar......Grazing on two red tide dinoflagellates, the potentially toxic Karenia mikimotoi and the non-toxic Gyrodinium instriatum, was examined in two species of marine copepods, Pseudocalanus elongatus and Temora longicornis. Both copepods cleared K. mikimotoi at rates that were a little lower...

  8. SELECTED ISSUES OF COMPETITIVENESS POTENTIAL OF FRUIT AND VEGETABLE PROCESSING COMPANIES LOCATED IN THE WIELKOPOLSKIE VOIVODESHIP

    Directory of Open Access Journals (Sweden)

    Joanna Smoluk-Sikorska

    2014-09-01

    Full Text Available The paper discusses results of the research concerning potential and strategy of competitiveness of companies of fruit and vegetable processing industry located in the Wielkopolskie voivodeship. Special attention was paid to the assessment of the companies’ financial situation, their production resources, management system and adopted development strategies. The investigated companies are characterised by strong domestic market position, which is mainly results of the assessment of their financial situation. They asses competitiveness potential very high, particularly human resources and related with them management skills. Furthermore, most of the companies assess the use of strategy of quality control and specialisation strategy as high or very high.

  9. Potential exposure to endocrine disrupting chemicals and selected adverse pregnancy outcomes

    DEFF Research Database (Denmark)

    Bengtsson, Jessica; Thygesen, Pernille Søgaard; Kaerlev, Linda

    2017-01-01

    potential occupational exposure to endocrine disrupting chemicals (EDC) of the mother during pregnancy is associated with preterm birth and low birth weight. Methods: Pregnant women referred to an Occupational Health Clinic (OHC) in two Danish regions (Copenhagen or Aarhus) between 1984 and 2010, suspected...

  10. MODULATION OF EVENT-RELATED POTENTIALS BY WORD REPETITION - THE ROLE OF VISUAL SELECTIVE ATTENTION

    NARCIS (Netherlands)

    OTTEN, LJ; RUGG, MD; DOYLE, MC

    1993-01-01

    Event-related potentials (ERPs) were recorded while subjects viewed visually presented words, some of which occurred twice. Each trial consisted of two colored letter strings, the requirement being to attend to and make a word/nonword discrimination for one of the strings. Attention was manipulated

  11. Effects of nicotine on visuo-spatial selective attention as indexed by event-related potentials.

    Science.gov (United States)

    Meinke, A; Thiel, C M; Fink, G R

    2006-08-11

    Nicotine has been shown to specifically reduce reaction times to invalidly cued targets in spatial cueing paradigms. In two experiments, we used event-related potentials to test whether the facilitative effect of nicotine upon the detection of invalidly cued targets is due to a modulation of perceptual processing, as indexed by early attention-related event-related potential components. Furthermore, we assessed whether the effect of nicotine on such unattended stimuli depends upon the use of exogenous or endogenous cues. In both experiments, the electroencephalogram was recorded while non-smokers completed discrimination tasks in Posner-type paradigms after chewing a nicotine polacrilex gum (Nicorette 2 mg) in one session and a placebo gum in another session. Nicotine reduced reaction times to invalidly cued targets when cueing was endogenous. In contrast, no differential effect of nicotine on reaction times was observed when exogenous cues were used. Electrophysiologically, we found a similar attentional modulation of the P1 and N1 components under placebo and nicotine but a differential modulation of later event-related potential components at a frontocentral site. The lack of a drug-dependent modulation of P1 and N1 in the presence of a behavioral effect suggests that the effect of nicotine in endogenous visuo-spatial cueing tasks is not due to an alteration of perceptual processes. Rather, the differential modulation of frontocentral event-related potentials suggests that nicotine acts at later stages of target processing.

  12. Substrate selection for fundamental studies of electrocatalysts and photoelectrodes: inert potential windows in acidic, neutral, and basic electrolyte.

    Directory of Open Access Journals (Sweden)

    Jesse D Benck

    Full Text Available The selection of an appropriate substrate is an important initial step for many studies of electrochemically active materials. In order to help researchers with the substrate selection process, we employ a consistent experimental methodology to evaluate the electrochemical reactivity and stability of seven potential substrate materials for electrocatalyst and photoelectrode evaluation. Using cyclic voltammetry with a progressively increased scan range, we characterize three transparent conducting oxides (indium tin oxide, fluorine-doped tin oxide, and aluminum-doped zinc oxide and four opaque conductors (gold, stainless steel 304, glassy carbon, and highly oriented pyrolytic graphite in three different electrolytes (sulfuric acid, sodium acetate, and sodium hydroxide. We determine the inert potential window for each substrate/electrolyte combination and make recommendations about which materials may be most suitable for application under different experimental conditions. Furthermore, the testing methodology provides a framework for other researchers to evaluate and report the baseline activity of other substrates of interest to the broader community.

  13. Analyzing production potential of selected food and legume crops for food security in Punjab, Pakistan

    International Nuclear Information System (INIS)

    Qasim, M.; Hassan, S.; Bashir, A.; Mehmood, I.; Mahmood, H. Z.

    2015-01-01

    The present study was designed to assess growth rate in area, yield and production of selected major food commodities and to project these parameters on the basis of estimated growth co-efficient. Time-series data for area, yield and production were collected for wheat, sugarcane, rice, mung and gram since 1980-81. The semi-log trend function was employed to find out the growth rate of selected commodities. The findings of the study showed the positive growth rates of area, production and yield of all selected food grain and legume crops. The estimated co-efficient for all growth models (area, production and yield) of selected commodities were statistically highly significant at 1 percentage level except yield of gram which was significant at 10 percentage level. The estimated annual growth rate of area for wheat, rice and sugarcane was 0.9 percentage, 2.1 percentage and 0.8 percentage, respectively with the production growth of 3.0 percentage, 3.8 percentage and 2.2 percentage, respectively and yield growth of 2.1 percentage, 1.6 percentage and 1.5 percentage, respectively. The results highlighted that the major contribution for expansion in production for rice and sugarcane was area while it was yield for wheat. In this scenario the wheat production can be enhanced by increasing its area than that of rice and sugarcane. The annual growth rate for gram and mung area was estimated about 1.0 v and 4.9 percentage, respectively, with the production growth rate of 2.3 percentage and 6.4 percentage while yield growth rate of 2.9 percentage and 1.4 percentage, respectively. Keeping in view the higher growth of gram yield the increase in its area may enhance its production more than that of mung. The proportionate higher increase in the area of wheat and gram may enhance the welfare of producers in particular and provide food security to masses in general. (author)

  14. Selective potentiation of the antitumor radiation effect by means of short-term hyperglycemia

    International Nuclear Information System (INIS)

    Yarmonenko, S.P.; Shapot, V.S.; Voloshina, E.A.; Gorozhanskaya, Eh.G.; Dyuskaliev, Zh.D.; Krimker, V.M.

    1981-01-01

    Experiments on mice have shown that short-term induced hyperglycemia caused by 5-fold intraperitoneal administration of glucose at a dose of 2.6 and 1.3 g/kg increases notably the radiation injury to a solid type of Ehrlich carcinoma. Short-term induced hyperglycemia is mostly effective after irradiation. During irradiation together with its antitumor effect enhanced in the presence of short-term induced hyperglycemia there is observed selective protection of the normal tissues resulting from a decrease of oxygen pressure in them

  15. Perils and potentials of self-selected entry to epidemiological studies and surveys

    DEFF Research Database (Denmark)

    Keiding, Niels; Louis, Thomas A.

    2016-01-01

    Low front-end cost and rapid accrual make Web-based surveys and enrolment in studies attractive, but participants are often self-selected with little reference to a well-defined study base. Of course, high quality studies must be internally valid (validity of inferences for the sample at hand......), but Web-based enrolment reactivates discussion of external validity (generalization of within-study inferences to a target population or context) in epidemiology and clinical trials. Survey research relies on a representative sample produced by a sampling frame, prespecified sampling process and weighting...

  16. Survey on basic knowledge about exposure and potential environmental and health risks for selected nanomaterials

    DEFF Research Database (Denmark)

    Mikkelsen, Sonja Hagen; Hansen, Erik; Christensen, Trine Boe

    Based on a literature review this report provides a general description as well as an environmental and health profile of 7 nanomaterials. The examined nanomaterials are selected because of expected high use or specific environmental and health properties. Fullerenes, iron, silver, nanoclay...... and titanium-, cerium-, and silicondioxides were studied in the project. Based on current uses, it is concluded that current applications of nano-iron and nanoclay can not cause unexpected “nano-associated” health or environmental problems. Although no specific risk associated with current uses of any of the 7...... other nanomaterials were identified, there are areas where there may be reason for attention and thus need for more knowledge....

  17. Method of Observation and their Effects in the Selection of Potential Football Goalkeepers

    Directory of Open Access Journals (Sweden)

    Zerf Mohammed

    2017-11-01

    Full Text Available The criteria and methods for goalkeeper selection are more strict and complex than those of field players. Founded on its principles, the present study tried to examine the strengths and weaknesses of selection process practised by Algerian coaches. Interpret by Algerian scientists in their subjectivity in evaluating the amount of body fat and its effect on physical performance. Seen it's built with the naked eye. Confirmed by FIFA in two categories normal vs overweight, they should work harder under these conditions. For this proposal, eight teams from the leagues of Oran, Algeria Championship second division were involved in the study. Their goalkeepers were classified into the following groups: total (GK = 28, Main goalkeeper (MG = 14 and replacement goalkeeper (RG = 14. Tested at the end of the outward phase by penalty kicks test, ‘T’ Drill Test, Ruler Drop Test (TR and anthropometric parameters (BH, BMI, BFP, BW. Backed on the applied statistical where our total sample is categorised in overweight, as well as no statistically significant differences between the two groups in all the comparisons practised. Our results confirm the weaknesses of traditional methods. Admit by similar studies in their subjective in evaluating the amount of body fat and its effect on physical performance correlate to anthropometric measurement.

  18. Genetic diversity of selected genes that are potentially economically important in feral sheep of New Zealand

    Directory of Open Access Journals (Sweden)

    Sedcole J Richard

    2010-12-01

    Full Text Available Abstract Background Feral sheep are considered to be a source of genetic variation that has been lost from their domestic counterparts through selection. Methods This study investigates variation in the genes KRTAP1-1, KRT33, ADRB3 and DQA2 in Merino-like feral sheep populations from New Zealand and its offshore islands. These genes have previously been shown to influence wool, lamb survival and animal health. Results All the genes were polymorphic, but no new allele was identified in the feral populations. In some of these populations, allele frequencies differed from those observed in commercial Merino sheep and other breeds found in New Zealand. Heterozygosity levels were comparable to those observed in other studies on feral sheep. Our results suggest that some of the feral populations may have been either inbred or outbred over the duration of their apparent isolation. Conclusion The variation described here allows us to draw some conclusions about the likely genetic origin of the populations and selective pressures that may have acted upon them, but they do not appear to be a source of new genetic material, at least for these four genes.

  19. Potential biochemical markers for selection of disease resistance in Vigna radiata

    International Nuclear Information System (INIS)

    Badere, R.S.; Koche, D.K.; Choudhary, A.D.; Pawar, S.E.

    2001-01-01

    The Vigna radiata (L.) Wilczek (Green gram), a major pulse crop is prone to damaging diseases caused by Erysiphe polygoni, Cercospora canescens and Rhizoctonia sp. Therefore, the development of multiple resistance is a major breeding objective in green gram. Resistance to powdery mildew has already been developed, however, there are no reports on the development of resistance to Cercospora in green gram. Owing to limitation of conventional screening methods, the improvement for multiple disease resistance is inadequate, in this crop. It needs an efficient and quick selection method, for screening the plant population at an early stage. It is well established that the resistant interaction, in plants, involves accumulation of antibiotic compound phytoalexin (Genestein in Vigna radiata) and induction of enzymes such as β-1,3 gulcanase and Chitinases. These compounds are not only induced by pathogens but also pathogen-derived elicitors. These biochemical compounds can be used as resistance indicative biochemical markers for screening the natural or mutagen induced genetic diversity in populations of Vigna radiata in non-destructive manner. It, however, needs a systematic study of plant defense response. This paper deals with the response of resistant and susceptible cultivars of vigna radiata to Cercospora elicitor and development of non-destructive selection method for disease resistance. (author)

  20. Renewable Biochemical Methane Potential through Anaerobic Co-digestion from Selective Feed Stocks

    Science.gov (United States)

    Thara, K.; Navis Karthika, Ignatius; Dheenadayalan, M. S., Dr

    2017-08-01

    Biochemical Methane Potential (BMP) analysis provides a measure of the anaerobic biodegradability of a given substrate. BMP test is also used to evaluate the potential biogas (methane) production between various Co-digestion substrates. This test is also used to determine the amount of organic carbon in a given material that can be an aerobically converted to methane-Biogas. Studies were carried out for the production of biogas from the leather solid waste. Co-digestion (simultaneous digestion of two or more substrates) studies were carried out in batch reactor using the fleshing (a solid waste generated during the processing of raw hides or skins into finished leather) along with the fruit and vegetable waste at mesophilic condition 35° C). The anaerobic methanogenic seed sludge prepared separately followed by standard BMP test, which was used as the seed inoculums. Recent research on this topic is reviewed in this current paper.

  1. Energy Efficiency Potential in Existing Commercial Buildings: Review of Selected Recent Studies

    Energy Technology Data Exchange (ETDEWEB)

    Belzer, David B.

    2009-04-03

    This report reviews six recent studies (from 2002 through 2006) by states and utilities to assess the energy saving potential in existing commercial buildings. The studies cover all or portions of California, Connecticut, Vermont, Colorado, Illinois, and the Pacific Northwest. The studies clearly reveal that lighting remains the single largest and most cost effective end use that can be reduced to save energy. Overall the study indicated that with existing technologies and costs, a reasonable range of economic savings potential in existing commercial buildings is between 10 and 20 percent of current energy use. While not a focus of the study, an additional conclusion is that implementation of commercial building monitoring and controls would also play an important role in the nation’s efforts to improve energy efficiency of existing buildings.

  2. Comparative Assessment Of Coastal Tourism Potentials Of Selected Areas In Rivers State Nigeria

    Directory of Open Access Journals (Sweden)

    Obinwanne

    2015-08-01

    Full Text Available ABSTRACT The study examined coastal tourism potentials in Rivers State with emphasis on Opobo Bonny and Port Harcourt to determine the area that has comparative advantage for tourism development to optimally utilize resources. The study was conducted in Bonny Opobo and Port Harcourt of River State Nigeria. The area occupies the land close to the Atlantic Ocean within 60km radius from the coast. A survey design was adopted for the study. The instruments used were observation checklist and interview schedule. The instruments were tested for validity and reliability using five experts drawn from the field. The data collected were analyzed using ethnographic description method of analysis to answer research questions. The natural attractions found include mangrove forest sacred forests sacred rivers lakes beaches fishing rivers natural sources of drinking water and sanctuary. The cultural heritage resources were historical monument shrines museums different cultural festivals cultural materials and slave port. The man-made attractions were recreational park zoological garden and tourism village. It was found that there were more tourism potentials in Port Harcourt study site more than Bonny and Opobo sites and therefore Port Harcourt has comparative advantage over Bonny and Opobo for tourism development. Therefore efforts should be made and scarce resources utilized towards developing those coastal areas with best potentials and comparative advantage over others.

  3. Guided selective deposition of nanoparticles by tuning of the surface potential

    Science.gov (United States)

    Eklöf, J.; Stolaś, A.; Herzberg, M.; Pekkari, A.; Tebikachew, B.; Gschneidtner, T.; Lara-Avila, S.; Hassenkam, T.; Moth-Poulsen, K.

    2017-07-01

    Guided deposition of nanoparticles onto different substrates is of great importance for a variety of applications such as biosensing, targeted cancer therapy, anti-bacterial coatings and single molecular electronics. It is therefore important to gain an understanding of what parameters are involved in the deposition of nanoparticles. In this work we have deposited 60 nm, negatively charged, citrate stabilized gold nanoparticles onto microstructures consisting of six different materials, (vanadium (V), silicon dioxide (SiO2), gold (Au), aluminum (Al), copper (Cu) and nickel (Ni)). The samples have then been investigated by scanning electron microscopy to extract the particle density. The surface potential was calculated from the measured surface charge density maps measured by atomic force microscopy while the samples were submerged in a KCl water solution. These values were compared with literature values of the isoelectric points (IEP) of different oxides formed on the metals in an ambient environment. According to measurements, Al had the highest surface potential followed by Ni and Cu. The same trend was observed for the nanoparticle densities. No particles were found on V, SiO2 and Au. The literature values of the IEP showed a different trend compared to the surface potential measurements concluding that IEP is not a reliable parameter for the prediction of NP deposition. Contribution to the Focus Issue Self-assemblies of Inorganic and Organic Nanomaterials edited by Marie-Paule Pileni.

  4. Recording strategies and selection potential of feed intake measured using the X-ray method in rainbow trout

    Directory of Open Access Journals (Sweden)

    Mäntysaari Esa A

    2006-06-01

    Full Text Available Abstract This study examines the way long-term feed intake should be recorded accurately for selective breeding purposes, and estimates selection potential in feed intake using the X-ray method to record individual daily feed intake in rainbow trout (Oncorhynchus mykiss. The analysis showed that the point estimates of daily feed intake displayed low repeatabilities (r = 0.09–0.32. This indicates that a minimum of three repeated records were needed to accurately record average feed intake at a fixed age. To effectively breed for feed intake over the whole growing period, it is necessary to determine average feed intake at different ages, since there were only moderate phenotypic and genetic correlations between average daily feed intake recorded at 140 g, 750 g and 2000 g wet mass. Heritability for average daily feed intake was low (average h2 = 0.10, indicating that modest genetic changes can be obtained in response to selection. It was concluded that selection to genetically change long-term feed intake can be successful, yet repeated observations at several life stages are needed to ensure the accuracy of feed intake estimates and the efficiency of selection.

  5. Fermented goats' milk produced with selected multiple starters as a potentially functional food.

    Science.gov (United States)

    Minervini, Fabio; Bilancia, Maria Teresa; Siragusa, Sonya; Gobbetti, Marco; Caponio, Francesco

    2009-09-01

    A screening among five lactic acid bacteria, used alone or in combination, led to select a mixed starter (Streptococcus thermophilus CR12, Lactobacillus casei LC01, Lactobacillus helveticus PR4, Lactobacillus plantarum 1288) capable to produce a fermented goats' milk containing gamma-aminobutyric acid (GABA) and angiotensin-I converting enzyme (ACE)-inhibitory peptides. The fermented milk was characterized by cell counts of lactic acid bacteria not lower than 7.0 log cfu g(-1), even after 45 days of storage at 4 degrees C. Fermentation of goats' milk resulted in the production of ca. 28 mg kg(-1) of GABA. Furthermore the fermented goats' milk had an in vitro ACE-inhibitory activity of ca. 73%. Prolonged cold storage did not significantly affect both the concentration of GABA and the ACE-inhibitory activity. Moreover, the taurine content did not significantly vary during both fermentation and the entire storage period.

  6. Visual encoding and fixation target selection in free viewing: presaccadic brain potentials

    Directory of Open Access Journals (Sweden)

    Andrey R Nikolaev

    2013-06-01

    Full Text Available In scrutinizing a scene, the eyes alternate between fixations and saccades. During a fixation, two component processes can be distinguished: visual encoding and selection of the next fixation target. We aimed to distinguish the neural correlates of these processes in the electrical brain activity prior to a saccade onset. Participants viewed color photographs of natural scenes, in preparation for a change detection task. Then, for each participant and each scene we computed an image heat map, with temperature representing the duration and density of fixations. The temperature difference between the start and end points of saccades was taken as a measure of the expected task-relevance of the information concentrated in specific regions of a scene. Visual encoding was evaluated according to whether subsequent change was correctly detected. Saccades with larger temperature difference were more likely to be followed by correct detection than ones with smaller temperature differences. The amplitude of presaccadic activity over anterior brain areas was larger for correct detection than for detection failure. This difference was observed for short scrutinizing but not for long explorative saccades, suggesting that presaccadic activity reflects top-down saccade guidance. Thus, successful encoding requires local scanning of scene regions which are expected to be task-relevant. Next, we evaluated fixation target selection. Saccades moving up in temperature were preceded by presaccadic activity of higher amplitude than those moving down. This finding suggests that presaccadic activity reflects attention deployed to the following fixation location. Our findings illustrate how presaccadic activity can elucidate concurrent brain processes related to the immediate goal of planning the next saccade and the larger-scale goal of constructing a robust representation of the visual scene.

  7. Selective isolation and differentiation of a stromal population of human embryonic stem cells with osteogenic potential

    DEFF Research Database (Denmark)

    Harkness, Linda M; Mahmood, Amer; Ditzel, Nicholas

    2011-01-01

    cultured in osteogenic differentiation media, up regulation of osteoblastic lineage markers (DLX5, MSX2, RUNX2, SPARC, ALP, COL1a1, BGLAP, IBSP, DCN, LOX-L4) and production of in vitro mineralized matrix was detected. hESC-stromal cells loaded on a carrier and implanted either subcutaneously...... or in a critical size calvarial defect in immune deficient mice for 10weeks, resulted in new bone formation and partial repair of the calvarial defect. In conclusion, hESC-stromal can be isolated from hESC cultures and represent a good source for obtaining cells with osteogenic differentiation potential suitable...

  8. Enterocin P Selectively Dissipates the Membrane Potential of Enterococcus faecium T136

    Science.gov (United States)

    Herranz, C.; Chen, Y.; Chung, H.-J.; Cintas, L. M.; Hernández, P. E.; Montville, T. J.; Chikindas, M. L.

    2001-01-01

    Enterocin P is a pediocin-like, broad-spectrum bacteriocin which displays a strong inhibitory activity against Listeria monocytogenes. The bacteriocin was purified from the culture supernatant of Enterococcus faecium P13, and its molecular mechanism of action against the sensitive strain E. faecium T136 was evaluated. Although enterocin P caused significant reduction of the membrane potential (ΔΨ) and the intracellular ATP pool of the indicator organism, the pH gradient (ΔpH) component of the proton motive force (Δp) was not dissipated. By contrast, enterocin P caused carboxyfluorescein efflux from E. faecium T136-derived liposomes. PMID:11282622

  9. An in silico high-throughput screen identifies potential selective inhibitors for the non-receptor tyrosine kinase Pyk2

    Directory of Open Access Journals (Sweden)

    Meirson T

    2017-05-01

    Full Text Available Tomer Meirson, Abraham O Samson, Hava Gil-Henn Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel Abstract: The non-receptor tyrosine kinase proline-rich tyrosine kinase 2 (Pyk2 is a critical mediator of signaling from cell surface growth factor and adhesion receptors to cell migration, proliferation, and survival. Emerging evidence indicates that signaling by Pyk2 regulates hematopoietic cell response, bone density, neuronal degeneration, angiogenesis, and cancer. These physiological and pathological roles of Pyk2 warrant it as a valuable therapeutic target for invasive cancers, osteoporosis, Alzheimer’s disease, and inflammatory cellular response. Despite its potential as a therapeutic target, no potent and selective inhibitor of Pyk2 is available at present. As a first step toward discovering specific potential inhibitors of Pyk2, we used an in silico high-throughput screening approach. A virtual library of six million lead-like compounds was docked against four different high-resolution Pyk2 kinase domain crystal structures and further selected for predicted potency and ligand efficiency. Ligand selectivity for Pyk2 over focal adhesion kinase (FAK was evaluated by comparative docking of ligands and measurement of binding free energy so as to obtain 40 potential candidates. Finally, the structural flexibility of a subset of the docking complexes was evaluated by molecular dynamics simulation, followed by intermolecular interaction analysis. These compounds may be considered as promising leads for further development of highly selective Pyk2 inhibitors. Keywords: virtual screen, efficiency metrics, MM-GBSA, molecular dynamics

  10. Potential and limitations of multidecadal satellite soil moisture observations for selected climate model evaluation studies

    Directory of Open Access Journals (Sweden)

    A. Loew

    2013-09-01

    Full Text Available Soil moisture is an essential climate variable (ECV of major importance for land–atmosphere interactions and global hydrology. An appropriate representation of soil moisture dynamics in global climate models is therefore important. Recently, a first multidecadal, observation-based soil moisture dataset has become available that provides information on soil moisture dynamics from satellite observations (ECVSM, essential climate variable soil moisture. The present study investigates the potential and limitations of this new dataset for several applications in climate model evaluation. We compare soil moisture data from satellite observations, reanalysis and simulations from a state-of-the-art land surface model and analyze relationships between soil moisture and precipitation anomalies in the different dataset. Other potential applications like model parameter optimization or model initialization are not investigated in the present study. In a detailed regional study, we show that ECVSM is capable to capture well the interannual and intraannual soil moisture and precipitation dynamics in the Sahelian region. Current deficits of the new dataset are critically discussed and summarized at the end of the paper to provide guidance for an appropriate usage of the ECVSM dataset for climate studies.

  11. Energy performance contracting - energy saving potential of selected energy conservation measures (ECM)

    Energy Technology Data Exchange (ETDEWEB)

    Johansson, M. (Dansk Energi Analyse A/S, Frederiksberg (Denmark)); Langkilde, G.; Olesen, Bjarne W. (Technical Univ. of Denmark, ICIEE, Kgs. Lyngby (Denmark)); Moerck, O. (Cenergia Energy Consultants, Herlev (Denmark)); Sundman, O. (DONG Energy, Copenhagen (Denmark)); Engelund Thomsen, K. (Aalborg Univ., SBi, Hoersholm (Denmark))

    2008-09-15

    This report has been developed under the research project 'Etablering af grundlag for energitjenester i Danmark' (project number: ENS-33031-0185) under the Danish research programme - EFP. The objective of this project has been to contribute to the utilisation of the large potential for energy conservations in the building sector within the public, industry and service sectors through the development of a better basis for decision making for both the Energy Service Companies (ESCOes) and the building owners. The EU directive on Energy Service Contracting points at the buildings as the area where the biggest potential market for energy services and energy efficiency improvements are. The EFP-project has two parts: (1) A Danish part and (2) participation in the international cooperation project 'Holistic Assesment Tool-Kit on Energy Efficient Retrofit Measures for Government Buildings (EnERGo)', Annex 46 under the IEA R and D program 'Energy Conservation In Buildings And Community Systems' (ECBCS). This report describes the Danish contributions to the IEA projects subtask B, which has a primary objective to develop a database of energy conservation measures (ECM) with descriptions and performance characteristics of these. (au)

  12. Microbial antagonism as a potential solution for controlling selected root pathogens of crops

    Science.gov (United States)

    Cooper, Sarah; Agnew, Linda; Pereg, Lily

    2016-04-01

    Root pathogens of crops can cause large reduction in yield, however, there is a limited range of effective methods to control such pathogens. Soilborne pathogens that infect roots often need to survive in the rhizosphere, where there is high competition from other organisms. In such hot spots of microbial activity and growth, supported by root exudates, microbes have evolved antagonistic mechanisms that give them competitive advantages in winning the limited resources. Among these mechanisms is antibiosis, with production of some significant antifungal compounds including, antibiotics, volatile organic compounds, hydrogen cyanide and lytic enzymes. Some of these mechanisms may suppress disease through controlling the growth of root pathogens. In this project we isolated various fungi and bacteria that suppress the growth of cotton pathogens in vitro. The pathogen-suppressive microbes were isolated from cotton production soils that are under different management strategies, with and without the use of organic amendments. The potential of pathogen-suppressing microbes for controlling the black root rot disease, caused by the soilborne pathogen Thielaviopsis basicola, was confirmed using soil assays. We identified isolates with potential use as inoculant for cotton production in Australia. Having isolated a diverse group of antagonistic microbes enhances the probability that some would survive well in the soil and provide an alternative approach to address the problem of root disease affecting agricultural crops.

  13. Energy performance contracting - energy saving potential of selected energy conservation measures (ECM)

    Energy Technology Data Exchange (ETDEWEB)

    Johansson, M [Dansk Energi Analyse A/S, Frederiksberg (Denmark); Langkilde, G; Olesen, Bjarne W [Technical Univ. of Denmark, ICIEE, Kgs. Lyngby (Denmark); Moerck, O [Cenergia Energy Consultants, Herlev (Denmark); Sundman, O [DONG Energy, Copenhagen (Denmark); Engelund Thomsen, K [Aalborg Univ., SBi, Hoersholm (Denmark)

    2008-09-15

    This report has been developed under the research project 'Etablering af grundlag for energitjenester i Danmark' (project number: ENS-33031-0185) under the Danish research programme - EFP. The objective of this project has been to contribute to the utilisation of the large potential for energy conservations in the building sector within the public, industry and service sectors through the development of a better basis for decision making for both the Energy Service Companies (ESCOes) and the building owners. The EU directive on Energy Service Contracting points at the buildings as the area where the biggest potential market for energy services and energy efficiency improvements are. The EFP-project has two parts: (1) A Danish part and (2) participation in the international cooperation project 'Holistic Assesment Tool-Kit on Energy Efficient Retrofit Measures for Government Buildings (EnERGo)', Annex 46 under the IEA R and D program 'Energy Conservation In Buildings And Community Systems' (ECBCS). This report describes the Danish contributions to the IEA projects subtask B, which has a primary objective to develop a database of energy conservation measures (ECM) with descriptions and performance characteristics of these. (au)

  14. High-temperature steam oxidation testing of select advanced replacement alloys for potential core internals

    Energy Technology Data Exchange (ETDEWEB)

    Tan, Lizhen [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Pint, Bruce A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2017-05-19

    Coupons from a total of fourteen commercial and custom fabricated alloys were exposed to 1 bar full steam with ~10 ppb oxygen content at 600 and 650°C. The coupons were weighed at 500-h intervals with a total exposure time of 5,000 h. The fourteen alloys are candidate alloys selected under the ARRM program, which include three ferritic steels (Grade 92, 439, and 14YWT), three austenitic stainless steels (316L, 310, and 800), seven Ni-base superalloys (X750, 725, C22, 690, 625, 625 direct-aging, and 625- plus), and one Zr-alloy (Zr–2.5Nb). Among the alloys, 316L and X750 are served as reference alloys for low- and high-strength alloys, respectively. The candidate Ni-base superalloy 718 was procured too late to be included in the tests. The corrosion rates of the candidate alloys can be approximately interpreted by their Cr, Ni and Fe content. The corrosion rate was significantly reduced with increasing Cr content and when Ni content is above ~15 wt%, but not much further reduced when Fe content is less than ~55 wt%. Simplified thermodynamics analyses of the alloy oxidation provided reasonable indications for the constituents of oxide scales formed on the alloys and explanations for the porosity and exfoliation phenomena because of the nature of specific types of oxides.

  15. Serologic survey for selected arboviruses and other potential pathogens in wildlife from Mexico.

    Science.gov (United States)

    Aguirre, A A; McLean, R G; Cook, R S; Quan, T J

    1992-07-01

    During 1988 and 1989, a serologic survey of wildlife was conducted in northeastern Mexico to determine the presence, prevalence, and distribution of arboviruses and other selected disease agents. Eighty mammal specimens were tested. Antibodies to vesicular stomatitis-Indiana, Venezuelan equine encephalitis-Mena II, Rio Grande virus, and vesicular stomatitis-New Jersey were detected predominantly in small mammals. Deer and mouflon (Ovis musimon) had antibodies to bluetongue and epizootic hemorrhagic disease. Two species had serologic evidence of recent exposure to Francisella tularensis. A white-tailed deer (Odocoileus virginianus) had antibodies to Anaplasma marginale. All specimens tested for antibodies against Yersinia pestis and Brucella abortus were negative. Sera from 315 birds were tested for antibody against five equine encephalitis viruses and six avian pathogens. During 1988, antibodies to Venezuelan equine encephalitis-Mena II, Venezuelan equine encephalitis-TC83, St. Louis encephalitis, eastern equine encephalitis, and western equine encephalitis were detected in birds of several species. Antibodies to Pasteurella multocida and Newcastle disease virus were also detected. Birds from five species presented antibodies to Mycoplasma meleagridis. Specimens tested for M. gallisepticum, M. synoviae, and Chlamydia psittaci were negative. To the best of our knowledge, this survey represents the first serologic evidence of bluetongue, Cache Valley virus, epizootic hemorrhagic disease, Jamestown Canyon virus, vesicular stomatitis-Indiana, vesicular stomatitis-New Jersey, Rio Grande virus, and tularemia reported among wildlife in Mexico.

  16. Phytoremediation potential of Alocasia microrrhiza grown on soil collected from selected dumpsites in Ekiti State, Nigeria

    Directory of Open Access Journals (Sweden)

    Asaolu S. S.

    2013-04-01

    Full Text Available This study investigates the effect of enhanced phytoextraction on the accumulation of heavy metals by Alocasia microrrhiza cultivated on soil collected from selected dumpsites in Ekiti State, Nigeria. The application of 1g/kg EDTA decreased the heights of plants relative to control, but significantly increased the concentration of heavy metals in various tissues of the plant. Notably, concentration of Pb and Cu were greater than the threshold value of 100mg/kg, indicative of the fact that Alocasia microrrhiza could be a good candidate for Pb and Cuphytoextraction. BF, TF and RR values (1.1–1.6, (4.3-4.8 and (1.4–2.3 revealed the effectiveness of the plant to translocate Pb and Cu to their harvestable portion. RRs values greater than one also indicated the efficiency of plant under chelate-induced phytoextraction. However, the concentration of heavy metals did not vary significantly at p < 0.05 (LSD test in all dumpsites investigated.

  17. Potential aluminium(III)- and gallium(III)-selective optical sensors based on porphyrazines.

    Science.gov (United States)

    Goslinski, Tomasz; Tykarska, Ewa; Kryjewski, Michal; Osmalek, Tomasz; Sobiak, Stanislaw; Gdaniec, Maria; Dutkiewicz, Zbigniew; Mielcarek, Jadwiga

    2011-01-01

    Porphyrazines possessing non-coordinating alkyl (propyl) and aralkyl (4-tert-butylphenyl) groups in the periphery were studied as optical sensors for a set of mono-, di- and trivalent cations. Investigated porphyrazines in the UV-Vis monitored titrations revealed significant responses towards aluminium and gallium cations, unlike other metal ions studied. Additionally, porphyrazine possessing 4-tert-butylphenyl peripheral substituents showed sensor property towards ruthenium cation and was chosen for further investigation. The presence of isosbestic points in absorption spectra for its titration with aluminium, gallium and ruthenium cations, accompanied by a linear Benesi-Hildebrand plot, proved complex formation. The continuous variation method was used to determine binding stoichiometry in 1:1 porphyrazine-metal ratio. X-Ray studies and density functional theory calculations were employed to investigate octa(4-tert-butylphenyl)porphyrazine structure. The results helped to explain the observed selectivity towards certain ions. Interaction between ion and porphyrazine meso nitrogen in a Lewis acid-Lewis base manner is proposed.

  18. Keynote address: cellular reduction of nitroimidazole drugs: potential for selective chemotherapy and diagnosis of hypoxic cells

    International Nuclear Information System (INIS)

    Chapman, J.D.; Lee, J.; Meeker, B.E.

    1989-01-01

    Nitroimidazole drugs were initially developed as selective radiosensitizers of hypoxic cells and, consequently, as adjuvants to improve the local control probabilities of current radiotherapies. Misonidazole (MISO), the prototype radiosensitizing drug, was found in Phase I clinical studies to cause dose-limiting neurotoxicities (mainly peripheral neuropathies). MISO was also found to be cytotoxic in the absence of radiation and to covalently bind to cellular molecules, both processes demonstrating rates much higher in hypoxic compared with oxygenated cells. It is likely that neurotoxicity, cellular cytotoxicity and adduct formation results from reactions between reduction intermediates of MISO and cellular target molecules. Spin-offs from radiosensitizer research include the synthesis and characterization of more potent hypoxic cytotoxins and the exploitation of sensitizer-adducts as probes for measuring cellular and tissue oxygen levels. Current developments in hypoxic cell cytotoxin and hypoxic cell marker research are reviewed with specific examples from studies which characterize the cellular reduction of TF-MISO, (1-(2-nitro-1-imidazolyl)-3[2,2,2-trifluoroethoxy]-2-propanol). 45 references

  19. Investigation of therapeutic potentials of some selected medicinal plants using neutron activation analysis

    International Nuclear Information System (INIS)

    Abubakar, Sani; Isa, Nasiru Fage; Usman, Ahmed Rufa’i; Khandaker, Mayeen Uddin; Abubakar, Nuraddeen

    2015-01-01

    Series of attempts were made to investigate concentrations of trace elements and their therapeutic properties in various medicinal plants. In this study, samples of some commonly used plants were collected from Bauchi State, Nigeria. They includes leaves of azadirachta indica (neem), Moringa Oleifera (moringa), jatropha curcas (purgin Nut), guiera senegalensis (custard apple) and anogeissus leiocarpus (African birch). These samples were analyzed for their trace elements contents with both short and long irradiation protocols of Instrumental Neutron Activation Analysis (INAA) at Nigerian Research Reactor-1 (NIRR-1) of Ahmadu Bello University, Zaria, Nigeria. The level of trace elements found varies from one sample to another, with some reported at hundreds of mg/Kg dry weight. The results have been compared with the available literature data. The presence of these trace elements indicates promising potentials of these plants for relief of certain ailments

  20. Investigation of therapeutic potentials of some selected medicinal plants using neutron activation analysis

    Energy Technology Data Exchange (ETDEWEB)

    Abubakar, Sani; Isa, Nasiru Fage [Bayero University, Kano Nigeria (Nigeria); Usman, Ahmed Rufa’i [University of Malaya, Kuala Lumpur (Malaysia); Umaru Musa Yar’adua University, Katsina Nigeria (Nigeria); Khandaker, Mayeen Uddin [University of Malaya, Kuala Lumpur (Malaysia); Abubakar, Nuraddeen [Center for Energy Research and Training, Ahmadu Bello University, Zaria Nigeria (Nigeria)

    2015-04-24

    Series of attempts were made to investigate concentrations of trace elements and their therapeutic properties in various medicinal plants. In this study, samples of some commonly used plants were collected from Bauchi State, Nigeria. They includes leaves of azadirachta indica (neem), Moringa Oleifera (moringa), jatropha curcas (purgin Nut), guiera senegalensis (custard apple) and anogeissus leiocarpus (African birch). These samples were analyzed for their trace elements contents with both short and long irradiation protocols of Instrumental Neutron Activation Analysis (INAA) at Nigerian Research Reactor-1 (NIRR-1) of Ahmadu Bello University, Zaria, Nigeria. The level of trace elements found varies from one sample to another, with some reported at hundreds of mg/Kg dry weight. The results have been compared with the available literature data. The presence of these trace elements indicates promising potentials of these plants for relief of certain ailments.

  1. Investigation of therapeutic potentials of some selected medicinal plants using neutron activation analysis

    Science.gov (United States)

    Abubakar, Sani; Usman, Ahmed Rufa'i.; Isa, Nasiru Fage; Khandaker, Mayeen Uddin; Abubakar, Nuraddeen

    2015-04-01

    Series of attempts were made to investigate concentrations of trace elements and their therapeutic properties in various medicinal plants. In this study, samples of some commonly used plants were collected from Bauchi State, Nigeria. They includes leaves of azadirachta indica (neem), Moringa Oleifera (moringa), jatropha curcas (purgin Nut), guiera senegalensis (custard apple) and anogeissus leiocarpus (African birch). These samples were analyzed for their trace elements contents with both short and long irradiation protocols of Instrumental Neutron Activation Analysis (INAA) at Nigerian Research Reactor-1 (NIRR-1) of Ahmadu Bello University, Zaria, Nigeria. The level of trace elements found varies from one sample to another, with some reported at hundreds of mg/Kg dry weight. The results have been compared with the available literature data. The presence of these trace elements indicates promising potentials of these plants for relief of certain ailments.

  2. Evaluation and Selection of Potential Biomass Sources of North-East India towards Sustainable Bioethanol Production

    International Nuclear Information System (INIS)

    Nongthombam, Grihalakshmi D.; Labala, Rajendra K.; Das, Sudripta; Handique, Pratap J.; Talukdar, Narayan C.

    2017-01-01

    Vegetation biomass production in North-East India within Indo-Burma biodiversity hotspot is luxuriant and available from April to October to consider their potential for bioethanol production. Potential of six lignocellulosic biomass (LCB) sources; namely, sugarcane bagasse (BG), cassava aerial parts (CS), ficus fruits (Ficus cunia) (FF), “phumdi” (floating biomass), rice straw (RS), and sawdust were investigated for bioethanol production using standard techniques. Morphological and chemical changes were evaluated by Scanning electron microscopy and Fourier transform infrared spectroscopy and quantity of sugars and inhibitors in LCB were determined by High performance liquid chromatography. Hydrothermally treated BG, CS, and FF released 954.54, 1,354.33, and 1,347.94 mg/L glucose and 779.31, 612.27, and 1,570.11 mg/L of xylose, respectively. Inhibitors produced due to effect of hydrothermal pretreatment ranged from 42.8 to 145.78 mg/L acetic acid, below detection level (BDL) to 17.7 µg/L 5-hydroxymethylfurfural, and BDL to 56.78 µg/L furfural. The saccharification efficiency of hydrothermally treated LCB (1.35–28.64%) was significantly higher compared with their native counterparts (0.81–17.97%). Consolidated bioprocessing of the LCB using MTCC 1755 (Fusarium oxysporum) resulted in maximum ethanol concentration of 0.85 g/L and corresponded to 42 mg ethanol per gram of hydrothermally treated BG in 120 h followed by 0.83 g/L corresponding to 41.5 mg/g of untreated CS in 144 h. These ethanol concentrations corresponded to 23.43 and 21.54% of theoretical ethanol yield, respectively. LCB of CS and FF emerged as a suitable material to be subjected to test for enhanced ethanol production in future experiments through efficient fermentative microbial strains, appropriate enzyme loadings, and standardization of other fermentation parameters.

  3. Evaluation and Selection of Potential Biomass Sources of North-East India towards Sustainable Bioethanol Production

    Energy Technology Data Exchange (ETDEWEB)

    Nongthombam, Grihalakshmi D., E-mail: griha789@gmail.com; Labala, Rajendra K.; Das, Sudripta [Institute of Bioresources and Sustainable Development (IBSD), Imphal (India); Handique, Pratap J. [Department of Biotechnology, Gauhati University, Guwahati (India); Talukdar, Narayan C., E-mail: griha789@gmail.com [Division of Life Sciences, Institute of Advanced Study in Science and Technology, Guwahati (India)

    2017-07-11

    Vegetation biomass production in North-East India within Indo-Burma biodiversity hotspot is luxuriant and available from April to October to consider their potential for bioethanol production. Potential of six lignocellulosic biomass (LCB) sources; namely, sugarcane bagasse (BG), cassava aerial parts (CS), ficus fruits (Ficus cunia) (FF), “phumdi” (floating biomass), rice straw (RS), and sawdust were investigated for bioethanol production using standard techniques. Morphological and chemical changes were evaluated by Scanning electron microscopy and Fourier transform infrared spectroscopy and quantity of sugars and inhibitors in LCB were determined by High performance liquid chromatography. Hydrothermally treated BG, CS, and FF released 954.54, 1,354.33, and 1,347.94 mg/L glucose and 779.31, 612.27, and 1,570.11 mg/L of xylose, respectively. Inhibitors produced due to effect of hydrothermal pretreatment ranged from 42.8 to 145.78 mg/L acetic acid, below detection level (BDL) to 17.7 µg/L 5-hydroxymethylfurfural, and BDL to 56.78 µg/L furfural. The saccharification efficiency of hydrothermally treated LCB (1.35–28.64%) was significantly higher compared with their native counterparts (0.81–17.97%). Consolidated bioprocessing of the LCB using MTCC 1755 (Fusarium oxysporum) resulted in maximum ethanol concentration of 0.85 g/L and corresponded to 42 mg ethanol per gram of hydrothermally treated BG in 120 h followed by 0.83 g/L corresponding to 41.5 mg/g of untreated CS in 144 h. These ethanol concentrations corresponded to 23.43 and 21.54% of theoretical ethanol yield, respectively. LCB of CS and FF emerged as a suitable material to be subjected to test for enhanced ethanol production in future experiments through efficient fermentative microbial strains, appropriate enzyme loadings, and standardization of other fermentation parameters.

  4. Potential for bioremediation of agro-industrial effluents with high loads of pesticides by selected fungi.

    Science.gov (United States)

    Karas, Panagiotis A; Perruchon, Chiara; Exarhou, Katerina; Ehaliotis, Constantinos; Karpouzas, Dimitrios G

    2011-02-01

    Wastewaters from the fruit packaging industry contain a high pesticide load and require treatment before their environmental discharge. We provide first evidence for the potential bioremediation of these wastewaters. Three white rot fungi (WRF) (Phanerochaete chrysosporium, Trametes versicolor, Pleurotus ostreatus) and an Aspergillus niger strain were tested in straw extract medium (StEM) and soil extract medium (SEM) for degrading the pesticides thiabendazole (TBZ), imazalil (IMZ), thiophanate methyl (TM), ortho-phenylphenol (OPP), diphenylamine (DPA) and chlorpyrifos (CHL). Peroxidase (LiP, MnP) and laccase (Lac) activity was also determined to investigate their involvement in pesticide degradation. T. versicolor and P. ostreatus were the most efficient degraders and degraded all pesticides (10 mg l⁻¹) except TBZ, with maximum efficiency in StEM. The phenolic pesticides OPP and DPA were rapidly degraded by these two fungi with a concurrent increase in MnP and Lac activity. In contrast, these enzymes were not associated with the degradation of CHL, IMZ and TM implying the involvement of other enzymes. T. versicolor degraded spillage-level pesticide concentrations (50 mg l⁻¹) either fully (DPA, OPP) or partially (TBZ, IMZ). The fungus was also able to rapidly degrade a mixture of TM/DPA (50 mg l⁻¹), whereas it failed to degrade IMZ and TBZ when supplied in a mixture with OPP. Overall, T. versicolor and P. ostreatus showed great potential for the bioremediation of wastewaters from the fruit packaging industry. However, degradation of TBZ should be also achieved before further scaling up.

  5. Urine proteome analysis in Dent's disease shows high selective changes potentially involved in chronic renal damage.

    Science.gov (United States)

    Santucci, Laura; Candiano, Giovanni; Anglani, Franca; Bruschi, Maurizio; Tosetto, Enrica; Cremasco, Daniela; Murer, Luisa; D'Ambrosio, Chiara; Scaloni, Andrea; Petretto, Andrea; Caridi, Gianluca; Rossi, Roberta; Bonanni, Alice; Ghiggeri, Gian Marco

    2016-01-01

    Definition of the urinary protein composition would represent a potential tool for diagnosis in many clinical conditions. The use of new proteomic technologies allows detection of genetic and post-trasductional variants that increase sensitivity of the approach but complicates comparison within a heterogeneous patient population. Overall, this limits research of urinary biomarkers. Studying monogenic diseases are useful models to address this issue since genetic variability is reduced among first- and second-degree relatives of the same family. We applied this concept to Dent's disease, a monogenic condition characterised by low-molecular-weight proteinuria that is inherited following an X-linked trait. Results are presented here on a combined proteomic approach (LC-mass spectrometry, Western blot and zymograms for proteases and inhibitors) to characterise urine proteins in a large family (18 members, 6 hemizygous patients, 6 carrier females, and 6 normals) with Dent's diseases due to the 1070G>T mutation of the CLCN5. Gene ontology analysis on more than 1000 proteins showed that several clusters of proteins characterised urine of affected patients compared to carrier females and normal subjects: proteins involved in extracellular matrix remodelling were the major group. Specific analysis on metalloproteases and their inhibitors underscored unexpected mechanisms potentially involved in renal fibrosis. Studying with new-generation techniques for proteomic analysis of the members of a large family with Dent's disease sharing the same molecular defect allowed highly repetitive results that justify conclusions. Identification in urine of proteins actively involved in interstitial matrix remodelling poses the question of active anti-fibrotic drugs in Dent's patients. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Identifying Potential Conservation Corridors Along the Mongolia-Russia Border Using Resource Selection Functions: A Case Study on Argali Sheep

    Directory of Open Access Journals (Sweden)

    Buyanaa Chimeddorj

    2013-12-01

    Full Text Available The disruption of animal movements is known to affect wildlife populations, particularly large bodied, free-ranging mammals that require large geographic ranges to survive. Corridors commonly connect fragmented wildlife populations and their habitats, yet identifying corridors rarely uses data on habitat selection and movements of target species. New technologies and analytical tools make it possible to better integrate landscape patterns with spatial behavioral data. We show how resource selection functions can describe habitat suitability using continuous and multivariate metrics to determine potential wildlife movement corridors. During 2005–2010, we studied movements of argali sheep ( Ovis ammon near the Mongolia-Russia border using radio-telemetry and modeled their spatial distribution in relation to landscape features to create a spatially explicit habitat suitability surface to identify potential transboundary conservation corridors. Argali sheep habitat selection in western Mongolia positively correlated with elevation, ruggedness index, and distance to border. In other words, argali were tended use areas with higher elevation, rugged topography, and distances farther from the international border. We suggest that these spatial modeling approaches offer ways to design and identify wildlife corridors more objectively and holistically, and can be applied to many other target species.

  7. Hyaluronic acid binding ability of human sperm reflects cellular maturity and fertilizing potential: selection of sperm for intracytoplasmic sperm injection.

    Science.gov (United States)

    Huszar, Gabor; Ozkavukcu, Sinan; Jakab, Attila; Celik-Ozenci, Ciler; Sati, G Leyla; Cayli, Sevil

    2006-06-01

    The current concepts of sperm biochemical markers and the central role of the HspA2 chaperone protein, a measure of sperm cellular maturity and fertilizing potential, are reviewed. Because HspA2 is a component of the synaptonemal complex, low HspA2 levels and increased frequency of chromosomal aneuploidies are related in diminished maturity sperm. We also suggest a relationship between HspA2 expression in elongating spermatids and events of late spermiogenesis, such as cytoplasmic extrusion and plasma membrane remodeling that aid the formation of the zona pellucida binding and hyaluronic acid binding sites. The presence of hyaluronic acid receptor on the plasma membrane of mature sperm, coupled with hyaluronic acid coated glass or plastic surfaces, facilitates testing of sperm function and selection of single mature sperm for intracytoplasmic sperm injection. The frequencies of sperm with chromosomal disomy are reduced approximately fourfold to fivefold in hyaluronic acid selected sperm compared with semen sperm, comparable to the increase in such abnormalities in intracytoplasmic sperm injection offspring. Hyaluronic acid binding also excludes immature sperm with cytoplasmic extrusion, persistent histones, and DNA chain breaks. Hyaluronic acid mediated sperm selection is a novel technique that is comparable to sperm zona pellucida binding. Hyaluronic acid selected sperm will also alleviate the risks related to intracytoplasmic sperm injection fertilization with sperm of diminished maturity that currently cause worldwide concern.

  8. Mining potential biomarkers associated with space flight in Caenorhabditis elegans experienced Shenzhou-8 mission with multiple feature selection techniques

    International Nuclear Information System (INIS)

    Zhao, Lei; Gao, Ying; Mi, Dong; Sun, Yeqing

    2016-01-01

    Highlights: • A combined algorithm is proposed to mine biomarkers of spaceflight in C. elegans. • This algorithm makes the feature selection more reliable and robust. • Apply this algorithm to predict 17 positive biomarkers to space environment stress. • The strategy can be used as a general method to select important features. - Abstract: To identify the potential biomarkers associated with space flight, a combined algorithm, which integrates the feature selection techniques, was used to deal with the microarray datasets of Caenorhabditis elegans obtained in the Shenzhou-8 mission. Compared with the ground control treatment, a total of 86 differentially expressed (DE) genes in responses to space synthetic environment or space radiation environment were identified by two filter methods. And then the top 30 ranking genes were selected by the random forest algorithm. Gene Ontology annotation and functional enrichment analyses showed that these genes were mainly associated with metabolism process. Furthermore, clustering analysis showed that 17 genes among these are positive, including 9 for space synthetic environment and 8 for space radiation environment only. These genes could be used as the biomarkers to reflect the space environment stresses. In addition, we also found that microgravity is the main stress factor to change the expression patterns of biomarkers for the short-duration spaceflight.

  9. Mining potential biomarkers associated with space flight in Caenorhabditis elegans experienced Shenzhou-8 mission with multiple feature selection techniques

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Lei [Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026 (China); Gao, Ying [Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Shushanhu Road 350, Hefei 230031 (China); Mi, Dong, E-mail: mid@dlmu.edu.cn [Department of Physics, Dalian Maritime University, Dalian 116026 (China); Sun, Yeqing, E-mail: yqsun@dlmu.edu.cn [Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026 (China)

    2016-09-15

    Highlights: • A combined algorithm is proposed to mine biomarkers of spaceflight in C. elegans. • This algorithm makes the feature selection more reliable and robust. • Apply this algorithm to predict 17 positive biomarkers to space environment stress. • The strategy can be used as a general method to select important features. - Abstract: To identify the potential biomarkers associated with space flight, a combined algorithm, which integrates the feature selection techniques, was used to deal with the microarray datasets of Caenorhabditis elegans obtained in the Shenzhou-8 mission. Compared with the ground control treatment, a total of 86 differentially expressed (DE) genes in responses to space synthetic environment or space radiation environment were identified by two filter methods. And then the top 30 ranking genes were selected by the random forest algorithm. Gene Ontology annotation and functional enrichment analyses showed that these genes were mainly associated with metabolism process. Furthermore, clustering analysis showed that 17 genes among these are positive, including 9 for space synthetic environment and 8 for space radiation environment only. These genes could be used as the biomarkers to reflect the space environment stresses. In addition, we also found that microgravity is the main stress factor to change the expression patterns of biomarkers for the short-duration spaceflight.

  10. Selection and Characterization of Single Chain Antibody Fragments Specific for Hsp90 as a Potential Cancer Targeting Molecule

    Directory of Open Access Journals (Sweden)

    Edyta Petters

    2015-08-01

    Full Text Available Heat shock proteins play an essential role in facilitating malignant transformation and they have been recognized as important factors in human cancers. One of the key elements of the molecular chaperones machinery is Hsp90 and it has recently become a target for anticancer therapeutic approaches. The potential and importance of Hsp90-directed agents becomes apparent when one realizes that disruption of Hsp90 function may influence over 200 oncogenic client proteins. Here, we described the selection and characterization of Hsp90-specific antibody fragments from commercially available Tomlinson I and J phage display libraries. The affinities of Hsp90-binding scFv variants were measured using SPR method. Then, based on the best clone selected, we performed the affinity maturation procedure and obtained valuable Hsp90-specific clones. The selected binders were expressed and applied for immunostaining, ELISA and SPR analysis using model cancer cell lines. All performed experiments confirmed the ability of selected antibodies to interact with the Hsp90. Therefore, the presented Hsp90-specific scFv, might be a starting point for the development of a novel antibody-based strategy targeting cancer.

  11. Exploring Covalent Allosteric Inhibition of Antigen 85C from Mycobacterium tuberculosis by Ebselen Derivatives.

    Science.gov (United States)

    Goins, Christopher M; Dajnowicz, Steven; Thanna, Sandeep; Sucheck, Steven J; Parks, Jerry M; Ronning, Donald R

    2017-05-12

    Previous studies identified ebselen as a potent in vitro and in vivo inhibitor of the Mycobacterium tuberculosis (Mtb) antigen 85 (Ag85) complex, comprising three homologous enzymes required for the biosynthesis of the mycobacterial cell wall. In this study, the Mtb Ag85C enzyme was cocrystallized with azido and adamantyl ebselen derivatives, resulting in two crystallographic structures of 2.01 and 1.30 Å resolution, respectively. Both structures displayed the anticipated covalent modification of the solvent accessible, noncatalytic Cys209 residue forming a selenenylsulfide bond. Continuous difference density for both thiol modifiers allowed for the assessment of interactions that influence ebselen binding and inhibitor orientation that were unobserved in previous Ag85C ebselen structures. The k inact /K I values for ebselen, adamantyl ebselen, and azido ebselen support the importance of observed constructive chemical interactions with Arg239 for increased in vitro efficacy toward Ag85C. To better understand the in vitro kinetic properties of these ebselen derivatives, the energetics of specific protein-inhibitor interactions and relative reaction free energies were calculated for ebselen and both derivatives using density functional theory. These studies further support the different in vitro properties of ebselen and two select ebselen derivatives from our previously published ebselen library with respect to kinetics and protein-inhibitor interactions. In both structures, the α9 helix was displaced farther from the enzyme active site than the previous Ag85C ebselen structure, resulting in the restructuring of a connecting loop and imparting a conformational change to residues believed to play a role in substrate binding specific to Ag85C. These notable structural changes directly affect protein stability, reducing the overall melting temperature by up to 14.5 °C, resulting in the unfolding of protein at physiological temperatures. Additionally, this structural

  12. Tissue factor activates allosteric networks in factor VIIa through structural and dynamic changes

    DEFF Research Database (Denmark)

    Madsen, Jesper Jonasson; Persson, E.; Olsen, O. H.

    2015-01-01

    that are not likely to be inferred from mutagenesis studies. Furthermore, paths from Met306 to Ile153 (N-terminus) and Trp364, both representing hallmark residues of allostery, are 7% and 37% longer, respectively, in free FVIIa. Thus, there is significantly weaker coupling between the TF contact point and key......Background: Tissue factor (TF) promotes colocalization of enzyme (factorVIIa) and substrate (FX or FIX), and stabilizes the active conformation of FVIIa. Details on how TF induces structural and dynamic changes in the catalytic domain of FVIIa to enhance its efficiency remain elusive. Objective......: To elucidate the activation of allosteric networks in the catalytic domain of the FVIIa protease it is when bound to TF.MethodsLong-timescale molecular dynamics simulations of FVIIa, free and in complex with TF, were executed and analyzed by dynamic network analysis. Results: Allosteric paths of correlated...

  13. Photogrammetry and Its Potential Application in Medical Science on the Basis of Selected Literature.

    Science.gov (United States)

    Ey-Chmielewska, Halina; Chruściel-Nogalska, Małgorzata; Frączak, Bogumiła

    2015-01-01

    Photogrammetry is a science and technology which allows quantitative traits to be determined, i.e. the reproduction of object shapes, sizes and positions on the basis of their photographs. Images can be recorded in a wide range of wavelengths of electromagnetic radiation. The most common is the visible range, but near- and medium-infrared, thermal infrared, microwaves and X-rays are also used. The importance of photogrammetry has increased with the development of computer software. Digital image processing and real-time measurement have allowed the automation of many complex manufacturing processes. Photogrammetry has been widely used in many areas, especially in geodesy and cartography. In medicine, this method is used for measuring the widely understood human body for the planning and monitoring of therapeutic treatment and its results. Digital images obtained from optical-electronic sensors combined with computer technology have the potential of objective measurement thanks to the remote nature of the data acquisition, with no contact with the measured object and with high accuracy. Photogrammetry also allows the adoption of common standards for archiving and processing patient data.

  14. Implicit and explicit selective attention to smoking cues in smokers indexed by brain potentials.

    Science.gov (United States)

    Littel, Marianne; Franken, Ingmar H A

    2011-04-01

    Substance use disorders are characterized by cognitive processing biases, such as automatically detecting and orienting attention towards drug-related stimuli. However, it is unclear how, when and what kind of attention (i.e. implicit, explicit) interacts with the processing of these stimuli. In addition, it is unclear whether smokers are hypersensitive to emotionally significant cues in general or to smoking-related cues in particular. The present event-related potential study aimed to enhance insight in drug-related processing biases by manipulating attention for smoking and other motivationally relevant (emotional) cues in smokers and non-smokers using a visual oddball task. Each of the stimulus categories served as a target (explicit attention; counting) or as a non-target (implicit attention; oddball) category. Compared with non-smokers, smokers' P300 (350-600 ms) was enhanced to smoking pictures under both attentional conditions. P300 amplitude did not differ between groups in response to positive, negative, and neutral cues. It can be concluded from this study that attention manipulation affects the P300 differently in smokers and non-smokers. Smokers display a specific bias to smoking-related cues, and this bias is present during both explicit and implicit attentional processing. Overall, it can be concluded that both explicit and implicit attentional processes appear to play an important role in drug-related processing bias.

  15. Energy regulation in China: Objective selection, potential assessment and responsibility sharing by partial frontier analysis

    International Nuclear Information System (INIS)

    Xia, X.H.; Chen, Y.B.; Li, J.S.; Tasawar, H.; Alsaedi, A.; Chen, G.Q.

    2014-01-01

    To cope with the excessive growth of energy consumption, the Chinese government has been trying to strengthen the energy regulation system by introducing new initiatives that aim at controlling the total amount of energy consumption. A partial frontier analysis is performed in this paper to make a comparative assessment of the combinations of possible energy conservation objectives, new constraints and regulation strategies. According to the characteristics of the coordination of existing regulation structure and the optimality of regulation strategy, four scenarios are constructed and regional responsibilities are reasonably divided by fully considering the production technology in the economy. The relative importance of output objectives and the total amount controlling is compared and the impacts on the regional economy caused by the changes of regulation strategy are also evaluated for updating regulation policy. - Highlights: • New initiatives to control the total amount of energy consumption are evaluated. • Twenty-four regulation strategies and four scenarios are designed and compared. • Crucial regions for each sector and regional potential are identified. • The national goals of energy abatement are decomposed into regional responsibilities. • The changes of regulation strategy are evaluated for updating regulation policy

  16. Investigation of greenhouse gas reduction potential and change in technological selection in Indian power sector

    International Nuclear Information System (INIS)

    Mathur, Jyotirmay; Bansal, Narendra Kumar; Wagner, H.-J.

    2003-01-01

    Due to the growing energy needs along with increasing concerns towards control of greenhouse gas emissions, most developing countries are under pressure to find alternative methods for energy conversion and policies to make these technologies economically viable. One of the instruments that have been adopted by many industrial countries is that of the carbon tax. The rate of introducing carbon taxes however, depends upon the local economic conditions and market forces. The case of Indian power sector has been examined by using MARKAL model for introduction of carbon taxes at four different trajectories. Their implications on the power generation choices have been investigated for a time span of 25 years from the year 2000. In general large hydropower plants have emerged as the first choice followed by wind energy systems. However, cheaper availability of coal in India keeps scope of use of coal based technologies for which pressurised fluidised bed combustion technology has been found to be the balanced choice among fossil technologies. There exists a potential of reduction of greenhouse gas emissions by about 25% as compared to the 'business-as-usual' case in presence of high carbon tax rates

  17. Structural differences of matrix metalloproteinases with potential implications for inhibitor selectivity examined by the GRID/CPCA approach

    DEFF Research Database (Denmark)

    Terp, Gitte Elgaard; Cruciani, Gabriele; Christensen, Inge Thøger

    2002-01-01

    The matrix metalloproteinases (MMPs) are a family of proteolytic enzymes, which have been the focus of a lot of research in recent years because of their involvement in various disease conditions. In this study, structures of 10 enzymes (MMP1, MMP2, MMP3, MMP7, MMP8, MMP9, MMP12, MMP13, MMP14......, and MMP20) were examined with the intention of highlighting regions that could be potential sites for obtaining selectivity. For this purpose, the GRID/CPCA approach as implemented in GOLPE was used. Counterions were included to take into account the different electrostatic properties of the proteins......, and the GRID calculations were performed, allowing the protein side chains to move in response to interaction with the probes. In the search for selectivity, the MMPs are known to be a very difficult case because the enzymes of this family are very similar. The well-known differences in the S1' pocket were...

  18. In vitro screening of potential probiotic activities of selected lactobacilli isolated from unpasteurized milk products for incorporation into soft cheese.

    Science.gov (United States)

    Coeuret, Valérie; Gueguen, Micheline; Vernoux, Jean Paul

    2004-11-01

    The aim was to select potentially probiotic lactobacilli from 88 strains isolated from unpasteurized milk and cheese products, and to incorporate these bacteria in a viable state into a soft cheese, without changing its quality. The survival of these bacteria was assessed in acidic and bile conditions, after freezing at -80 degrees C. Four strains from unpasteurized Camembert--two Lactobacillus plantarum strains and two Lb. paracasei/casei strains--were identified and typed by PCR and PFGE and were found to display potentially probiotic characteristics in addition to resistance to low pH and bile. These characteristics were resistance to lysozyme, adhesion to CACO-2 cells, antimicrobial effects against common foodborne pathogens (Listeria monocytogenes, Staphylococcus aureus, Salmonella spp., Escherichia coli, innocuity following the ingestion of high doses by mice and appropriate antibiotic susceptibility profiles. The potential of Lb. plantarum strain UCMA 3037 for incorporation into a soft cheese (Pont-l'Eveque registered designation of origin (RDO)) was investigated. This strain grew well and survived in sufficient numbers (more than 10(7) cfu/g throughout the shelf-life of the product) in the cheese. This strain did not change the quality score of the product until the best before date (75 days after manufacture). Thus, unpasteurized Camembert is a natural source of potentially probiotic lactobacilli, which could be used as an additive in the development of potentially probiotic soft cheeses. Further work is required to demonstrate the persistence and efficacy of these strains in the human host upon ingestion.

  19. Diacylglycerol Acyltransferase 1 Is Regulated by Its N-Terminal Domain in Response to Allosteric Effectors.

    Science.gov (United States)

    Caldo, Kristian Mark P; Acedo, Jeella Z; Panigrahi, Rashmi; Vederas, John C; Weselake, Randall J; Lemieux, M Joanne

    2017-10-01

    Diacylglycerol acyltransferase 1 (DGAT1) is an integral membrane enzyme catalyzing the final and committed step in the acyl-coenzyme A (CoA)-dependent biosynthesis of triacylglycerol (TAG). The biochemical regulation of TAG assembly remains one of the least understood areas of primary metabolism to date. Here, we report that the hydrophilic N-terminal domain of Brassica napus DGAT1 (BnaDGAT1 1-113 ) regulates activity based on acyl-CoA/CoA levels. The N-terminal domain is not necessary for acyltransferase activity and is composed of an intrinsically disordered region and a folded segment. We show that the disordered region has an autoinhibitory function and a dimerization interface, which appears to mediate positive cooperativity, whereas the folded segment of the cytosolic region was found to have an allosteric site for acyl-CoA/CoA. Under increasing acyl-CoA levels, the binding of acyl-CoA with this noncatalytic site facilitates homotropic allosteric activation. Enzyme activation, on the other hand, is prevented under limiting acyl-CoA conditions (low acyl-CoA-to-CoA ratio), whereby CoA acts as a noncompetitive feedback inhibitor through interaction with the same folded segment. The three-dimensional NMR solution structure of the allosteric site revealed an α-helix with a loop connecting a coil fragment. The conserved amino acid residues in the loop interacting with CoA were identified, revealing details of this important regulatory element for allosteric regulation. Based on these results, a model is proposed illustrating the role of the N-terminal domain of BnaDGAT1 as a positive and negative modulator of TAG biosynthesis. © 2017 American Society of Plant Biologists. All Rights Reserved.

  20. Allosteric regulation by oleamide of the binding properties of 5-hydroxytryptamine7 receptors.

    Science.gov (United States)

    Hedlund, P B; Carson, M J; Sutcliffe, J G; Thomas, E A

    1999-12-01

    Oleamide belongs to a family of amidated lipids with diverse biological activities, including sleep induction and signaling modulation of several 5-hydroxytryptamine (5-HT) receptor subtypes, including 5-HT1A, 5-HT2A/2C, and 5-HT7. The 5-HT7 receptor, predominantly localized in the hypothalamus, hippocampus, and frontal cortex, stimulates cyclic AMP formation and is thought to be involved in the regulation of sleep-wake cycles. Recently, it was proposed that oleamide acts at an allosteric site on the 5-HT7 receptor to regulate cyclic AMP formation. We have further investigated the interaction between oleamide and 5-HT7 receptors by performing radioligand binding assays with HeLa cells transfected with the 5-HT7 receptor. Methiothepin, clozapine, and 5-HT all displaced specific [3H]5-HT (100 nM) binding, with pK(D) values of 7.55, 7.85, and 8.39, respectively. Oleamide also displaced [3H]5-HT binding, but the maximum inhibition was only 40% of the binding. Taking allosteric (see below) cooperativity into account, a K(D) of 2.69 nM was calculated for oleamide. In saturation binding experiments, oleamide caused a 3-fold decrease in the affinity of [3H]5-HT for the 5-HT7 receptor, without affecting the number of binding sites. A Schild analysis showed that the induced shift in affinity of [3H]5-HT reached a plateau, unlike that of a competitive inhibitor, illustrating the allosteric nature of the interaction between oleamide and the 5-HT7 receptor. Oleic acid, the product of oleamide hydrolysis, had a similar effect on [3H]5-HT binding, whereas structural analogs of oleamide, trans-9,10-octadecenamide, cis-8,9-octadecenamide, and erucamide, did not alter [3H]5-HT binding significantly. The findings support the hypothesis that oleamide acts via an allosteric site on the 5-HT7 receptor regulating receptor affinity.

  1. Allosteric ligands and their binding sites define γ-aminobutyric acid (GABA) type A receptor subtypes.

    Science.gov (United States)

    Olsen, Richard W

    2015-01-01

    GABAA receptors (GABA(A)Rs) mediate rapid inhibitory transmission in the brain. GABA(A)Rs are ligand-gated chloride ion channel proteins and exist in about a dozen or more heteropentameric subtypes exhibiting variable age and brain regional localization and thus participation in differing brain functions and diseases. GABA(A)Rs are also subject to modulation by several chemotypes of allosteric ligands that help define structure and function, including subtype definition. The channel blocker picrotoxin identified a noncompetitive channel blocker site in GABA(A)Rs. This ligand site is located in the transmembrane channel pore, whereas the GABA agonist site is in the extracellular domain at subunit interfaces, a site useful for low energy coupled conformational changes of the functional channel domain. Two classes of pharmacologically important allosteric modulatory ligand binding sites reside in the extracellular domain at modified agonist sites at other subunit interfaces: the benzodiazepine site and the high-affinity, relevant to intoxication, ethanol site. The benzodiazepine site is specific for certain GABA(A)R subtypes, mainly synaptic, while the ethanol site is found at a modified benzodiazepine site on different, extrasynaptic, subtypes. In the transmembrane domain are allosteric modulatory ligand sites for diverse chemotypes of general anesthetics: the volatile and intravenous agents, barbiturates, etomidate, propofol, long-chain alcohols, and neurosteroids. The last are endogenous positive allosteric modulators. X-ray crystal structures of prokaryotic and invertebrate pentameric ligand-gated ion channels, and the mammalian GABA(A)R protein, allow homology modeling of GABA(A)R subtypes with the various ligand sites located to suggest the structure and function of these proteins and their pharmacological modulation. © 2015 Elsevier Inc. All rights reserved.

  2. Structure and allosteric effects of low-molecular-weight activators on the protein kinase PDK1

    DEFF Research Database (Denmark)

    Hindie, Valerie; Stroba, Adriana; Zhang, Hua

    2009-01-01

    -dependent activation of AGC kinases. The AGC kinase PDK1 is activated by the docking of a phosphorylated motif from substrates. Here we present the crystallography of PDK1 bound to a rationally developed low-molecular-weight activator and describe the conformational changes induced by small compounds in the crystal...... molecular details of the allosteric changes induced by small compounds that trigger the activation of PDK1 through mimicry of phosphorylation-dependent conformational changes....

  3. Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteins.

    Science.gov (United States)

    Soltan Ghoraie, Laleh; Burkowski, Forbes; Zhu, Mu

    2015-03-01

    Recent studies have highlighted the role of coupled side-chain fluctuations alone in the allosteric behavior of proteins. Moreover, examination of X-ray crystallography data has recently revealed new information about the prevalence of alternate side-chain conformations (conformational polymorphism), and attempts have been made to uncover the hidden alternate conformations from X-ray data. Hence, new computational approaches are required that consider the polymorphic nature of the side chains, and incorporate the effects of this phenomenon in the study of information transmission and functional interactions of residues in a molecule. These studies can provide a more accurate understanding of the allosteric behavior. In this article, we first present a novel approach to generate an ensemble of conformations and an efficient computational method to extract direct couplings of side chains in allosteric proteins, and provide sparse network representations of the couplings. We take the side-chain conformational polymorphism into account, and show that by studying the intrinsic dynamics of an inactive structure, we are able to construct a network of functionally crucial residues. Second, we show that the proposed method is capable of providing a magnified view of the coupled and conformationally polymorphic residues. This model reveals couplings between the alternate conformations of a coupled residue pair. To the best of our knowledge, this is the first computational method for extracting networks of side chains' alternate conformations. Such networks help in providing a detailed image of side-chain dynamics in functionally important and conformationally polymorphic sites, such as binding and/or allosteric sites. © 2014 Wiley Periodicals, Inc.

  4. Allosteric mechanisms within the adenosine A2A-dopamine D2 receptor heterotetramer

    Science.gov (United States)

    Ferré, Sergi; Bonaventura, Jordi; Tomasi, Dardo; Navarro, Gemma; Moreno, Estefanía; Cortés, Antonio; Lluís, Carme; Casadó, Vicent; Volkow, Nora D.

    2017-01-01

    The structure constituted by a G protein coupled receptor (GPCR) homodimer and a G protein provides a main functional unit and oligomeric entities can be viewed as multiples of dimers. For GPCR heteromers, experimental evidence supports a tetrameric structure, comprised of two different homodimers, each able to signal with its preferred G protein. GPCR homomers and heteromers can act as the conduit of allosteric interactions between orthosteric ligands. The well-known agonist/agonist allosteric interaction in the adenosine A2A receptor (A2AR)-dopamine D2 receptor (D2R) heteromer, by which A2AR agonists decrease the affinity of D2R agonists, gave the first rationale for the use of A2AR antagonists in Parkinson’s disease. We review new pharmacological findings that can be explained in the frame of a tetrameric structure of the A2AR-D2R heteromer: first, ligand-independent allosteric modulations by the D2R that result in changes of the binding properties of A2AR ligands; second, differential modulation of the intrinsic efficacy of D2R ligands for G protein-dependent and independent signaling; third, the canonical antagonistic Gs-Gi interaction within the frame of the heteromer; and fourth, the ability of A2AR antagonists, including caffeine, to also exert the same allosteric modulations of D2R ligands than A2AR agonists, while A2AR agonists and antagonists counteract each other’s effects. These findings can have important clinical implications when evaluating the use of A2AR antagonists. They also call for the need of monitoring caffeine intake when evaluating the effect of D2R ligands, when used as therapeutic agents in neuropsychiatric disorders or as probes in imaging studies. PMID:26051403

  5. Estimation of Leakage Potential of Selected Sites in Interstate and Tri-State Canals Using Geostatistical Analysis of Selected Capacitively Coupled Resistivity Profiles, Western Nebraska, 2004

    Science.gov (United States)

    Vrabel, Joseph; Teeple, Andrew; Kress, Wade H.

    2009-01-01

    With increasing demands for reliable water supplies and availability estimates, groundwater flow models often are developed to enhance understanding of surface-water and groundwater systems. Specific hydraulic variables must be known or calibrated for the groundwater-flow model to accurately simulate current or future conditions. Surface geophysical surveys, along with selected test-hole information, can provide an integrated framework for quantifying hydrogeologic conditions within a defined area. In 2004, the U.S. Geological Survey, in cooperation with the North Platte Natural Resources District, performed a surface geophysical survey using a capacitively coupled resistivity technique to map the lithology within the top 8 meters of the near-surface for 110 kilometers of the Interstate and Tri-State Canals in western Nebraska and eastern Wyoming. Assuming that leakage between the surface-water and groundwater systems is affected primarily by the sediment directly underlying the canal bed, leakage potential was estimated from the simple vertical mean of inverse-model resistivity values for depth levels with geometrically increasing layer thickness with depth which resulted in mean-resistivity values biased towards the surface. This method generally produced reliable results, but an improved analysis method was needed to account for situations where confining units, composed of less permeable material, underlie units with greater permeability. In this report, prepared by the U.S. Geological Survey in cooperation with the North Platte Natural Resources District, the authors use geostatistical analysis to develop the minimum-unadjusted method to compute a relative leakage potential based on the minimum resistivity value in a vertical column of the resistivity model. The minimum-unadjusted method considers the effects of homogeneous confining units. The minimum-adjusted method also is developed to incorporate the effect of local lithologic heterogeneity on water

  6. Assessment of toxic and endocrine potential of substances migrating from selected toys and baby products.

    Science.gov (United States)

    Szczepańska, Natalia; Namieśnik, Jacek; Kudłak, Błażej

    2016-12-01

    Analysis of literature data shows that there is limited information about the harmful biological effects of mixture of compounds from the EDC group that are released from the surface of toys and objects intended for children and infants. One of the tools that can be used to obtain such information is appropriate bioanalytical tests. The aim of this research involved determining whether tests that use living organisms as an active element (Vibrio fischeri-Microtox®, Heterocypris incongruens-Ostrocodtoxkit F™ and the XenoScreen YES/YAS™ test of oestrogenic/androgenic activity) can be a tool for estimating the combined toxic effects induced by xenobiotics released from objects intended for children. To reproduce the conditions to which objects are exposed during their use, liquids with a composition corresponding to that of human bodily fluids (artificial sweat and saliva) were used. This research focused on the main parameters influencing the intensification of the migration process (temperature, contact time and composition of the extraction mixture). The studies aimed to estimate the endocrine potential of the extracts showed that compounds released from the surface of studied objects exhibit antagonistic androgenic activity. While on the basis of the results of Microtox® test, one can state that the largest quantity of toxic compounds are released in the first 2 h of using the object. The FTIR spectra analyses confirmed that no degradation of polymeric material took place. On the basis of the results obtained, it was unanimously concluded that contact of the object with bodily fluids may result in the release of a large number of xenobiotics, which has disadvantageous effects on the metabolic processes of the indicator organisms.

  7. Assessing potential dietary toxicity of heavy metals in selected vegetables and food crops.

    Science.gov (United States)

    Islam, Ejaz ul; Yang, Xiao-e; He, Zhen-li; Mahmood, Qaisar

    2007-01-01

    Heavy metals, such as cadmium, copper, lead, chromium and mercury, are important environmental pollutants, particularly in areas with high anthropogenic pressure. Their presence in the atmosphere, soil and water, even in traces can cause serious problems to all organisms, and heavy metal bioaccumulation in the food chain especially can be highly dangerous to human health. Heavy metals enter the human body mainly through two routes namely: inhalation and ingestion, ingestion being the main route of exposure to these elements in human population. Heavy metals intake by human populations through food chain has been reported in many countries. Soil threshold for heavy metal toxicity is an important factor affecting soil environmental capacity of heavy metal and determines heavy metal cumulative loading limits. For soil-plant system, heavy metal toxicity threshold is the highest permissible content in the soil (total or bioavailable concentration) that does not pose any phytotoxic effects or heavy metals in the edible parts of the crops does not exceed food hygiene standards. Factors affecting the thresholds of dietary toxicity of heavy metal in soil-crop system include: soil type which includes soil pH, organic matter content, clay mineral and other soil chemical and biochemical properties; and crop species or cultivars regulated by genetic basis for heavy metal transport and accumulation in plants. In addition, the interactions of soil-plant root-microbes play important roles in regulating heavy metal movement from soil to the edible parts of crops. Agronomic practices such as fertilizer and water managements as well as crop rotation system can affect bioavailability and crop accumulation of heavy metals, thus influencing the thresholds for assessing dietary toxicity of heavy metals in the food chain. This paper reviews the phytotoxic effects and bioaccumulation of heavy metals in vegetables and food crops and assesses soil heavy metal thresholds for potential dietary

  8. Potential Sources for Lipid Soluble Food Colorants from Selected Malaysian Traditional Vegetables

    International Nuclear Information System (INIS)

    Rashidi Othman; Fatimah Azzahra Mohd Zaifuddin; Norazian Mohd Hassan

    2015-01-01

    Colour is one important characteristic to food products as it dictates consumers first perception on the foods flavour and quality. In the current food industry, most of the colorants used were derived from synthetic sources. However, due to negative health impacts of the synthetic colorants, the urgency to find natural colorants and impose it to food products is of great importance. In this study, a group of plant pigments which are potentially introduced as natural food colorants were quantified from 24 species of local traditional vegetables (ulam), characterized as neoxanthin, violaxanthin, lutein, zeaxanthin, β-cryptoxanthine, α-carotene and β-carotene by using HPLC. It was shown that Sauropus androgynous contained the highest amount of neoxanthin, violaxanthin and β-cryptoxanthine at 142.40±3.57, 28.06±0.65 and 0.07±0.00 mg/ g dry weight (DW), respectively. In contrast, highest content of lutein and α-carotene were observed in Centella asiatica at 16.53±0.97 and 2.14±0.12 mg/ g DW, accordingly. Meanwhile, Piper sarmentosum contained the highest zeaxanthin level (123.45±12.3 mg/ g DW) and Oenanthe javanica has the largest amount of β-carotene (3.09±0.06 mg/ g DW). The extracted yellow-to-red lipid soluble pigments can be further developed into commercial food colorant to replace the synthetic colorants in the market thus improving social awareness towards natural products as well as strengthening the national economy. (author)

  9. Development of live attenuated Streptococcus agalactiae as potential vaccines by selecting for resistance to sparfloxacin.

    Science.gov (United States)

    Pridgeon, Julia W; Klesius, Phillip H

    2013-05-31

    To develop attenuated bacteria as potential live vaccines, sparfloxacin was used in this study to modify 40 isolates of Streptococcus agalactiae. Majority of S. agalactiae used in this study were able to develop at least 80-fold resistance to sparfloxacin. When the virulence of the sparfloxacin-resistant S. agalactiae isolates were tested in 10-12g Nile tilapia by intraperitoneal injection at dose of 2×10(7)CFU/fish, 31 were found to be avirulent to fish. Of the 31 avirulent sparfloxacin-resistant S. agalactiae isolates, 30 provided 75-100% protection to 10-12g Nile tilapia against challenges with a virulent S. agalactiae isolate Sag 50. When the virulence of the 30 sparfloxacin-resistant S. agalactiae isolates was tested in 3-5g Nile tilapia by intraperitoneal injection at dose of 2×10(7)CFU/fish, six were found to be avirulent to 3-5g Nile tilapia. Of the six avirulent sparfloxacin-resistant S. agalactiae isolates, four provided 3-5g Nile tilapia 100% protection against challenges with homologous isolates, including Sag 97-spar isolate that was non-hemolytic. However, Sag 97-spar failed to provide broad cross-protection against challenges with heterologous isolates. When Nile tilapia was vaccinated with a polyvalent vaccine consisting of 30 sparfloxacin-resistant S. agalactiae isolates at dose of 2×10(6)CFU/fish, the polyvalent vaccine provided significant (PS. agalactiae. Taken together, our results suggest that a polyvalent vaccine consisting of various strains of S. agalactiae might be essential to provide broader protection to Nile tilapia against infections caused by S. agalactiae. Published by Elsevier Ltd.

  10. Identification of an allosteric binding site for RORγt inhibition

    Energy Technology Data Exchange (ETDEWEB)

    Scheepstra, Marcel; Leysen, Seppe; vanAlmen, Geert C.; Miller, J. Richard; Piesvaux, Jennifer; Kutilek, Victoria; van Eenennaam, Hans; Zhang, Hongjun; Barr, Kenneth; Nagpal, Sunil; Soisson, Stephen M.; Kornienko, Maria; Wiley, Kristen; Elsen, Nathaniel; Sharma, Sujata; Correll, Craig C.; Trotter, B. Wesley; van der Stelt, Mario; Oubrie, Arthur; Ottmann, Christian; Parthasarathy, Gopal; Brunsveld, Luc (Merck); (Eindhoven)

    2015-12-07

    RORγt is critical for the differentiation and proliferation of Th17 cells associated with several chronic autoimmune diseases. We report the discovery of a novel allosteric binding site on the nuclear receptor RORγt. Co-crystallization of the ligand binding domain (LBD) of RORγt with a series of small-molecule antagonists demonstrates occupancy of a previously unreported allosteric binding pocket. Binding at this non-canonical site induces an unprecedented conformational reorientation of helix 12 in the RORγt LBD, which blocks cofactor binding. The functional consequence of this allosteric ligand-mediated conformation is inhibition of function as evidenced by both biochemical and cellular studies. RORγt function is thus antagonized in a manner molecularly distinct from that of previously described orthosteric RORγt ligands. This brings forward an approach to target RORγt for the treatment of Th17-mediated autoimmune diseases. The elucidation of an unprecedented modality of pharmacological antagonism establishes a mechanism for modulation of nuclear receptors.

  11. Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction.

    Science.gov (United States)

    Razo-Mejia, Manuel; Barnes, Stephanie L; Belliveau, Nathan M; Chure, Griffin; Einav, Tal; Lewis, Mitchell; Phillips, Rob

    2018-04-25

    Allosteric regulation is found across all domains of life, yet we still lack simple, predictive theories that directly link the experimentally tunable parameters of a system to its input-output response. To that end, we present a general theory of allosteric transcriptional regulation using the Monod-Wyman-Changeux model. We rigorously test this model using the ubiquitous simple repression motif in bacteria by first predicting the behavior of strains that span a large range of repressor copy numbers and DNA binding strengths and then constructing and measuring their response. Our model not only accurately captures the induction profiles of these strains, but also enables us to derive analytic expressions for key properties such as the dynamic range and [EC 50 ]. Finally, we derive an expression for the free energy of allosteric repressors that enables us to collapse our experimental data onto a single master curve that captures the diverse phenomenology of the induction profiles. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  12. Activation of Hsp90 Enzymatic Activity and Conformational Dynamics through Rationally Designed Allosteric Ligands.

    Science.gov (United States)

    Sattin, Sara; Tao, Jiahui; Vettoretti, Gerolamo; Moroni, Elisabetta; Pennati, Marzia; Lopergolo, Alessia; Morelli, Laura; Bugatti, Antonella; Zuehlke, Abbey; Moses, Mike; Prince, Thomas; Kijima, Toshiki; Beebe, Kristin; Rusnati, Marco; Neckers, Len; Zaffaroni, Nadia; Agard, David A; Bernardi, Anna; Colombo, Giorgio

    2015-09-21

    Hsp90 is a molecular chaperone of pivotal importance for multiple cell pathways. ATP-regulated internal dynamics are critical for its function and current pharmacological approaches block the chaperone with ATP-competitive inhibitors. Herein, a general approach to perturb Hsp90 through design of new allosteric ligands aimed at modulating its functional dynamics is proposed. Based on the characterization of a first set of 2-phenylbenzofurans showing stimulatory effects on Hsp90 ATPase and conformational dynamics, new ligands were developed that activate Hsp90 by targeting an allosteric site, located 65 Å from the active site. Specifically, analysis of protein responses to first-generation activators was exploited to guide the design of novel derivatives with improved ability to stimulate ATP hydrolysis. The molecules' effects on Hsp90 enzymatic, conformational, co-chaperone and client-binding properties were characterized through biochemical, biophysical and cellular approaches. These designed probes act as allosteric activators of the chaperone and affect the viability of cancer cell lines for which proper functioning of Hsp90 is necessary. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A

    Energy Technology Data Exchange (ETDEWEB)

    Quinlan, Casey L.; Kaiser, Stephen E.; Bolaños, Ben; Nowlin, Dawn; Grantner, Rita; Karlicek-Bryant, Shannon; Feng, Jun Li; Jenkinson, Stephen; Freeman-Cook, Kevin; Dann, Stephen G.; Wang, Xiaoli; Wells, Peter A.; Fantin, Valeria R.; Stewart, Al E.; Grant, Stephan K. (Pfizer)

    2017-05-29

    S-Adenosyl-L-methionine (SAM) is an enzyme cofactor used in methyl transfer reactions and polyamine biosynthesis. The biosynthesis of SAM from ATP and L-methionine is performed by the methionine adenosyltransferase enzyme family (Mat; EC 2.5.1.6). Human methionine adenosyltransferase 2A (Mat2A), the extrahepatic isoform, is often deregulated in cancer. We identified a Mat2A inhibitor, PF-9366, that binds an allosteric site on Mat2A that overlaps with the binding site for the Mat2A regulator, Mat2B. Studies exploiting PF-9366 suggested a general mode of Mat2A allosteric regulation. Allosteric binding of PF-9366 or Mat2B altered the Mat2A active site, resulting in increased substrate affinity and decreased enzyme turnover. These data support a model whereby Mat2B functions as an inhibitor of Mat2A activity when methionine or SAM levels are high, yet functions as an activator of Mat2A when methionine or SAM levels are low. The ramification of Mat2A activity modulation in cancer cells is also described.

  14. Potential Selection Effects when Estimating Associations Between the Infancy Peak or Adiposity Rebound and Later Body Mass Index in Children

    DEFF Research Database (Denmark)

    Börnhorst, Claudia; Siani, Alfonso; Tornaritis, Michalis

    2017-01-01

    Introduction:This study aims to evaluate a potential selection effect caused by exclusion of children with non-identifiable infancy peak (IP) and adiposity rebound (AR) when estimating associations between age and BMI at IP and AR and later weight status. Subjects and methods: In 4 744 children.......98). In the total study group, BMI values in infancy and childhood were positively associated with later BMI z-scores where associations increased with age. Associations between BMI velocities and later BMI z-scores were largest at ages 5 and 6. Results differed for children with non-identifiable IP and AR...

  15. Toxicity, sublethal effects, and potential modes of action of select fungicides on freshwater fish and invertebrates

    Science.gov (United States)

    Elskus, Adria A.

    2012-01-01

    Despite decades of agricultural and urban use of fungicides and widespread detection of these pesticides in surface waters, relatively few data are available on the effects of fungicides on fish and invertebrates in the aquatic environment. Nine fungicides are reviewed in this report: azoxystrobin, boscalid, chlorothalonil, fludioxonil, myclobutanil, fenarimol, pyraclostrobin, pyrimethanil, and zoxamide. These fungicides were identified as emerging chemicals of concern because of their high or increasing global use rates, detection frequency in surface waters, or likely persistence in the environment. A review of the literature revealed significant sublethal effects of fungicides on fish, aquatic invertebrates, and ecosystems, including zooplankton and fish reproduction, fish immune function, zooplankton community composition, metabolic enzymes, and ecosystem processes, such as leaf decomposition in streams, among other biological effects. Some of these effects can occur at fungicide concentrations well below single-species acute lethality values (48- or 96-hour concentration that effects a response in 50 percent of the organisms, that is, effective concentration killing 50 percent of the organisms in 48 or 96 hours) and chronic sublethal values (for example, 21-day no observed adverse effects concentration), indicating that single-species toxicity values may dramatically underestimate the toxic potency of some fungicides. Fungicide modes of toxic action in fungi can sometimes reflect the biochemical and (or) physiological effects of fungicides observed in vertebrates and invertebrates; however, far more studies are needed to explore the potential to predict effects in nontarget organisms based on specific fungicide modes of toxic action. Fungicides can also have additive and (or) synergistic effects when used with other fungicides and insecticides, highlighting the need to study pesticide mixtures that occur in surface waters. For fungicides that partition to

  16. Mathematical model of the binding of allosteric effectors to the Escherichia coli PII signal transduction protein GlnB.

    Science.gov (United States)

    da Rocha, Ricardo Alves; Weschenfelder, Thiago André; de Castilhos, Fernanda; de Souza, Emanuel Maltempi; Huergo, Luciano Fernandes; Mitchell, David Alexander

    2013-04-16

    PII proteins are important regulators of nitrogen metabolism in a wide variety of organisms: the binding of the allosteric effectors ATP, ADP, and 2-oxoglutarate (2-OG) to PII proteins affects their ability to interact with target proteins. We modeled the simultaneous binding of ATP, ADP, and 2-OG to one PII protein, namely GlnB of Escherichia coli, using a modeling approach that allows the prediction of the proportions of individual binding states. Four models with different binding rules were compared. We selected one of these models (that assumes that the binding of the first nucleotide to GlnB makes it harder for subsequent nucleotides to bind) and used it to explore how physiological concentrations of ATP, ADP, and 2-OG would affect the proportions of those states of GlnB that interact with the target proteins ATase and NtrB. Our simulations indicate that GlnB can, as suggested by previous researchers, act as a sensor of both 2-OG and the ATP:ADP ratio. We conclude that our modeling approach will be an important tool in future studies concerning the PII binding states and their interactions with target proteins.

  17. Bacteria Associated to Plants Naturally Selected in a Historical PCB Polluted Soil Show Potential to Sustain Natural Attenuation.

    Science.gov (United States)

    Vergani, Lorenzo; Mapelli, Francesca; Marasco, Ramona; Crotti, Elena; Fusi, Marco; Di Guardo, Antonio; Armiraglio, Stefano; Daffonchio, Daniele; Borin, Sara

    2017-01-01

    The exploitation of the association between plants and microorganisms is a promising approach able to boost natural attenuation processes for soil clean-up in vast polluted areas characterized by mixed chemical contamination. We aimed to explore the selection of root-associated bacterial communities driven by different plant species spontaneously established in abandoned agricultural soils within a historical polluted site in north Italy. The site is highly contaminated by chlorinated persistent organic pollutants, mainly constituted by polychlorobiphenyls (PCBs), together with heavy metals and metalloids, in variable concentrations and uneven distribution. The overall structure of the non-vegetated and root-associated soil fractions bacterial communities was described by high-throughput sequencing of the 16S rRNA gene, and a collection of 165 rhizobacterial isolates able to use biphenyl as unique carbon source was assayed for plant growth promotion (PGP) traits and bioremediation potential. The results showed that the recruitment of specific bacterial communities in the root-associated soil fractions was driven by both soil fractions and plant species, explaining 21 and 18% of the total bacterial microbiome variation, respectively. PCR-based detection in the soil metagenome of bacterial bphA gene, encoding for the biphenyl dioxygenase α subunit, indicated that the soil in the site possesses metabolic traits linked to PCB degradation. Biphenyl-utilizing bacteria isolated from the rhizosphere of the three different plant species showed low phylogenetic diversity and well represented functional traits, in terms of PGP and bioremediation potential. On average, 72% of the strains harbored the bphA gene and/or displayed catechol 2,3-dioxygenase activity, involved in aromatic ring cleavage. PGP traits, including 1-aminocyclopropane-1-carboxylic acid deaminase activity potentially associated to plant stress tolerance induction, were widely distributed among the isolates

  18. Bacteria Associated to Plants Naturally Selected in a Historical PCB Polluted Soil Show Potential to Sustain Natural Attenuation

    KAUST Repository

    Vergani, Lorenzo

    2017-07-25

    The exploitation of the association between plants and microorganisms is a promising approach able to boost natural attenuation processes for soil clean-up in vast polluted areas characterized by mixed chemical contamination. We aimed to explore the selection of root-associated bacterial communities driven by different plant species spontaneously established in abandoned agricultural soils within a historical polluted site in north Italy. The site is highly contaminated by chlorinated persistent organic pollutants, mainly constituted by polychlorobiphenyls (PCBs), together with heavy metals and metalloids, in variable concentrations and uneven distribution. The overall structure of the non-vegetated and root-associated soil fractions bacterial communities was described by high-throughput sequencing of the 16S rRNA gene, and a collection of 165 rhizobacterial isolates able to use biphenyl as unique carbon source was assayed for plant growth promotion (PGP) traits and bioremediation potential. The results showed that the recruitment of specific bacterial communities in the root-associated soil fractions was driven by both soil fractions and plant species, explaining 21 and 18% of the total bacterial microbiome variation, respectively. PCR-based detection in the soil metagenome of bacterial bphA gene, encoding for the biphenyl dioxygenase α subunit, indicated that the soil in the site possesses metabolic traits linked to PCB degradation. Biphenyl-utilizing bacteria isolated from the rhizosphere of the three different plant species showed low phylogenetic diversity and well represented functional traits, in terms of PGP and bioremediation potential. On average, 72% of the strains harbored the bphA gene and/or displayed catechol 2,3-dioxygenase activity, involved in aromatic ring cleavage. PGP traits, including 1-aminocyclopropane-1-carboxylic acid deaminase activity potentially associated to plant stress tolerance induction, were widely distributed among the isolates

  19. Bacteria Associated to Plants Naturally Selected in a Historical PCB Polluted Soil Show Potential to Sustain Natural Attenuation

    Directory of Open Access Journals (Sweden)

    Lorenzo Vergani

    2017-07-01

    Full Text Available The exploitation of the association between plants and microorganisms is a promising approach able to boost natural attenuation processes for soil clean-up in vast polluted areas characterized by mixed chemical contamination. We aimed to explore the selection of root-associated bacterial communities driven by different plant species spontaneously established in abandoned agricultural soils within a historical polluted site in north Italy. The site is highly contaminated by chlorinated persistent organic pollutants, mainly constituted by polychlorobiphenyls (PCBs, together with heavy metals and metalloids, in variable concentrations and uneven distribution. The overall structure of the non-vegetated and root-associated soil fractions bacterial communities was described by high-throughput sequencing of the 16S rRNA gene, and a collection of 165 rhizobacterial isolates able to use biphenyl as unique carbon source was assayed for plant growth promotion (PGP traits and bioremediation potential. The results showed that the recruitment of specific bacterial communities in the root-associated soil fractions was driven by both soil fractions and plant species, explaining 21 and 18% of the total bacterial microbiome variation, respectively. PCR-based detection in the soil metagenome of bacterial bphA gene, encoding for the biphenyl dioxygenase α subunit, indicated that the soil in the site possesses metabolic traits linked to PCB degradation. Biphenyl-utilizing bacteria isolated from the rhizosphere of the three different plant species showed low phylogenetic diversity and well represented functional traits, in terms of PGP and bioremediation potential. On average, 72% of the strains harbored the bphA gene and/or displayed catechol 2,3-dioxygenase activity, involved in aromatic ring cleavage. PGP traits, including 1-aminocyclopropane-1-carboxylic acid deaminase activity potentially associated to plant stress tolerance induction, were widely distributed

  20. Characterization of silver nanoparticles in selected consumer products and its relevance for predicting children’s potential exposures

    Science.gov (United States)

    Tulve, Nicolle S.; Stefaniak, Aleksandr B.; Vance, Marina E.; Rogers, Kim; Mwilu, Samuel; LeBouf, Ryan F.; Schwegler-Berry, Diane; Willis, Robert; Thomas, Treye A.; Marr, Linsey C.

    2015-01-01

    Due to their antifungal, antibacterial, antiviral, and antimicrobial properties, silver nanoparticles (AgNPs) are used in consumer products intended for use by children or in the home. Children may be especially affected by the normal use of consumer products because of their physiological functions, developmental stage, and activities and behaviors. Despite much research to date, children’s potential exposures to AgNPs are not well characterized. Our objectives were to characterize selected consumer products containing AgNPs and to use the data to estimate a child’s potential non-dietary ingestion exposure. We identified and cataloged 165 consumer products claiming to contain AgNPs that may be used by or near children or found in the home. Nineteen products (textile, liquid, plastic) were selected for further analysis. We developed a tiered analytical approach to determine silver content, form (particulate or ionic), size, morphology, agglomeration state, and composition. Silver was detected in all products except one sippy cup body. Among products in a given category, silver mass contributions were highly variable and not always uniformly distributed within products, highlighting the need to sample multiple areas of a product. Electron microscopy confirmed the presence of AgNPs. Using this data, a child’s potential non-dietary ingestion exposure to AgNPs when drinking milk formula from a sippy cup is 1.53 μg Ag/kg. Additional research is needed to understand the number and types of consumer products containing silver and the concentrations of silver in these products in order to more accurately predict children’s potential aggregate and cumulative exposures to AgNPs. PMID:25747543

  1. A method for selecting potential geosites. The case of glacial geosites in the Chablais area (French and Swiss Prealps)

    Science.gov (United States)

    Perret, Amandine; Reynard, Emmanuel

    2014-05-01

    Since 2009, an Interreg IVA project (123 Chablais), dealing with the promotion of natural and cultural heritage in the Chablais area, has been developed. It is linked to the creation of the Chablais Geopark. In a context of development of smart forms of tourism, the objective was to develop a strategy promoting the glacial heritage to a wide public in an area where the glaciers have almost disappeared. The recognition of specific places as geoheritage is the result of a double process: a scientific one, based on more or less sophisticated methods, and a social one, that is the acknowledgment by the society. One of the first scientific tasks is to produce a list of "potential geosites" that will be assessed in more details. However, this selection is often a weak point of inventories. It often seems like a "black box" without any transparency. In this project (123 Chablais) we carried out an inventory of glacial geosites, using the method developed by Reynard et al. (2007, 2012). However, a method has been created to enlighten the selection process, and to enhance choices in geoheritage management. As it was not possible to consider all sites in the Chablais area, a mixed selection approach was developed, halfway between completeness and specificity (Martin, 2012). The first step was the creation of a list of "points of interest", established using different sources: literature review, fieldwork and use of GIS to cross information. A selection was then performed according to two criteria: correspondence with a glacial stage (time axis) and belonging to a type of forms (spatial axis). Finally, selected sites aimed at providing a representative overview of the regional glacial witnesses. Therefore, representative sites of the regional geology were selected as well as sites presenting regional peculiarities Temporal and spatial attributes were given to the 101 points of interest identified. From a temporal point of view, this inventory aimed at presenting the main

  2. VU0477573: Partial Negative Allosteric Modulator of the Subtype 5 Metabotropic Glutamate Receptor with In Vivo Efficacy.

    Science.gov (United States)

    Nickols, Hilary Highfield; Yuh, Joannes P; Gregory, Karen J; Morrison, Ryan D; Bates, Brittney S; Stauffer, Shaun R; Emmitte, Kyle A; Bubser, Michael; Peng, Weimin; Nedelcovych, Michael T; Thompson, Analisa; Lv, Xiaohui; Xiang, Zixiu; Daniels, J Scott; Niswender, Colleen M; Lindsley, Craig W; Jones, Carrie K; Conn, P Jeffrey

    2016-01-01

    Negative allosteric modulators (NAMs) of metabotropic glutamate receptor subtype 5 (mGlu5) have potential applications in the treatment of fragile X syndrome, levodopa-induced dyskinesia in Parkinson disease, Alzheimer disease, addiction, and anxiety; however, clinical and preclinical studies raise concerns that complete blockade of mGlu5 and inverse agonist activity of current mGlu5 NAMs contribute to adverse effects that limit the therapeutic use of these compounds. We report the discovery and characterization of a novel mGlu5 NAM, N,N-diethyl-5-((3-fluorophenyl)ethynyl)picolinamide (VU0477573) that binds to the same allosteric site as the prototypical mGlu5 NAM MPEP but displays weak negative cooperativity. Because of this weak cooperativity, VU0477573 acts as a "partial NAM" so that full occupancy of the MPEP site does not completely inhibit maximal effects of mGlu5 agonists on intracellular calcium mobilization, inositol phosphate (IP) accumulation, or inhibition of synaptic transmission at the hippocampal Schaffer collateral-CA1 synapse. Unlike previous mGlu5 NAMs, VU0477573 displays no inverse agonist activity assessed using measures of effects on basal [(3)H]inositol phosphate (IP) accumulation. VU0477573 acts as a full NAM when measuring effects on mGlu5-mediated extracellular signal-related kinases 1/2 phosphorylation, which may indicate functional bias. VU0477573 exhibits an excellent pharmacokinetic profile and good brain penetration in rodents and provides dose-dependent full mGlu5 occupancy in the central nervous system (CNS) with systemic administration. Interestingly, VU0477573 shows robust efficacy, comparable to the mGlu5 NAM MTEP, in models of anxiolytic activity at doses that provide full CNS occupancy of mGlu5 and demonstrate an excellent CNS occupancy-efficacy relationship. VU0477573 provides an exciting new tool to investigate the efficacy of partial NAMs in animal models. Copyright © 2015 by The American Society for Pharmacology and

  3. An allosteric gating model recapitulates the biophysical properties of IK,L expressed in mouse vestibular type I hair cells.

    Science.gov (United States)

    Spaiardi, Paolo; Tavazzani, Elisa; Manca, Marco; Milesi, Veronica; Russo, Giancarlo; Prigioni, Ivo; Marcotti, Walter; Magistretti, Jacopo; Masetto, Sergio

    2017-11-01

    Vestibular type I and type II hair cells and their afferent fibres send information to the brain regarding the position and movement of the head. The characteristic feature of type I hair cells is the expression of a low-voltage-activated outward rectifying K + current, I K,L , whose biophysical properties and molecular identity are still largely unknown. In vitro, the afferent nerve calyx surrounding type I hair cells causes unstable intercellular K + concentrations, altering the biophysical properties of I K,L . We found that in the absence of the calyx, I K,L in type I hair cells exhibited unique biophysical activation properties, which were faithfully reproduced by an allosteric channel gating scheme. These results form the basis for a molecular and pharmacological identification of I K,L . Type I and type II hair cells are the sensory receptors of the mammalian vestibular epithelia. Type I hair cells are characterized by their basolateral membrane being enveloped in a single large afferent nerve terminal, named the calyx, and by the expression of a low-voltage-activated outward rectifying K + current, I K,L . The biophysical properties and molecular profile of I K,L are still largely unknown. By using the patch-clamp whole-cell technique, we examined the voltage- and time-dependent properties of I K,L in type I hair cells of the mouse semicircular canal. We found that the biophysical properties of I K,L were affected by an unstable K + equilibrium potential (V eq K + ). Both the outward and inward K + currents shifted V eq K + consistent with K + accumulation or depletion, respectively, in the extracellular space, which we attributed to a residual calyx attached to the basolateral membrane of the hair cells. We therefore optimized the hair cell dissociation protocol in order to isolate mature type I hair cells without their calyx. In these cells, the uncontaminated I K,L showed a half-activation at -79.6 mV and a steep voltage dependence (2.8 mV). I K,L also

  4. Differential modulation of thresholds for intracranial self-stimulation by mGlu5 positive and negative allosteric modulators: implications for effects on drug self-administration

    Directory of Open Access Journals (Sweden)

    M. Foster eOlive

    2012-01-01

    Full Text Available Pharmacological manipulation of the type 5 metabotropic glutamate (mGlu5 receptor alters various addiction related behaviors such as drug self-administration and the extinction and reinstatement of drug-seeking behavior. However, the effects of pharmacological modulation of mGlu5 receptors on brain reward function have not been widely investigated. We examined the effects of acute administration of positive and negative allosteric modulators (PAMs and NAMs, respectively on brain reward function by assessing thresholds for intracranial self-stimulation (ICSS. In addition, when acute effects were observed, we examined potential changes in altered ICSS thresholds following repeated administration. Male Sprague-Dawley rats were implanted with bipolar electrodes into the medial forebrain bundle and trained to respond for ICSS, followed by assessment of effects of mGlu5 ligands on ICSS thresholds using a discrete trials current intensity threshold determination procedure. Acute administration of the selective mGlu5 NAMs MTEP (0, 0.3, 1 or 3 mg/kg and fenobam (0, 3, 10, or 30 mg/kg dose-dependently increased ICSS thresholds (~70% at the highest dose tested, suggesting a deficit in brain reward function. Acute administration of the mGlu5 PAMs CDPPB (0, 10, 30 and 60 mg/kg or ADX47273 (0, 10, 30 and 60 mg/kg was without effect at any dose tested. When administered once daily for 5 consecutive days, the development of tolerance to the ability of threshold-elevating doses of MTEP and fenobam to increase ICSS thresholds was observed. We conclude that mGlu5 PAMs and NAMs differentially affect brain reward function, and that tolerance to the ability of mGlu5 NAMs to reduce brain reward function develops with repeated administration. These brain reward deficits should be taken into consideration when interpreting acute effects of mGlu5 NAMs on drug self-administration, and repeated administration may be an effective method to reduce these deficits.

  5. Marker-assisted selection as a potential tool for genetic improvement in developing countries: debating the issues

    International Nuclear Information System (INIS)

    Robinson, J.; Ruane, J.

    2007-01-01

    Marker-assisted selection (MAS) is a complementary technology, for use in conjunction with more established conventional methods of genetic selection, for plant and animal improvement. It has generated a good deal of expectations, many of which have yet to be realized. Although documentation is limited, the current impact of MAS on products delivered to farmers seems small. While the future possibilities and potential impacts of MAS are considerable, there are also obstacles to its use, particularly in developing countries. Principal among these are issues relating to current high costs of the technology and its appropriateness, given that publicly funded agricultural research in many developing countries is suboptimal and development priorities do not necessarily include genetic improvement programmes. Other potential obstacles to the uptake of MAS in developing countries include limited infrastructure, the absence of conventional selection and breeding programmes, poor private sector involvement and lack of research on specific crops of importance in developing countries. Intellectual property rights may also be an important constraint to development and uptake of MAS in the developing world. It is hoped that through partnerships between developing and developed country institutions and individuals, including public-private sector collaboration, MAS costs can be reduced, resources pooled and shared and capacity developed. With the assistance of the Consultative Group on International Agricultural Research (CGIAR) and international organizations such as FAO, developing countries can benefit more from MAS. These were some of the outcomes of a moderated e-mail conference, entitled 'Molecular Marker- Assisted Selection as a Potential Tool for Genetic Improvement of Crops, Forest Trees, Livestock and Fish in Developing Countries', that FAO hosted at the end of 2003. During the four-week conference, 627 people subscribed and 85 messages were posted, about 60 percent

  6. Potential Response to Selection of HSP70 as a Component of Innate Immunity in the Abalone Haliotis rufescens

    Science.gov (United States)

    Brokordt, Katherina B.; González, Roxana C.; Farías, William J.; Winkler, Federico M.

    2015-01-01

    Assessing components of the immune system may reflect disease resistance. In some invertebrates, heat shock proteins (HSPs) are immune effectors and have been described as potent activators of the innate immune response. Several diseases have become a threat to abalone farming worldwide; therefore, increasing disease resistance is considered to be a long-term goal for breeding programs. A trait will respond to selection only if it is determined partially by additive genetic variation. The aim of this study was to estimate the heritability (h 2) and the additive genetic coefficient of variation (CV A) of HSP70 as a component of innate immunity of the abalone Haliotis rufescens, in order to assess its potential response to selection. These genetic components were estimated for the variations in the intracellular (in haemocytes) and extracellular (serum) protein levels of HSP70 in response to an immunostimulant agent in 60 full-sib families of H. rufescens. Levels of HSP70 were measured twice in the same individuals, first when they were young and again when they were pre-harvest adults, to estimate the repeatability (R), the h 2 and the potential response to selection of these traits at these life stages. High HSP70 levels were observed in abalones subjected to immunostimulation in both the intracellular and extracellular haemolymph fractions. This is the first time that changes in serum levels of HSP70 have been reported in response to an immune challenge in molluscs. HSP70 levels in both fractions and at both ages showed low h 2 and R, with values that were not significantly different from zero. However, HSP70 induced levels had a CV A of 13.3–16.2% in young adults and of 2.7–8.1% in pre-harvest adults. Thus, despite its low h 2, HSP70 synthesis in response to an immune challenge in red abalone has the potential to evolve through selection because of its large phenotypic variation and the presence of additive genetic variance, especially in young animals. PMID

  7. Potential Response to Selection of HSP70 as a Component of Innate Immunity in the Abalone Haliotis rufescens.

    Directory of Open Access Journals (Sweden)

    Katherina B Brokordt

    Full Text Available Assessing components of the immune system may reflect disease resistance. In some invertebrates, heat shock proteins (HSPs are immune effectors and have been described as potent activators of the innate immune response. Several diseases have become a threat to abalone farming worldwide; therefore, increasing disease resistance is considered to be a long-term goal for breeding programs. A trait will respond to selection only if it is determined partially by additive genetic variation. The aim of this study was to estimate the heritability (h2 and the additive genetic coefficient of variation (CVA of HSP70 as a component of innate immunity of the abalone Haliotis rufescens, in order to assess its potential response to selection. These genetic components were estimated for the variations in the intracellular (in haemocytes and extracellular (serum protein levels of HSP70 in response to an immunostimulant agent in 60 full-sib families of H. rufescens. Levels of HSP70 were measured twice in the same individuals, first when they were young and again when they were pre-harvest adults, to estimate the repeatability (R, the h2 and the potential response to selection of these traits at these life stages. High HSP70 levels were observed in abalones subjected to immunostimulation in both the intracellular and extracellular haemolymph fractions. This is the first time that changes in serum levels of HSP70 have been reported in response to an immune challenge in molluscs. HSP70 levels in both fractions and at both ages showed low h2 and R, with values that were not significantly different from zero. However, HSP70 induced levels had a CVA of 13.3-16.2% in young adults and of 2.7-8.1% in pre-harvest adults. Thus, despite its low h2, HSP70 synthesis in response to an immune challenge in red abalone has the potential to evolve through selection because of its large phenotypic variation and the presence of additive genetic variance, especially in young animals.

  8. Evaluation of Phenolic Content Variability along with Antioxidant, Antimicrobial, and Cytotoxic Potential of Selected Traditional Medicinal Plants from India.

    Science.gov (United States)

    Singh, Garima; Passsari, Ajit K; Leo, Vincent V; Mishra, Vineet K; Subbarayan, Sarathbabu; Singh, Bhim P; Kumar, Brijesh; Kumar, Sunil; Gupta, Vijai K; Lalhlenmawia, Hauzel; Nachimuthu, Senthil K

    2016-01-01

    Plants have been used since ancient times as an important source of biologically active substances. The aim of the present study was to investigate the phytochemical constituents (flavonoids and phenolics), antioxidant potential, cytotoxicity against HepG2 (human hepato carcinoma) cancer cell lines, and the antimicrobial activity of the methanol extract of selected traditional medicinal plants collected from Mizoram, India. A number of phenolic compounds were detected using HPLC-DAD-ESI-TOF-MS, mainly Luteolin, Kaempferol, Myricetin, Gallic Acid, Quercetin and Rutin, some of which have been described for the first time in the selected plants. The total phenolic and flavonoid contents showed high variation ranging from 4.44 to 181.91 μg of Gallic Acid equivalent per milligram DW (GAE/mg DW) and 3.17 to 102.2 μg of Quercetin/mg, respectively. The antioxidant capacity was determined by DPPH (IC50 values ranges from 34.22 to 131.4 μg/mL), ABTS (IC50 values ranges from 24.08 to 513.4 μg/mL), and reducing power assays. Antimicrobial activity was assayed against gram positive (Staphylococcus aureus), gram negative (Escherichia coli, Pseudomonas aeruginosa), and yeast (Candida albicans) demonstrating that the methanol extracts of some plants were efficacious antimicrobial agents. Additionally, cytotoxicity was assessed on human hepato carcinoma (HepG2) cancer cell lines and found that the extracts of Albizia lebbeck, Dillenia indica, and Bombax ceiba significantly decreased the cell viability at low concentrations with IC50 values of 24.03, 25.09, and 29.66 μg/mL, respectively. This is the first report of detection of phenolic compounds along with antimicrobial, antioxidant and cytotoxic potential of selected medicinal plants from India, which indicates that these plants might be valuable source for human and animal health.

  9. Evaluation of phenolic content variability, antioxidant, antimicrobial and cytotoxic potential of selected traditional medicinal plants from India

    Directory of Open Access Journals (Sweden)

    Garima eSingh

    2016-03-01

    Full Text Available Plants have been used since ancient times as an important source of biologically active substances. The aim of the present study was to investigate the phytochemical constituents (flavonoids and phenolics, antioxidant potential, cytotoxicity against HepG2 (human hepato carcinoma cancer cell lines and the antimicrobial activity of the methanol extract of selected traditional medicinal plants collected from Mizoram, India. A number of phenolic compounds were detected using HPLC-DAD-ESI-TOF-MS, mainly Luteolin, Kaempferol, Myricetin, Gallic Acid, Quercetin and Rutin, some of which have been described for the first time in the selected plants. The total phenolic and flavonoid contents showed high variation ranging from 4.44 to 181.91 µg of Gallic Acid equivalent per milligram DW (GAE/mg DW and 3.17 to 102.2 µg of Quercetin/mg, respectively. The antioxidant capacity was determined by DPPH (IC50 values ranges from 34.22 to 131.4 µg/mL, ABTS (IC50 values ranges from 24.08 to 513.4 µg/mL and reducing power assays. Antimicrobial activity was assayed against gram positive (Staphylococcus aureus, gram negative (Escherichia coli, Pseudomonas aeruginosa and yeast (Candida albicans demonstrating that the methanol extracts of some plants were efficacious antimicrobial agents. Additionally, cytotoxicity was assessed on human hepato carcinoma (HepG2 cancer cell lines and found that the extracts of Albizia lebbeck, Dillenia indica and Bombax ceiba significantly decreased the cell viability at low concentrations with IC50 values of 24.03, 25.09 and 29.66 µg/mL, respectively. This is the first report of detection of phenolic compounds along with antimicrobial, antioxidant and cytotoxic potential of selected medicinal plants from India, which indicates that these plants might be valuable source for human and animal health.

  10. Potentiating mGluR5 Function with a Positive Allosteric Modulator Enhances Adaptive Learning

    Science.gov (United States)

    Xu, Jian; Zhu, Yongling; Kraniotis, Stephen; He, Qionger; Marshall, John J.; Nomura, Toshihiro; Stauffer, Shaun R.; Lindsley, Craig W.; Conn, P. Jeffrey; Contractor, Anis

    2013-01-01

    Metabotropic glutamate receptor 5 (mGluR5) plays important roles in modulating neural activity and plasticity and has been associated with several neuropathological disorders. Previous work has shown that genetic ablation or pharmacological inhibition of mGluR5 disrupts fear extinction and spatial reversal learning, suggesting that mGluR5…

  11. The cognition-enhancing activity of E1R, a novel positive allosteric modulator of sigma-1 receptors

    Science.gov (United States)

    Zvejniece, L; Vavers, E; Svalbe, B; Vilskersts, R; Domracheva, I; Vorona, M; Veinberg, G; Misane, I; Stonans, I; Kalvinsh, I; Dambrova, M

    2014-01-01

    Background and Purpose Here, we describe the in vitro and in vivo effects of (4R,5S)-2-(5-methyl-2-oxo-4-phenyl-pyrrolidin-1-yl)-acetamide (E1R), a novel positive allosteric modulator of sigma-1 receptors. Experimental Approach E1R was tested for sigma receptor binding activity in a [3H](+)-pentazocine assay, in bradykinin (BK)-induced intracellular Ca2+ concentration ([Ca2+]i) assays and in an electrically stimulated rat vas deferens model. E1R's effects on cognitive function were tested using passive avoidance (PA) and Y-maze tests in mice. A selective sigma-1 receptor antagonist (NE-100), was used to study the involvement of the sigma-1 receptor in the effects of E1R. The open-field test was used to detect the effects of E1R on locomotion. Key Results Pretreatment with E1R enhanced the selective sigma-1 receptor agonist PRE-084's stimulating effect during a model study employing electrically stimulated rat vasa deferentia and an assay measuring the BK-induced [Ca2+]i increase. Pretreatment with E1R facilitated PA retention in a dose-related manner. Furthermore, E1R alleviated the scopolamine-induced cognitive impairment during the PA and Y-maze tests in mice. The in vivo and in vitro effects of E1R were blocked by treatment with the selective sigma-1 receptor antagonist NE-100. E1R did not affect locomotor activity. Conclusion and Implications E1R is a novel 4,5-disubstituted derivative of piracetam that enhances cognition and demonstrates efficacy against scopolamine-induced cholinergic dysfunction in mice. These effects are attributed to its positive modulatory action on the sigma-1 receptor and this activity may be relevant when developing new drugs for treating cognitive symptoms related to neurodegenerative diseases. PMID:24490863

  12. Sediment sources in a small agricultural catchment: A composite fingerprinting approach based on the selection of potential sources

    Science.gov (United States)

    Zhou, Huiping; Chang, Weina; Zhang, Longjiang

    2016-08-01

    Fingerprinting techniques have been widely used as a reasonable and reliable means for investigating sediment sources, especially in relatively large catchments in which there are significant differences in surface materials. However, the discrimination power of fingerprint properties for small catchments, in which the surface materials are relatively homogeneous and human interference is marked, may be affected by fragmentary or confused source information. Using fingerprinting techniques can be difficult, and there is still a need for further studies to verify the effectiveness of such techniques in these small catchments. A composite fingerprinting approach was used in this study to investigate the main sources of sediment output, as well as their relative contributions, from a small catchment (30 km2) with high levels of farming and mining activities. The impact of the selection of different potential sediment sources on the derivation of composite fingerprints and its discrimination power were also investigated by comparing the results from different combinations of potential source types. The initial source types and several samples that could cause confusion were adjusted. These adjustments improved the discrimination power of the composite fingerprints. The results showed that the composite fingerprinting approach used in this study had a discriminatory efficiency of 89.2% for different sediment sources and that the model had a mean goodness of fit of 0.90. Cultivated lands were the main sediment source. The sediment contribution of the studied cultivated lands ranged from 39.9% to 87.8%, with a mean of 76.6%, for multiple deposited sediment samples. The mean contribution of woodlands was 21.7%. Overall, the sediment contribution from mining and road areas was relatively low. The selection of potential sources is an important factor in the application of fingerprinting techniques and warrants more attention in future studies, as is the case with other

  13. Molecular sampling of the allosteric binding pocket of the TSH receptor provides discriminative pharmacophores for antagonist and agonists.

    Science.gov (United States)

    Hoyer, Inna; Haas, Ann-Karin; Kreuchwig, Annika; Schülein, Ralf; Krause, Gerd

    2013-02-01

    The TSHR (thyrotropin receptor) is activated endogenously by the large hormone thyrotropin and activated pathologically by auto-antibodies. Both activate and bind at the extracellular domain. Recently, SMLs (small-molecule ligands) have been identified, which bind in an allosteric binding pocket within the transmembrane domain. Modelling driven site-directed mutagenesis of amino acids lining this pocket led to the delineation of activation and inactivation sensitive residues. Modified residues showing CAMs (constitutively activating mutations) indicate signalling-sensitive positions and mark potential trigger points for agonists. Silencing mutations lead to an impairment of basal activity and mark contact points for antagonists. Mapping these residues on to a structural model of TSHR indicates locations where an SML may switch the receptor to an inactive or active conformation. In the present article, we report the effects of SMLs on these signalling-sensitive amino acids at the TSHR. Surprisingly, the antagonistic effect of SML compound 52 was reversed to an agonistic effect, when tested at the CAM Y667A. Switching agonism to antagonism and the reverse by changing either SMLs or residues covering the binding pocket provides detailed knowledge about discriminative pharmacophores. It prepares the basis for rational optimization of new high-affinity antagonists to interfere with the pathogenic activation of the TSHR.

  14. A potential food-grade cloning vector for Streptococcus thermophilus that uses cadmium resistance as the selectable marker.

    Science.gov (United States)

    Wong, Wing Yee; Su, Ping; Allison, Gwen E; Liu, Chun-Qiang; Dunn, Noel W

    2003-10-01

    A potential food-grade cloning vector, pND919, was constructed and transformed into S. thermophilus ST3-1, a plasmid-free strain. The vector contains DNAs from two different food-approved organisms, Streptococcus thermophilus and Lactococcus lactis. The 5.0-kb pND919 is a derivative of the cloning vector pND918 (9.3 kb) and was constructed by deletion of the 4.3-kb region of pND918 which contained DNA from non-food-approved organisms. pND919 carries a heterologous native cadmium resistance selectable marker from L. lactis M71 and expresses the Cd(r) phenotype in S. thermophilus transformants. With the S. thermophilus replicon derived from the shuttle vector pND913, pND919 is able to replicate in the two S. thermophilus industrial strains tested, ST3-1 and ST4-1. Its relatively high retention rate in S. thermophilus further indicates its usefulness as a potential food-grade cloning vector. To our knowledge, this is the first report of a replicative potential food-grade vector for the industrially important organism S. thermophilus.

  15. AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems.

    Science.gov (United States)

    LeVine, Michael V; Weinstein, Harel

    2015-05-01

    In performing their biological functions, molecular machines must process and transmit information with high fidelity. Information transmission requires dynamic coupling between the conformations of discrete structural components within the protein positioned far from one another on the molecular scale. This type of biomolecular "action at a distance" is termed allostery . Although allostery is ubiquitous in biological regulation and signal transduction, its treatment in theoretical models has mostly eschewed quantitative descriptions involving the system's underlying structural components and their interactions. Here, we show how Ising models can be used to formulate an approach to allostery in a structural context of interactions between the constitutive components by building simple allosteric constructs we termed Allosteric Ising Models (AIMs). We introduce the use of AIMs in analytical and numerical calculations that relate thermodynamic descriptions of allostery to the structural context, and then show that many fundamental properties of allostery, such as the multiplicative property of parallel allosteric channels, are revealed from the analysis of such models. The power of exploring mechanistic structural models of allosteric function in more complex systems by using AIMs is demonstrated by building a model of allosteric signaling for an experimentally well-characterized asymmetric homodimer of the dopamine D2 receptor.

  16. Function-Oriented Synthesis of Marine Phidianidine Derivatives as Potential PTP1B Inhibitors with Specific Selectivity

    Directory of Open Access Journals (Sweden)

    Jin Liu

    2018-03-01

    Full Text Available Phidianidines A and B are two novel marine indole alkaloids bearing an uncommon 1,2,4-oxadiazole ring and exhibiting various biological activities. Our previous research showed that the synthesized phidianidine analogs had the potential to inhibit the activity of protein tyrosine phosphatase 1B (PTP1B, a validated target for Type II diabetes, which indicates that these analogs are worth further structural modification. Therefore, in this paper, a series of phidianidine derivatives were designed and rapidly synthesized with a function-oriented synthesis (FOS strategy. Their inhibitory effects on PTP1B and T-cell protein tyrosine phosphatase (TCPTP were evaluated, and several compounds displayed significant inhibitory potency and specific selectivity over PTP1B. The structure–activity relationship (SAR and molecular docking analyses are also described.

  17. Function-Oriented Synthesis of Marine Phidianidine Derivatives as Potential PTP1B Inhibitors with Specific Selectivity.

    Science.gov (United States)

    Liu, Jin; Chen, Yu; Li, Jing-Ya; Luo, Cheng; Li, Jia; Chen, Kai-Xian; Li, Xu-Wen; Guo, Yue-Wei

    2018-03-20

    Phidianidines A and B are two novel marine indole alkaloids bearing an uncommon 1,2,4-oxadiazole ring and exhibiting various biological activities. Our previous research showed that the synthesized phidianidine analogs had the potential to inhibit the activity of protein tyrosine phosphatase 1B (PTP1B), a validated target for Type II diabetes, which indicates that these analogs are worth further structural modification. Therefore, in this paper, a series of phidianidine derivatives were designed and rapidly synthesized with a function-oriented synthesis (FOS) strategy. Their inhibitory effects on PTP1B and T-cell protein tyrosine phosphatase (TCPTP) were evaluated, and several compounds displayed significant inhibitory potency and specific selectivity over PTP1B. The structure-activity relationship (SAR) and molecular docking analyses are also described.

  18. The Oleaginous Yeast Meyerozyma guilliermondii BI281A as a New Potential Biodiesel Feedstock: Selection and Lipid Production Optimization.

    Science.gov (United States)

    Ramírez-Castrillón, Mauricio; Jaramillo-Garcia, Victoria P; Rosa, Priscila D; Landell, Melissa F; Vu, Duong; Fabricio, Mariana F; Ayub, Marco A Z; Robert, Vincent; Henriques, João A P; Valente, Patricia

    2017-01-01

    A high throughput screening (HTS) methodology for evaluation of cellular lipid content based on Nile red fluorescence reads using black background 96-wells test plates and a plate reader equipment allowed the rapid intracellular lipid estimation of strains from a Brazilian phylloplane yeast collection. A new oleaginous yeast, Meyerozyma guilliermondii BI281A, was selected, for which the gravimetric determination of total lipids relative to dry weight was 52.38% for glucose or 34.97% for pure glycerol. The lipid production was optimized obtaining 108 mg/L of neutral lipids using pure glycerol as carbon source, and the strain proved capable of accumulating oil using raw glycerol from a biodiesel refinery. The lipid profile showed monounsaturated fatty acids (MUFA) varying between 56 or 74% in pure or raw glycerol, respectively. M. guilliermondii BI281A bears potential as a new biodiesel feedstock.

  19. The Oleaginous Yeast Meyerozyma guilliermondii BI281A as a New Potential Biodiesel Feedstock: Selection and Lipid Production Optimization

    Directory of Open Access Journals (Sweden)

    Mauricio Ramírez-Castrillón

    2017-09-01

    Full Text Available A high throughput screening (HTS methodology for evaluation of cellular lipid content based on Nile red fluorescence reads using black background 96-wells test plates and a plate reader equipment allowed the rapid intracellular lipid estimation of strains from a Brazilian phylloplane yeast collection. A new oleaginous yeast, Meyerozyma guilliermondii BI281A, was selected, for which the gravimetric determination of total lipids relative to dry weight was 52.38% for glucose or 34.97% for pure glycerol. The lipid production was optimized obtaining 108 mg/L of neutral lipids using pure glycerol as carbon source, and the strain proved capable of accumulating oil using raw glycerol from a biodiesel refinery. The lipid profile showed monounsaturated fatty acids (MUFA varying between 56 or 74% in pure or raw glycerol, respectively. M. guilliermondii BI281A bears potential as a new biodiesel feedstock.

  20. Distribution and Potential Mobility of Selected Heavy Metals in a Fluvial Environment Under the Influence of Tanneries

    Directory of Open Access Journals (Sweden)

    Rodrigues M. L. K.

    2013-04-01

    Full Text Available In this study we evaluated the occurrence of heavy metals in a fluvial environment under the influence of tanneries – the Cadeia and Feitoria rivers basin (RS, south Brazil, highlighting the distribution and potential mobility of the selected elements. Every three months, over one year-period, selected heavy metals and ancillary parameters were analyzed in water and sediment samples taken at ten sites along the rivers. Water analyses followed APHA recommendations, and sediment analyses were based on methods from USEPA (SW846 and European Community (BCR sequential extraction. The determinations were performed by ICP/OES, except for Hg (CV/ETA. Statistical factor analysis was applied to water and sediment data sets, in order to obtain a synthesis of the environmental diagnosis. The results revealed that water quality decreased along the rivers, and mainly on the dry period (January, showing the influence of tannery plants vicinity and flow variations. Except for Fe, Al, and eventually Mn, heavy metal contents in water were in agreement with Brazilian standards. Concerning sediments, Al, Cu, Fe, Ni, Mn, Ti, and Zn concentrations appeared to reflect the base levels, while Cr and Hg were enriched in the deposits from the lower part of the basin. The partition of heavy metals among the sediment geochemical phases showed higher mobility of Mn along the sampling sites, followed by Cr in the lower reach of the basin, most affected by tanneries. Since Cr was predominantly associated to the oxidizable fraction, its potential mobilization from contaminated sediments would be associated to redox conditions. The detection of Hg in the tissue of a bottom-fish species indicated that the environmental conditions are apparently favoring the remobilization of this metal from contaminated sediments.

  1. Selective serotonin reuptake inhibitors potentiate the rapid antidepressant-like effects of serotonin4 receptor agonists in the rat.

    Directory of Open Access Journals (Sweden)

    Guillaume Lucas

    2010-02-01

    Full Text Available We have recently reported that serotonin(4 (5-HT(4 receptor agonists have a promising potential as fast-acting antidepressants. Here, we assess the extent to which this property may be optimized by the concomitant use of conventional antidepressants.We found that, in acute conditions, the 5-HT(4 agonist prucalopride was able to counteract the inhibitory effect of the selective serotonin reuptake inhibitors (SSRI fluvoxamine and citalopram on 5-HT neuron impulse flow, in Dorsal Raphé Nucleus (DRN cells selected for their high (>1.8 Hz basal discharge. The co-administration of both prucalopride and RS 67333 with citalopram for 3 days elicited an enhancement of DRN 5-HT neuron average firing rate, very similar to what was observed with either 5-HT(4 agonist alone. At the postsynaptic level, this translated into the manifestation of a tonus on hippocampal postsynaptic 5-HT(1A receptors, that was two to three times stronger when the 5-HT(4 agonist was combined with citalopram. Similarly, co-administration of citalopram synergistically potentiated the enhancing effect of RS 67333 on CREB protein phosphorylation within the hippocampus. Finally, in the Forced Swimming Test, the combination of RS 67333 with various SSRIs (fluvoxamine, citalopram and fluoxetine was more effective to reduce time of immobility than the separate administration of each compound.These findings strongly suggest that the adjunction of an SSRI to a 5-HT(4 agonist may help to optimize the fast-acting antidepressant efficacy of the latter.

  2. Selective replication of oncolytic virus M1 results in a bystander killing effect that is potentiated by Smac mimetics.

    Science.gov (United States)

    Cai, Jing; Lin, Yuan; Zhang, Haipeng; Liang, Jiankai; Tan, Yaqian; Cavenee, Webster K; Yan, Guangmei

    2017-06-27

    Oncolytic virotherapy is a treatment modality that uses native or genetically modified viruses that selectively replicate in and kill tumor cells. Viruses represent a type of pathogen-associated molecular pattern and thereby induce the up-regulation of dozens of cytokines via activating the host innate immune system. Second mitochondria-derived activator of caspases (Smac) mimetic compounds (SMCs), which antagonize the function of inhibitor of apoptosis proteins (IAPs) and induce apoptosis, sensitize tumor cells to multiple cytokines. Therefore, we sought to determine whether SMCs sensitize tumor cells to cytokines induced by the oncolytic M1 virus, thus enhancing a bystander killing effect. Here, we report that SMCs potentiate the oncolytic effect of M1 in vitro, in vivo, and ex vivo. This strengthened oncolytic efficacy resulted from the enhanced bystander killing effect caused by the M1 virus via cytokine induction. Through a microarray analysis and subsequent validation using recombinant cytokines, we identified IL-8, IL-1A, and TRAIL as the key cytokines in the bystander killing effect. Furthermore, SMCs increased the replication of M1, and the accumulation of virus protein induced irreversible endoplasmic reticulum stress- and c-Jun N-terminal kinase-mediated apoptosis. Nevertheless, the combined treatment with M1 and SMCs had little effect on normal and human primary cells. Because SMCs selectively and significantly enhance the bystander killing effect and the replication of oncolytic virus M1 specifically in cancer cells, this combined treatment may represent a promising therapeutic strategy.

  3. [Effects of anxiety and the COMT gene on cortical evoked potentials and performance effectiveness of selective attention].

    Science.gov (United States)

    Alfimova, M V; Golimbet, V E; Lebedeva, I S; Korovaĭtseva, G I; Lezheĭko, T V

    2014-01-01

    We studied influence of the anxiety-related trait Harm Avoidance and the COMT gene, which is an important modulator of prefrontal functioning, on event-related potentials in oddball paradigm and performance effectiveness of selective attention. For 50 individuals accuracy and time of searching words among letters at any desired rate and then under an instruction to perform the task as quickly and accurate as possible were measured. Scores on the Harm Avoidance scale from Cloninger's Temperament and Character Inventory, N100 and P300 parameters, and COMTVa1158Met genotypes were obtained for them as well. Searching accuracy and time were mainly related to N100 amplitude. The COMT genotype and Harm Avoidance did not affect N100 amplitude; however, the N100 amplitude modulated their effects on accuracy and time dynamics. Harm Avoidance was positively correlated with P300 latency. The results suggest that anxiety and the COMT gene effects on performance effectiveness of selective attention depend on cognitive processes reflected in N100 parameters.

  4. Selective attention to sound location or pitch studied with event-related brain potentials and magnetic fields.

    Science.gov (United States)

    Degerman, Alexander; Rinne, Teemu; Särkkä, Anna-Kaisa; Salmi, Juha; Alho, Kimmo

    2008-06-01

    Event-related brain potentials (ERPs) and magnetic fields (ERFs) were used to compare brain activity associated with selective attention to sound location or pitch in humans. Sixteen healthy adults participated in the ERP experiment, and 11 adults in the ERF experiment. In different conditions, the participants focused their attention on a designated sound location or pitch, or pictures presented on a screen, in order to detect target sounds or pictures among the attended stimuli. In the Attend Location condition, the location of sounds varied randomly (left or right), while their pitch (high or low) was kept constant. In the Attend Pitch condition, sounds of varying pitch (high or low) were presented at a constant location (left or right). Consistent with previous ERP results, selective attention to either sound feature produced a negative difference (Nd) between ERPs to attended and unattended sounds. In addition, ERPs showed a more posterior scalp distribution for the location-related Nd than for the pitch-related Nd, suggesting partially different generators for these Nds. The ERF source analyses found no source distribution differences between the pitch-related Ndm (the magnetic counterpart of the Nd) and location-related Ndm in the superior temporal cortex (STC), where the main sources of the Ndm effects are thought to be located. Thus, the ERP scalp distribution differences between the location-related and pitch-related Nd effects may have been caused by activity of areas outside the STC, perhaps in the inferior parietal regions.

  5. Potential social, institutional, and environmental impacts of selected energy-conservation measures in two Washington communities. [Seattle and Yakima

    Energy Technology Data Exchange (ETDEWEB)

    Edelson, E.; Olsen, M.

    1980-03-01

    The likely environmental, social, and institutional impacts of selected energy-conservation measures in two communities in Washington state are reported. The five conservation measures investigated in this study were: (1) retrofitting existing buildings; (2) district heating and Integrated Community Energy Systems (ICES); (3) small automobiles and vehicle redesign; (4) land-use and housing modifications; and (5) electric-utility rate reform. Twenty potential impact areas were selected for analysis. These areas were divided into five categories of environmental impacts, economic impacts, community impacts, personal impacts, and overall quality of life in the community. The research was conducted in Seattle and Yakima, Washington. In each location, about two dozen public officials and business, labor, and community leaders were interviewed. Their diverse views are summarized. The Seattle respondents saw energy conservation as a highly desirable policy with a number of temporary, transitional problems arising as energy-conservation measures were implemented. Yakima respondents, in contrast, did not expect to encounter many serious energy problems in the foreseeable future and consequently viewed energy conservation as a relatively minor community concern. Moreover, they anticipated that many conservation measures, if implemented by the government, would encounter either apathy or resistance in their community. Two broad generalizations can bedrawn from these interviews: (1) energy conservation will basically be beneficial for the natural environment and our society; and (2) if energy conservation does become a dominant thrust in our society, it could stimulate and reinforce a much broader process of fundamental social change. (LCL)

  6. Selection of Lactic Acid Bacteria with Probiotic Potential Isolated from the Fermentation Process of "Cupuaçu" (Theobroma grandiflorum).

    Science.gov (United States)

    Ornellas, Roberta Maria Santos; Santos, Tiza Teles; Arcucio, Leonardo Borges; Sandes, Sávio Henrique Cicco; Oliveira, Mayara Messias; Dias, Cristiano Villela; de Carvalho Silva, Samuel; Uetanabaro, Ana Paula Trovatti; Vinderola, Gabriel; Nicoli, Jacques Robert

    2017-01-01

    In the present study, nine lactic acid bacteria isolated from the fermentation process of "cupuaçu" (Theobroma grandiflorum) were selected for probiotic use. In vitro (resistance to gastrointestinal environment, in vitro antagonism and co-aggregation with pathogens) and in vivo (intestinal colonization and ex vivo antagonism in germ-free mice, cumulative mortality, translocation to liver and spleen, histopathological examination of liver and ileum and mRNA cytokine gene expression during an experimental infection with S. Typhimurium) assays were used. Among the nine Lactobacillus strains isolated from the "cupuaçu" fermentation, L. plantarum 81 and L. plantarum 90 were selected as potential probiotics based on better results obtained in in vitro evaluations (production of diffusible inhibitory compounds and co-aggregation) as well as in vivo experiments (resistance to gastrointestinal environment, ex vivo antagonism, higher survival after enteropathogen challenge, lower hepatic translocation of enteropathogen, lower histopathological lesions in ileum and liver and anti-inflammatory pattern of immunological response). Concluding, L. plantarum 81 and L. plantarum 90 showed in vitro and in vivo capacities for probiotic use through different mechanisms of protection and its origin would allow an easier adaptation in an alimentary matrix for its administration.

  7. Orexin A/Hypocretin Modulates Leptin Receptor-Mediated Signaling by Allosteric Modulations Mediated by the Ghrelin GHS-R1A Receptor in Hypothalamic Neurons.

    Science.gov (United States)

    Medrano, Mireia; Aguinaga, David; Reyes-Resina, Irene; Canela, Enric I; Mallol, Josefa; Navarro, Gemma; Franco, Rafael

    2018-06-01

    The hypothalamus is a key integrator of nutrient-seeking signals in the form of hormones and metabolites originated in both the central nervous system and the periphery. The main autocrine and paracrine target of orexinergic-related hormones such as leptin, orexin/hypocretin, and ghrelin are neuropeptide Y neurons located in the arcuate nucleus of the hypothalamus. The aim of this study was to investigate the expression and the molecular and functional relationships between leptin, orexin/hypocretin and ghrelin receptors. Biophysical studies in a heterologous system showed physical interactions between them, with potential formation of heterotrimeric complexes. Functional assays showed robust allosteric interactions particularly different when the three receptors are expressed together. Further biochemical and pharmacological assays provided evidence of heterotrimer functional expression in primary cultures of hypothalamic neurons. These findings constitute evidence of close relationships in the action of the three hormones already starting at the receptor level in hypothalamic cells.

  8. Structural and kinetic studies of the allosteric transition in Sulfolobus solfataricus uracil phosphoribosyltransferase: Permanent activation by engineering of the C-terminus

    DEFF Research Database (Denmark)

    Christoffersen, Stig; Kadziola, Anders; Johansson, Eva

    2009-01-01

    and PPi, in the other sites. Combined with three existing structures of uracil phosphoribosyltransferase in complex with UMP and the allosteric inhibitor cytidine triphosphate (CTP), these structures provide valuable insight into the mechanism of allosteric transition from inhibited to active enzyme...

  9. Mesoscale Assessment of CO2 Storage Potential and Geological Suitability for Target Area Selection in the Sichuan Basin

    Directory of Open Access Journals (Sweden)

    Yujie Diao

    2017-01-01

    Full Text Available In China, south of the Yangtze River, there are a large number of carbon sources, while the Sichuan Basin is the largest sedimentary basin; it makes sense to select the targets for CO2 geological storage (CGUS early demonstration. For CO2 enhanced oil and gas, coal bed methane recovery (CO2-EOR, EGR, and ECBM, or storage in these depleted fields, the existing oil, gas fields, or coal seams could be the target areas in the mesoscale. This paper proposed a methodology of GIS superimposed multisource information assessment of geological suitability for CO2 enhanced water recovery (CO2-EWR or only storage in deep saline aquifers. The potential per unit area of deep saline aquifers CO2 storage in Central Sichuan is generally greater than 50 × 104 t/km2 at P50 probability level, with Xujiahe group being the main reservoir. CO2 storage potential of depleted gas fields is 53.73 × 108 t, while it is 33.85 × 108 t by using CO2-EGR technology. This paper recommended that early implementation of CGUS could be carried out in the deep saline aquifers and depleted gas fields in the Sichuan Basin, especially that of the latter because of excellent traps, rich geological data, and well-run infrastructures.

  10. Glass and Glass-Ceramic Materials from Simulated Composition of Lunar and Martian Soils: Selected Properties and Potential Applications

    Science.gov (United States)

    Ray, C. S.; Sen, S.; Reis, S. T.; Kim, C. W.

    2005-01-01

    In-situ resource processing and utilization on planetary bodies is an important and integral part of NASA's space exploration program. Within this scope and context, our general effort is primarily aimed at developing glass and glass-ceramic type materials using lunar and martian soils, and exploring various applications of these materials for planetary surface operations. Our preliminary work to date have demonstrated that glasses can be successfully prepared from melts of the simulated composition of both lunar and martian soils, and the melts have a viscosity-temperature window appropriate for drawing continuous glass fibers. The glasses are shown to have the potential for immobilizing certain types of nuclear wastes without deteriorating their chemical durability and thermal stability. This has a direct impact on successfully and economically disposing nuclear waste generated from a nuclear power plant on a planetary surface. In addition, these materials display characteristics that can be manipulated using appropriate processing protocols to develop glassy or glass-ceramic magnets. Also discussed in this presentation are other potential applications along with a few selected thermal, chemical, and structural properties as evaluated up to this time for these materials.

  11. Mutations that silence constitutive signaling activity in the allosteric ligand-binding site of the thyrotropin receptor.

    Science.gov (United States)

    Haas, Ann-Karin; Kleinau, Gunnar; Hoyer, Inna; Neumann, Susanne; Furkert, Jens; Rutz, Claudia; Schülein, Ralf; Gershengorn, Marvin C; Krause, Gerd

    2011-01-01

    The thyrotropin receptor (TSHR) exhibits elevated cAMP signaling in the basal state and becomes fully activated by thyrotropin. Previously we presented evidence that small-molecule ligands act allosterically within the transmembrane region in contrast to the orthosteric extracellular hormone-binding sites. Our goal in this study was to identify positions that surround the allosteric pocket and that are sensitive for inactivation of TSHR. Homology modeling combined with site-directed mutagenesis and functional characterization revealed seven mutants located in the allosteric binding site that led to a decrease of basal cAMP signaling activity. The majority of these silencing mutations, which constrain the TSHR in an inactive conformation, are found in two clusters when mapped onto the 3D structural model. We suggest that the amino acid positions identified herein are indicating locations where small-molecule antagonists, both neutral antagonists and inverse agonists, might interfere with active TSHR conformations.

  12. Economic potential analysis of cogeneration using natural gas in the selected sectors; Analise do potencial economico de cogeracao a gas natural nos setores selecionados

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-07-01

    This chapter presents the results of the economic potential of the natural gas cogeneration under topping regime, in the selected sectors of beverage industry, editorial and graphic industries, shopping centers, hospitals and hotels.

  13. SB265610 is an allosteric, inverse agonist at the human CXCR2 receptor

    Science.gov (United States)

    Bradley, ME; Bond, ME; Manini, J; Brown, Z; Charlton, SJ

    2009-01-01

    Background and purpose: In several previous studies, the C-X-C chemokine receptor (CXCR)2 antagonist 1-(2-bromo-phenyl)-3-(7-cyano-3H-benzotriazol-4-yl)-urea (SB265610) has been described as binding competitively with the endogenous agonist. This is in contrast to many other chemokine receptor antagonists, where the mechanism of antagonism has been described as allosteric. Experimental approach: To determine whether it displays a unique mechanism among the chemokine receptor antagonists, the mode of action of SB265610 was investigated at the CXCR2 receptor using radioligand and [35S]-GTPγS binding approaches in addition to chemotaxis of human neutrophils. Key results: In equilibrium saturation binding studies, SB265610 depressed the maximal binding of [125I]-interleukin-8 ([125I]-IL-8) without affecting the Kd. In contrast, IL-8 was unable to prevent binding of [3H]-SB265610. Kinetic binding experiments demonstrated that this was not an artefact of irreversible or slowly reversible binding. In functional experiments, SB265610 caused a rightward shift of the concentration-response curves to IL-8 and growth-related oncogene α, but also a reduction in maximal response elicited by each agonist. Fitting these data to an operational allosteric ternary complex model suggested that, once bound, SB265610 completely blocks receptor activation. SB265610 also inhibited basal [35S]-GTPγS binding in this preparation. Conclusions and implications: Taken together, these data suggest that SB265610 behaves as an allosteric inverse agonist at the CXCR2 receptor, binding at a region distinct from the agonist binding site to prevent receptor activation, possibly by interfering with G protein coupling. PMID:19422399

  14. Intrasteric control of AMPK via the gamma1 subunit AMP allosteric regulatory site.

    Science.gov (United States)

    Adams, Julian; Chen, Zhi-Ping; Van Denderen, Bryce J W; Morton, Craig J; Parker, Michael W; Witters, Lee A; Stapleton, David; Kemp, Bruce E

    2004-01-01

    AMP-activated protein kinase (AMPK) is a alphabetagamma heterotrimer that is activated in response to both hormones and intracellular metabolic stress signals. AMPK is regulated by phosphorylation on the alpha subunit and by AMP allosteric control previously thought to be mediated by both alpha and gamma subunits. Here we present evidence that adjacent gamma subunit pairs of CBS repeat sequences (after Cystathionine Beta Synthase) form an AMP binding site related to, but distinct from the classical AMP binding site in phosphorylase, that can also bind ATP. The AMP binding site of the gamma(1) CBS1/CBS2 pair, modeled on the structures of the CBS sequences present in the inosine monophosphate dehydrogenase crystal structure, contains three arginine residues 70, 152, and 171 and His151. The yeast gamma homolog, snf4 contains a His151Gly substitution, and when this is introduced into gamma(1), AMP allosteric control is substantially lost and explains why the yeast snf1p/snf4p complex is insensitive to AMP. Arg70 in gamma(1) corresponds to the site of mutation in human gamma(2) and pig gamma(3) genes previously identified to cause an unusual cardiac phenotype and glycogen storage disease, respectively. Mutation of any of AMP binding site Arg residues to Gln substantially abolishes AMP allosteric control in expressed AMPK holoenzyme. The Arg/Gln mutations also suppress the previously described inhibitory properties of ATP and render the enzyme constitutively active. We propose that ATP acts as an intrasteric inhibitor by bridging the alpha and gamma subunits and that AMP functions to derepress AMPK activity.

  15. An application of zeta potential method for the selection of nano-fluids to enhance IVR capability

    International Nuclear Information System (INIS)

    Pham Quynh Trang; Kim, Tae Il; Chang, Soon Heung

    2009-01-01

    In-vessel Retention (IVR) is one of the key severe accident management strategies that have been applied currently for advanced light water reactors such as APR1000 or APR1400. The concept of IVR consists of external cooling of the reactor vessel by flooding the reactor cavity to remove the decay heat from the molten core through the lower head of the vessel. However, the heat removal process is limited by the occurrence of critical heat flux (CHF) at the reactor vessel outer surface that may lead to a sharp increase of local temperature, damaging the integrity of the reactor vessel. In order to obtain higher power of nuclear reactors and to assure the achievement of the IVR capability during accident conditions, an enhancement of CHF at the outer surface of the vessel is required. The potential use of nano-fluids to increase the CHF is among the main IVR enhancing approaches. In this study, Al 2 O 3 and CNT nano-fluids with different concentrations have been used as the potential coolant to enhance IVR capabilities. The dispersion stability of the nano-fluids was verified by zeta potential measurements. The results showed effects of time, concentration and pH on the stability of nanofluids. Three types of nano-fluids were selected as the candidates to apply for the IVR. A series of experiments have been performed in this study to understand the pool-boiling critical heat flux behavior on downward facing surfaces submerged in a pool of nano-fluids at very low concentration. The inclination angle was changed from horizontal to vertical to investigate the effect of orientation on CHF enhancement which is needed for the application in IVR

  16. Discovery of a novel allosteric modulator of 5-HT3 receptor

    DEFF Research Database (Denmark)

    Trattnig, Sarah M; Harpsøe, Kasper; Thygesen, Sarah B

    2012-01-01

    The ligand-gated ion channels in the Cysloop receptor superfamily mediate the effects of neurotransmitters acetylcholine, serotonin, GABA and glycine. Cysloop receptor signaling is susceptible to modulation by ligands acting through numerous allosteric sites. Here we report the discovery of a novel...... receptor guided by a homology model, PU02 is demonstrated to act through a transmembrane intersubunit site situated in the upper three helical turns of TM2 and TM3 in the (+)subunit and TM1 and TM2 in the (minus)subunit. The Ser248, Leu288, Ile290, Thr294 and Gly306 residues are identified as important...

  17. Allosteric control of internal electron transfer in cytochrome cd1 nitrite reductase

    DEFF Research Database (Denmark)

    Farver, Ole; Kroneck, Peter M H; Zumft, Walter G

    2003-01-01

    Cytochrome cd1 nitrite reductase is a bifunctional multiheme enzyme catalyzing the one-electron reduction of nitrite to nitric oxide and the four-electron reduction of dioxygen to water. Kinetics and thermodynamics of the internal electron transfer process in the Pseudomonas stutzeri enzyme have...... been studied and found to be dominated by pronounced interactions between the c and the d1 hemes. The interactions are expressed both in dramatic changes in the internal electron-transfer rates between these sites and in marked cooperativity in their electron affinity. The results constitute a prime...... example of intraprotein control of the electron-transfer rates by allosteric interactions....

  18. Complex pharmacology of novel allosteric free fatty acid 3 receptor ligands

    DEFF Research Database (Denmark)

    Hudson, Brian D; Christiansen, Elisabeth; Murdoch, Hannah

    2014-01-01

    this series resulted in compounds completely lacking activity, acting as FFA3 PAMs, or appearing to act as FFA3-negative allosteric modulators. However, the pharmacology of this series was further complicated in that certain analogs displaying overall antagonism of FFA3 function actually appeared to generate......, considerable care must be taken to define the pharmacological characteristics of specific compounds before useful predictions of their activity and their use in defining specific roles of FFA3 in either in vitro and in vivo settings can be made....

  19. Characterization of the apoptotic response induced by the cyanine dye D112: a potentially selective anti-cancer compound.

    Directory of Open Access Journals (Sweden)

    Ning Yang

    Full Text Available Chemotherapeutic drugs that are used in anti-cancer treatments often cause the death of both cancerous and noncancerous cells. This non-selective toxicity is the root cause of untoward side effects that limits the effectiveness of therapy. In order to improve chemotherapeutic options for cancer patients, there is a need to identify novel compounds with higher discrimination for cancer cells. In the past, methine dyes that increase the sensitivity of photographic emulsions have been investigated for anti-cancer properties. In the 1970's, Kodak Laboratories initiated a screen of approximately 7000 dye structural variants for selective toxicity. Among these, D112 was identified as a promising compound with elevated toxicity against a colon cancer cell line in comparison to a non-transformed cell line. Despite these results changing industry priorities led to a halt in further studies on D112. We decided to revive investigations on D112 and have further characterized D112-induced cellular toxicity. We identified that in response to D112 treatment, the T-cell leukemia cell line Jurkat showed caspase activation, mitochondrial depolarization, and phosphatidylserine externalization, all of which are hallmarks of apoptosis. Chemical inhibition of caspase enzymatic activity and blockade of the mitochondrial pathway through Bcl-2 expression inhibited D112-induced apoptosis. At lower concentrations, D112 induced growth arrest. To gain insight into the molecular mechanism of D112 induced mitochondrial dysfunction, we analyzed the intracellular localization of D112, and found that D112 associated with mitochondria. Interestingly, in the cell lines that we tested, D112 showed increased toxicity toward transformed versus non-transformed cells. Results from this work identify D112 as a potentially interesting molecule warranting further investigation.

  20. Selection for high muscle fat in rainbow trout induces potentially higher chylomicron synthesis and PUFA biosynthesis in the intestine.

    Science.gov (United States)

    Kamalam, Biju Sam; Panserat, Stephane; Aguirre, Peyo; Geurden, Inge; Fontagné-Dicharry, Stéphanie; Médale, Françoise

    2013-02-01

    Two lines of rainbow trout divergently selected for muscle fat content, fat line (F) and lean line (L) were used to investigate the effect of genetic selection on digestion, intestinal nutrient transport and fatty acid bioconversion, in relation to dietary starch intake. This study involved a digestibility trial for 2 weeks using Cr(2)O(3) as inert marker, followed by a feeding trial for 4 weeks. For the entire duration, juvenile trout from the two lines were fed diets with or without gelatinized starch. Blood, pyloric ceca, midgut and hindgut were sampled at 24 h after the last meal. Transcripts of the proteins involved in nutrient transport and fatty acid bioconversion were abundant in the proximal intestine. GLUT2 transcripts were slightly higher in the F line ceca than in the L line. Dietary starch intake did not enhance the transcription of intestinal glucose transporters, SGLT1 and GLUT2; but it was associated with the higher expression of ApoA1 and PepT1 in the midgut. Significantly, the F line exhibited higher intestinal mRNA levels of MTP, ApoA4, Elovl2, Elovl5 and D6D than the L line, linked to chylomicron assembly and fatty acid bioconversion. Apparent digestibility coefficients of protein, lipid and starch were high in both lines, but not significantly different between them. In conclusion, we found a higher potential of chylomicron synthesis and fatty acid bioconversion in the intestine of F line, but no adaptive transcriptional response of glucose transporters to dietary starch and no genotypic differences in nutrient digestibility. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. The potential of selected macroalgal species for treatment of AMD at different pH ranges in temperate regions.

    Science.gov (United States)

    Oberholster, Paul J; Cheng, Po-Hsun; Botha, Anna-Maria; Genthe, Bettina

    2014-09-01

    The metal bioaccumulation potential of selected macroalgae species at different pH ranges was study for usage as part of a possible secondary passive acid mine drainage (AMD) treatment technology in algae ponds. Two separate studies were conducted to determine the suitability of macroalgae for passive treatment when metabolic processes in macrophytes and microorganisms in constructed wetlands decrease during winter months. In the field study, the bioconcentration of metals (mg/kg dry weight) measured in the benthic macroalgae mats was in the following order: site 1. Oedogonium crassum Al > Fe > Mn > Zn; site 2. Klebsormidium klebsii, Al > Fe > Mn > Zn; site 3. Microspora tumidula, Fe > Al > Mn > Zn and site 4. M. tumidula, Fe > Mn > Al > Zn. In the laboratory study, cultured macroalgae K. klebsii, O. crassum and M. tumidula isolated from the field sampling sites were exposed to three different pH values (3, 5 and 7), while bioaccumulation of the metals, Al, Fe, Mn and Zn and glutathione S-transferase (GST) activity were measured in the different selected algae species at a constant water temperature of 14 °C. Bioaccumulation of Al was the highest for O. crassum followed by K. klebsii and M. tumidula (p macroalgae O. crassum at all three tested pH values under constant low water temperature. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Studies of the in vitro anticancer, antimicrobial and antioxidant potentials of selected Yemeni medicinal plants from the island Soqotra

    Science.gov (United States)

    2009-01-01

    Background Recent years have witnessed that there is a revival of interest in drug discovery from medicinal plants for the maintenance of health in all parts of the world. The aim of this work was to investigate 26 plants belonging to 17 families collected from a unique place in Yemen (Soqotra Island) for their in vitro anticancer, antimicrobial and antioxidant activities. Methods The 26 plants were extracted with methanol and hot water to yield 52 extracts. Evaluation for in vitro anticancer activity was done against three human cancer cell lines (A-427, 5637 and MCF-7) by using an established microtiter plate assay based on cellular staining with crystal violet. Antimicrobial activity was tested against three Gram-positive bacteria, two Gram-negative bacteria, one yeast species and three multiresistant Staphylococcus strains by using an agar diffusion method and the determination of MIC against three Gram-positive bacteria with the broth micro-dilution assay. Antioxidant activity was investigated by measuring the scavenging activity of the DPPH radical. Moreover, a phytochemical screening of the methanolic extracts was done. Results Notable cancer cell growth inhibition was observed for extracts from Ballochia atro-virgata, Eureiandra balfourii and Hypoestes pubescens, with IC50 values ranging between 0.8 and 8.2 μg/ml. The methanol extracts of Acanthospermum hispidum, Boswellia dioscorides, Boswellia socotrana, Commiphora ornifolia and Euphorbia socotrana also showed noticeable antiproliferative potency with IC50 values 15 mm and MIC values ≤ 250 μg/ml. In addition, the methanolic extracts of Acacia pennivenia, Boswellia dioscorides, Boswellia socotrana and Commiphora ornifolia showed good antioxidant potential at low concentrations (more than 80% at 50 μg/ml). Conclusion Our results show once again that medicinal plants can be promising sources of natural products with potential anticancer, antimicrobial and antioxidative activity. The results will guide

  3. The potential of aspen clonal forestry in Alberta: breeding regions and estimates of genetic gain from selection.

    Directory of Open Access Journals (Sweden)

    Tim Gylander

    Full Text Available BACKGROUND: Aspen naturally grows in large, single-species, even-aged stands that regenerate clonally after fire disturbance. This offers an opportunity for an intensive clonal forestry system that closely emulates the natural life history of the species. In this paper, we assess the potential of genetic tree improvement and clonal deployment to enhance the productivity of aspen forests in Alberta. We further investigate geographic patterns of genetic variation in aspen and infer forest management strategies under uncertain future climates. METHODOLOGY/PRINCIPAL FINDINGS: Genetic variation among 242 clones from Alberta was evaluated in 13 common garden trials after 5-8 growing seasons in the field. Broad-sense heritabilities for height and diameter at breast height (DBH ranged from 0.36 to 0.64, allowing 5-15% genetic gains in height and 9-34% genetic gains in DBH. Geographic partitioning of genetic variance revealed predominant latitudinal genetic differentiation. We further observed that northward movement of clones almost always resulted in increased growth relative to local planting material, while southward movement had a strong opposite effect. CONCLUSION/SIGNIFICANCE: Aspen forests are an important natural resource in western Canada that is used for pulp and oriented strandboard production, accounting for ~40% of the total forest harvest. Moderate to high broad-sense heritabilities in growth traits suggest good potential for a genetic tree improvement program with aspen. Significant productivity gains appear possible through clonal selection from existing trials. We propose two breeding regions for Alberta, and suggest that well-tested southern clones may be used in the northern breeding region, accounting for a general warming trend observed over the last several decades in Alberta.

  4. The potential of task shifting selected maternal interventions to auxiliary midwives in Myanmar: a mixed-method study.

    Science.gov (United States)

    Than, Kyu Kyu; Tin, Khaing Nwe; La, Thazin; Thant, Kyaw Soe; Myint, Theingi; Beeson, James G; Luchters, Stanley; Morgan, Alison

    2018-01-03

    An estimated 282 women die for every 100,000 live births in Myanmar, most due to preventable causes. Auxiliary Midwives (AMWs) in Myanmar are responsible for providing a package of care during pregnancy and childbirth to women in rural hard to reach areas where skilled birth attendants (Midwives) are not accessible. This study aims to examine the role of AMWs in Myanmar and to assess the current practices of three proposed essential maternal interventions (oral supplement distribution to pregnant women; administration of misoprostol to prevent postpartum haemorrhage; management of puerperal sepsis with oral antibiotics) in order to facilitate a formal integration of these tasks to AMWs in Myanmar. A mixed methods study was conducted in Magwe Region, Myanmar involving a survey of 262 AMWs, complemented by 15 focus group discussions with midwives (MWs), AMWs, mothers and community members, and 10 key informant interviews with health care providers at different levels within the health care system. According to current government policy, AMWs are responsible for identifying pregnant women, screening for danger signs and facilitating early referral, provision of counselling on nutrition and birth preparedness for women in hard-to-reach areas. AMWs also assist at normal deliveries and help MWs provide immunization services. In practice, they also provide oral supplements to pregnant women (84%), provide antibiotics to mothers during the puerperium (43%), and provide misoprostol to prevent postpartum haemorrhage (41%). The current practices of AMWs demonstrate the potential for task shifting on selected essential maternal interventions. However, to integrate these interventions into formal practice they must be complemented with appropriate training, clear guidelines on drug use, systematic recording and reporting, supportive monitoring and supervision and a clear political commitment towards task shifting. With the current national government's commitment towards one

  5. Generation of “LYmph Node Derived Antibody Libraries” (LYNDAL) for selecting fully human antibody fragments with therapeutic potential.

    Science.gov (United States)

    Diebolder, Philipp; Keller, Armin; Haase, Stephanie; Schlegelmilch, Anne; Kiefer, Jonathan D; Karimi, Tamana; Weber, Tobias; Moldenhauer, Gerhard; Kehm, Roland; Eis-Hübinger, Anna M; Jäger, Dirk; Federspil, Philippe A; Herold-Mende, Christel; Dyckhoff, Gerhard; Kontermann, Roland E; Arndt, Michaela A E; Krauss, Jürgen

    2014-01-01

    The development of efficient strategies for generating fully human monoclonal antibodies with unique functional properties that are exploitable for tailored therapeutic interventions remains a major challenge in the antibody technology field. Here, we present a methodology for recovering such antibodies from antigen-encountered human B cell repertoires. As the source for variable antibody genes, we cloned immunoglobulin G (IgG)-derived B cell repertoires from lymph nodes of 20 individuals undergoing surgery for head and neck cancer. Sequence analysis of unselected “LYmph Node Derived Antibody Libraries” (LYNDAL) revealed a naturally occurring distribution pattern of rearranged antibody sequences, representing all known variable gene families and most functional germline sequences. To demonstrate the feasibility for selecting antibodies with therapeutic potential from these repertoires, seven LYNDAL from donors with high serum titers against herpes simplex virus (HSV) were panned on recombinant glycoprotein B of HSV-1. Screening for specific binders delivered 34 single-chain variable fragments (scFvs) with unique sequences. Sequence analysis revealed extensive somatic hypermutation of enriched clones as a result of affinity maturation. Binding of scFvs to common glycoprotein B variants from HSV-1 and HSV-2 strains was highly specific, and the majority of analyzed antibody fragments bound to the target antigen with nanomolar affinity. From eight scFvs with HSV-neutralizing capacity in vitro,the most potent antibody neutralized 50% HSV-2 at 4.5 nM as a dimeric (scFv)2. We anticipate our approach to be useful for recovering fully human antibodies with therapeutic potential.

  6. The Potential of Aspen Clonal Forestry in Alberta: Breeding Regions and Estimates of Genetic Gain from Selection

    Science.gov (United States)

    Gylander, Tim; Hamann, Andreas; Brouard, Jean S.; Thomas, Barb R.

    2012-01-01

    Background Aspen naturally grows in large, single-species, even-aged stands that regenerate clonally after fire disturbance. This offers an opportunity for an intensive clonal forestry system that closely emulates the natural life history of the species. In this paper, we assess the potential of genetic tree improvement and clonal deployment to enhance the productivity of aspen forests in Alberta. We further investigate geographic patterns of genetic variation in aspen and infer forest management strategies under uncertain future climates. Methodology/Principal Findings Genetic variation among 242 clones from Alberta was evaluated in 13 common garden trials after 5–8 growing seasons in the field. Broad-sense heritabilities for height and diameter at breast height (DBH) ranged from 0.36 to 0.64, allowing 5–15% genetic gains in height and 9–34% genetic gains in DBH. Geographic partitioning of genetic variance revealed predominant latitudinal genetic differentiation. We further observed that northward movement of clones almost always resulted in increased growth relative to local planting material, while southward movement had a strong opposite effect. Conclusion/Significance Aspen forests are an important natural resource in western Canada that is used for pulp and oriented strandboard production, accounting for ∼40% of the total forest harvest. Moderate to high broad-sense heritabilities in growth traits suggest good potential for a genetic tree improvement program with aspen. Significant productivity gains appear possible through clonal selection from existing trials. We propose two breeding regions for Alberta, and suggest that well-tested southern clones may be used in the northern breeding region, accounting for a general warming trend observed over the last several decades in Alberta. PMID:22957006

  7. Lack of conventional oxygen-linked proton and anion binding sites does not impair allosteric regulation of oxygen binding in dwarf caiman hemoglobin

    Science.gov (United States)

    Fago, Angela; Malte, Hans; Storz, Jay F.; Gorr, Thomas A.

    2013-01-01

    In contrast to other vertebrate hemoglobins (Hbs) whose high intrinsic O2 affinities are reduced by red cell allosteric effectors (mainly protons, CO2, organic phosphates, and chloride ions), crocodilian Hbs exhibit low sensitivity to organic phosphates and high sensitivity to bicarbonate (HCO3−), which is believed to augment Hb-O2 unloading during diving and postprandial alkaline tides when blood HCO3− levels and metabolic rates increase. Examination of α- and β-globin amino acid sequences of dwarf caiman (Paleosuchus palpebrosus) revealed a unique combination of substitutions at key effector binding sites compared with other vertebrate and crocodilian Hbs: β82Lys→Gln, β143His→Val, and β146His→Tyr. These substitutions delete positive charges and, along with other distinctive changes in residue charge and polarity, may be expected to disrupt allosteric regulation of Hb-O2 affinity. Strikingly, however, P. palpebrosus Hb shows a strong Bohr effect, and marked deoxygenation-linked binding of organic phosphates (ATP and DPG) and CO2 as carbamate (contrasting with HCO3− binding in other crocodilians). Unlike other Hbs, it polymerizes to large complexes in the oxygenated state. The highly unusual properties of P. palpebrosus Hb align with a high content of His residues (potential sites for oxygenation-linked proton binding) and distinctive surface Cys residues that may form intermolecular disulfide bridges upon polymerization. On the basis of its singular properties, P. palpebrosus Hb provides a unique opportunity for studies on structure-function coupling and the evolution of compensatory mechanisms for maintaining tissue O2 delivery in Hbs that lack conventional effector-binding residues. PMID:23720132

  8. Prediction of malting quality traits in barley based on genome-wide marker data to assess the potential of genomic selection.

    Science.gov (United States)

    Schmidt, Malthe; Kollers, Sonja; Maasberg-Prelle, Anja; Großer, Jörg; Schinkel, Burkhard; Tomerius, Alexandra; Graner, Andreas; Korzun, Viktor

    2016-02-01

    Genomic prediction of malting quality traits in barley shows the potential of applying genomic selection to improve selection for malting quality and speed up the breeding process. Genomic selection has been applied to various plant species, mostly for yield or yield-related traits such as grain dry matter yield or thousand kernel weight, and improvement of resistances against diseases. Quality traits have not been the main scope of analysis for genomic selection, but have rather been addressed by marker-assisted selection. In this study, the potential to apply genomic selection to twelve malting quality traits in two commercial breeding programs of spring and winter barley (Hordeum vulgare L.) was assessed. Phenotypic means were calculated combining multilocational field trial data from 3 or 4 years, depending on the trait investigated. Three to five locations were available in each of these years. Heritabilities for malting traits ranged between 0.50 and 0.98. Predictive abilities (PA), as derived from cross validation, ranged between 0.14 to 0.58 for spring barley and 0.40-0.80 for winter barley. Small training sets were shown to be sufficient to obtain useful PAs, possibly due to the narrow genetic base in this breeding material. Deployment of genomic selection in malting barley breeding clearly has the potential to reduce cost intensive phenotyping for quality traits, increase selection intensity and to shorten breeding cycles.

  9. Cardiolipin modulates allosterically peroxynitrite detoxification by horse heart cytochrome c

    Energy Technology Data Exchange (ETDEWEB)

    Ascenzi, Paolo, E-mail: ascenzi@uniroma3.it [Department of Biology and Interdepartmental Laboratory for Electron Microscopy, University Roma Tre, I-00146 Roma (Italy); Ciaccio, Chiara [Department of Experimental Medicine and Biochemical Sciences, University of Roma ' Tor Vergata' , I-00133 Roma (Italy); Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, I-70126 Bari (Italy); Sinibaldi, Federica; Santucci, Roberto [Department of Experimental Medicine and Biochemical Sciences, University of Roma ' Tor Vergata' , I-00133 Roma (Italy); Coletta, Massimo [Department of Experimental Medicine and Biochemical Sciences, University of Roma ' Tor Vergata' , I-00133 Roma (Italy); Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, I-70126 Bari (Italy)

    2011-01-07

    Research highlights: {yields} Cardiolipin binding to cytochrome c. {yields} Cardiolipin-dependent peroxynitrite isomerization by cytochrome c. {yields} Cardiolipin-cytochrome c complex plays pro-apoptotic effects. {yields} Cardiolipin-cytochrome c complex plays anti-apoptotic effects. -- Abstract: Upon interaction with bovine heart cardiolipin (CL), horse heart cytochrome c (cytc) changes its tertiary structure disrupting the heme-Fe-Met80 distal bond, reduces drastically the midpoint potential out of the range required for its physiological role, binds CO and NO with high affinity, and displays peroxidase activity. Here, the effect of CL on peroxynitrite isomerization by ferric cytc (cytc-Fe(III)) is reported. In the absence of CL, hexa-coordinated cytc does not catalyze peroxynitrite isomerization. In contrast, CL facilitates cytc-Fe(III)-mediated isomerization of peroxynitrite in a dose-dependent fashion inducing the penta-coordination of the heme-Fe(III)-atom. The value of the second order rate constant for CL-cytc-Fe(III)-mediated isomerization of peroxynitrite (k{sub on}) is (3.2 {+-} 0.4) x 10{sup 5} M{sup -1} s{sup -1}. The apparent dissociation equilibrium constant for CL binding to cytc-Fe(III) is (5.1 {+-} 0.8) x 10{sup -5} M. These results suggest that CL-cytc could play either pro-apoptotic or anti-apoptotic effects facilitating lipid peroxidation and scavenging of reactive nitrogen species, such as peroxynitrite, respectively.

  10. Zinc-mediated Allosteric Inhibition of Caspase-6*

    Science.gov (United States)

    Velázquez-Delgado, Elih M.; Hardy, Jeanne A.

    2012-01-01

    Zinc and caspase-6 have independently been implicated in several neurodegenerative disorders. Depletion of zinc intracellularly leads to apoptosis by an unknown mechanism. Zinc inhibits cysteine proteases, including the apoptotic caspases, leading to the hypothesis that zinc-mediated inhibition of caspase-6 might contribute to its regulation in a neurodegenerative context. Using inductively coupled plasma optical emission spectroscopy, we observed that caspase-6 binds one zinc per monomer, under the same conditions where the zinc leads to complete loss of enzymatic activity. To understand the molecular details of zinc binding and inhibition, we performed an anomalous diffraction experiment above the zinc edge. The anomalous difference maps showed strong 5σ peaks, indicating the presence of one zinc/monomer bound at an exosite distal from the active site. Zinc was not observed bound to the active site. The zinc in the exosite was liganded by Lys-36, Glu-244, and His-287 with a water molecule serving as the fourth ligand, forming a distorted tetrahedral ligation sphere. This exosite appears to be unique to caspase-6, as the residues involved in zinc binding were not conserved across the caspase family. Our data suggest that binding of zinc at the exosite is the primary route of inhibition, potentially locking caspase-6 into the inactive helical conformation. PMID:22891250

  11. Characterization of Imidazopyridine Compounds as Negative Allosteric Modulators of Proton-Sensing GPR4 in Extracellular Acidification-Induced Responses.

    Directory of Open Access Journals (Sweden)

    Ayaka Tobo

    Full Text Available G protein-coupled receptor 4 (GPR4, previously proposed as the receptor for sphingosylphosphorylcholine, has recently been identified as the proton-sensing G protein-coupled receptor (GPCR coupling to multiple intracellular signaling pathways, including the Gs protein/cAMP and G13 protein/Rho. In the present study, we characterized some imidazopyridine compounds as GPR4 modulators that modify GPR4 receptor function. In the cells that express proton-sensing GPCRs, including GPR4, OGR1, TDAG8, and G2A, extracellular acidification stimulates serum responsive element (SRE-driven transcriptional activity, which has been shown to reflect Rho activity, with different proton sensitivities. Imidazopyridine compounds inhibited the moderately acidic pH-induced SRE activity only in GPR4-expressing cells. Acidic pH-stimulated cAMP accumulation, mRNA expression of inflammatory genes, and GPR4 internalization within GPR4-expressing cells were all inhibited by the GPR4 modulator. We further compared the inhibition property of the imidazopyridine compound with psychosine, which has been shown to selectively inhibit actions induced by proton-sensing GPCRs, including GPR4. In the GPR4 mutant, in which certain histidine residues were mutated to phenylalanine, proton sensitivity was significantly shifted to the right, and psychosine failed to further inhibit acidic pH-induced SRE activation. On the other hand, the imidazopyridine compound almost completely inhibited acidic pH-induced action in mutant GPR4. We conclude that some imidazopyridine compounds show specificity to GPR4 as negative allosteric modulators with a different action mode from psychosine, an antagonist susceptible to histidine residues, and are useful for characterizing GPR4-mediated acidic pH-induced biological actions.

  12. Characterization of Imidazopyridine Compounds as Negative Allosteric Modulators of Proton-Sensing GPR4 in Extracellular Acidification-Induced Responses.

    Science.gov (United States)

    Tobo, Ayaka; Tobo, Masayuki; Nakakura, Takashi; Ebara, Masashi; Tomura, Hideaki; Mogi, Chihiro; Im, Dong-Soon; Murata, Naoya; Kuwabara, Atsushi; Ito, Saki; Fukuda, Hayato; Arisawa, Mitsuhiro; Shuto, Satoshi; Nakaya, Michio; Kurose, Hitoshi; Sato, Koichi; Okajima, Fumikazu

    2015-01-01

    G protein-coupled receptor 4 (GPR4), previously proposed as the receptor for sphingosylphosphorylcholine, has recently been identified as the proton-sensing G protein-coupled receptor (GPCR) coupling to multiple intracellular signaling pathways, including the Gs protein/cAMP and G13 protein/Rho. In the present study, we characterized some imidazopyridine compounds as GPR4 modulators that modify GPR4 receptor function. In the cells that express proton-sensing GPCRs, including GPR4, OGR1, TDAG8, and G2A, extracellular acidification stimulates serum responsive element (SRE)-driven transcriptional activity, which has been shown to reflect Rho activity, with different proton sensitivities. Imidazopyridine compounds inhibited the moderately acidic pH-induced SRE activity only in GPR4-expressing cells. Acidic pH-stimulated cAMP accumulation, mRNA expression of inflammatory genes, and GPR4 internalization within GPR4-expressing cells were all inhibited by the GPR4 modulator. We further compared the inhibition property of the imidazopyridine compound with psychosine, which has been shown to selectively inhibit actions induced by proton-sensing GPCRs, including GPR4. In the GPR4 mutant, in which certain histidine residues were mutated to phenylalanine, proton sensitivity was significantly shifted to the right, and psychosine failed to further inhibit acidic pH-induced SRE activation. On the other hand, the imidazopyridine compound almost completely inhibited acidic pH-induced action in mutant GPR4. We conclude that some imidazopyridine compounds show specificity to GPR4 as negative allosteric modulators with a different action mode from psychosine, an antagonist susceptible to histidine residues, and are useful for characterizing GPR4-mediated acidic pH-induced biological actions.

  13. Sex-dependent anti-stress effect of an α5 subunit containing GABAA receptor positive allosteric modulator

    Directory of Open Access Journals (Sweden)

    Sean C. Piantadosi

    2016-11-01

    Full Text Available Rationale: Current first-line treatments for stress-related disorders such as Major Depressive Disorder (MDD act on monoaminergic systems and take weeks to achieve a therapeutic effect with poor response and low remission rates. Recent research has implicated the GABAergic system in the pathophysiology of depression, including deficits in interneurons targeting the dendritic compartment of cortical pyramidal cells. Objectives: The present study evaluates whether SH-053-2'F-R-CH3 (denoted α5-PAM, a positive allosteric modulator selective for α5-subunit containing GABAA receptors found predominantly on cortical pyramidal cell dendrites has anti-stress effects. Methods: Female and male C57BL6/J mice were exposed to unpredictable chronic mild stress (UCMS and treated with α5-PAM acutely (30 minutes prior to assessing behavior or chronically before being assessed behaviorally. Results: Acute and chronic α5-PAM treatments produce a pattern of decreased stress-induced behaviors (denoted as behavioral emotionality across various tests in female, but not in male mice. Behavioral Z-scores calculated across a panel of tests designed to best model the range and heterogeneity of human symptomatology confirmed that acute and chronic α5-PAM treatments consistently produce significant decreases in behavioral emotionality in several independent cohorts of females. The behavioral responses to α5-PAM could not be completely accounted for by differences in drug brain disposition between female and male mice. In mice exposed to UCMS, expression of the Gabra5 gene was increased in the frontal cortex after acute treatment and in hippocampus after chronic treatment with α5-PAM in females only, and these expression changes correlated with behavioral emotionality. Conclusions: We showed that acute and chronic positive modulation of α5 subunit-containing GABAA receptors elicit anti-stress effects in a sex-dependent manner, suggesting novel therapeutic modalities.

  14. Notes on stochastic (bio)-logic gates: computing with allosteric cooperativity.

    Science.gov (United States)

    Agliari, Elena; Altavilla, Matteo; Barra, Adriano; Dello Schiavo, Lorenzo; Katz, Evgeny

    2015-05-15

    Recent experimental breakthroughs have finally allowed to implement in-vitro reaction kinetics (the so called enzyme based logic) which code for two-inputs logic gates and mimic the stochastic AND (and NAND) as well as the stochastic OR (and NOR). This accomplishment, together with the already-known single-input gates (performing as YES and NOT), provides a logic base and paves the way to the development of powerful biotechnological devices. However, as biochemical systems are always affected by the presence of noise (e.g. thermal), standard logic is not the correct theoretical reference framework, rather we show that statistical mechanics can work for this scope: here we formulate a complete statistical mechanical description of the Monod-Wyman-Changeaux allosteric model for both single and double ligand systems, with the purpose of exploring their practical capabilities to express noisy logical operators and/or perform stochastic logical operations. Mixing statistical mechanics with logics, and testing quantitatively the resulting findings on the available biochemical data, we successfully revise the concept of cooperativity (and anti-cooperativity) for allosteric systems, with particular emphasis on its computational capabilities, the related ranges and scaling of the involved parameters and its differences with classical cooperativity (and anti-cooperativity).

  15. Enzyme activity and allosteric characteristics of gamma-irradiated solid aspartate transcarbamylase

    International Nuclear Information System (INIS)

    Bigler, W.N.; Tolbert, B.M.

    1977-01-01

    Aspartate transcarbamylase purified from E. coli was lyophilized, irradiated in vacuo with γ radiation from a cesium-137 source, redissolved in buffer under a nitrogen atmosphere, and assayed for enzyme activity. Lyophilized and redissolved enzyme had normal catalytic and allosteric kinetic characteristics. The average D 37 observed with saturating substrate, 25 mM aspartate, was 4.1 Mrad. With less than saturating substrate, 5 mM aspartate, the activity increases from zero to 1.6 Mrad and then decreases with a D 37 of 7.2 Mrad. Inclusion of 1 mM CTP, an allosteric inhibitor, in the 5 mM aspartate assays results in a more pronounced maximum in the activity curve occurring at slightly higher dose, 2.2 Mrad. Inhibitability by CTP has a D 37 of 2.3 Mrad with doses below the activity maximum. Enzyme lyophilized in the presence of 1 mM CTP has a D 37 of 2.9 Mrad. ATCase activity changes caused by irradiation of lyophylized bacteria were qualitatively like the changes observed in the detailed studies with the purified enzyme. Apparent radiation sensitivities of ATCase in lyophilized bacteria were observed to vary with the technique used to disrupt the resuspended bacteria

  16. Engineering integrated digital circuits with allosteric ribozymes for scaling up molecular computation and diagnostics.

    Science.gov (United States)

    Penchovsky, Robert

    2012-10-19

    Here we describe molecular implementations of integrated digital circuits, including a three-input AND logic gate, a two-input multiplexer, and 1-to-2 decoder using allosteric ribozymes. Furthermore, we demonstrate a multiplexer-decoder circuit. The ribozymes are designed to seek-and-destroy specific RNAs with a certain length by a fully computerized procedure. The algorithm can accurately predict one base substitution that alters the ribozyme's logic function. The ability to sense the length of RNA molecules enables single ribozymes to be used as platforms for multiple interactions. These ribozymes can work as integrated circuits with the functionality of up to five logic gates. The ribozyme design is universal since the allosteric and substrate domains can be altered to sense different RNAs. In addition, the ribozymes can specifically cleave RNA molecules with triplet-repeat expansions observed in genetic disorders such as oculopharyngeal muscular dystrophy. Therefore, the designer ribozymes can be employed for scaling up computing and diagnostic networks in the fields of molecular computing and diagnostics and RNA synthetic biology.

  17. Structural Insights into the Allosteric Operation of the Lon AAA+ Protease.

    Science.gov (United States)

    Lin, Chien-Chu; Su, Shih-Chieh; Su, Ming-Yuan; Liang, Pi-Hui; Feng, Chia-Cheng; Wu, Shih-Hsiung; Chang, Chung-I

    2016-05-03

    The Lon AAA+ protease (LonA) is an evolutionarily conserved protease that couples the ATPase cycle into motion to drive substrate translocation and degradation. A hallmark feature shared by AAA+ proteases is the stimulation of ATPase activity by substrates. Here we report the structure of LonA bound to three ADPs, revealing the first AAA+ protease assembly where the six protomers are arranged alternately in nucleotide-free and bound states. Nucleotide binding induces large coordinated movements of conserved pore loops from two pairs of three non-adjacent protomers and shuttling of the proteolytic groove between the ATPase site and a previously unknown Arg paddle. Structural and biochemical evidence supports the roles of the substrate-bound proteolytic groove in allosteric stimulation of ATPase activity and the conserved Arg paddle in driving substrate degradation. Altogether, this work provides a molecular framework for understanding how ATP-dependent chemomechanical movements drive allosteric processes for substrate degradation in a major protein-destruction machine. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Interdomain allosteric regulation of Polo kinase by Aurora B and Map205 is required for cytokinesis

    Science.gov (United States)

    Kachaner, David; Pinson, Xavier; El Kadhi, Khaled Ben; Normandin, Karine; Talje, Lama; Lavoie, Hugo; Lépine, Guillaume; Carréno, Sébastien; Kwok, Benjamin H.; Hickson, Gilles R.

    2014-01-01

    Drosophila melanogaster Polo and its human orthologue Polo-like kinase 1 fulfill essential roles during cell division. Members of the Polo-like kinase (Plk) family contain an N-terminal kinase domain (KD) and a C-terminal Polo-Box domain (PBD), which mediates protein interactions. How Plks are regulated in cytokinesis is poorly understood. Here we show that phosphorylation of Polo by Aurora B is required for cytokinesis. This phosphorylation in the activation loop of the KD promotes the dissociation of Polo from the PBD-bound microtubule-associated protein Map205, which acts as an allosteric inhibitor of Polo kinase activity. This mechanism allows the release of active Polo from microtubules of the central spindle and its recruitment to the site of cytokinesis. Failure in Polo phosphorylation results in both early and late cytokinesis defects. Importantly, the antagonistic regulation of Polo by Aurora B and Map205 in cytokinesis reveals that interdomain allosteric mechanisms can play important roles in controlling the cellular functions of Plks. PMID:25332165

  19. Multilocation trial of potential selected mutant lines of groundnut (arachis hypogaea) at 3 location in Peninsular Malaysia

    International Nuclear Information System (INIS)

    Abdul Rahim Harun; Rusli Ibrahim; Khairuddin Abdul Rahim; Shuhaimi Shamsuddin

    2002-01-01

    Two fixed mutant lines of groundnut derived from cultivar Matjan were selected for their yield potential at M 1 0 generation. Multilocation trial of these mutants (MJ40/42 and MJ20/165-5) was carried out to evaluate genotype stability at different climate and soil types in Peninsular Malaysia. The mutant lines were planted and compared with their parent (Matjan) and control variety (MKT1). The identified locations were in Taiping (Perak), Machang (Kelantan), and Air Hitam (Johor). The soils at the locations were of the Serdang, Bungor and Rengam series, respectively. The trial was carried out simultaneously in the same year at each location. Mutant MJ20/165-5 showed stable performance at all location compared to other genotypes tested. Its yield was higher than the parent in Kelantan and Johor trial and showed similar performance in Perak. This mutant also showed better yield performance than the control varieties in the Kelantan trial. Meanwhile, mutant line MJ40/42 gave better yield in Kelantan and Johor but did not perform well in Perak as compared to its parent and control varieties. (Author)

  20. Herbal Therapies for Type 2 Diabetes Mellitus: Chemistry, Biology, and Potential Application of Selected Plants and Compounds

    Directory of Open Access Journals (Sweden)

    Cicero L. T. Chang

    2013-01-01

    Full Text Available Diabetes mellitus has been recognized since antiquity. It currently affects as many as 285 million people worldwide and results in heavy personal and national economic burdens. Considerable progress has been made in orthodox antidiabetic drugs. However, new remedies are still in great demand because of the limited efficacy and undesirable side effects of current orthodox drugs. Nature is an extraordinary source of antidiabetic medicines. To date, more than 1200 flowering plants have been claimed to have antidiabetic properties. Among them, one-third have been scientifically studied and documented in around 460 publications. In this review, we select and discuss blood glucose-lowering medicinal herbs that have the ability to modulate one or more of the pathways that regulate insulin resistance, β-cell function, GLP-1 homeostasis, and glucose (reabsorption. Emphasis is placed on phytochemistry, anti-diabetic bioactivities, and likely mechanism(s. Recent progress in the understanding of the biological actions, mechanisms, and therapeutic potential of compounds and extracts of plant origin in type 2 diabetes is summarized. This review provides a source of up-to-date information for further basic and clinical research into herbal therapy for type 2 diabetes. Emerging views on therapeutic strategies for type 2 diabetes are also discussed.

  1. Piroxicam inhibits NMDA receptor-mediated excitotoxicity through allosteric inhibition of the GluN2B subunit: an in silico study elucidating a novel mechanism of action of the drug.

    Science.gov (United States)

    Mazumder, Muhammed Khairujjaman; Borah, Anupom

    2014-12-01

    Hyperactivation of GluN2B subunit containing N-methyl-d-aspartate receptors (NMDARs) significantly contributes to the development of several neurodegenerative diseases through a process called excitotoxicity. NMDARs are voltage-gated Ca2+ channels which when activated lead to excessive influx of Ca2+ into neurons thereby exacerbating several calcium-dependent pathways that cause oxidative stress and apoptosis. Several drugs are presently in use to counter the NMDAR-mediated excitotoxic events among which Ifenprodil and its derivatives are GluN2B selective allosteric antagonists. Certain non-steroidal anti-inflammatory drugs (NSAIDs) have also been reported to inhibit NMDARs and the resultant pathologies. Meanwhile, Piroxicam, which is a NSAID, has been reported to be protective in cerebral ischemia-induced neurodegeneration through various pathways. Since Piroxicam has more number of interacting groups as compared to other NSAIDs and also has structural similarities with Ifenprodil, we thought it prudent that Piroxicam may inhibit NMDARs similar to Ifenprodil. By using molecular docking as a tool, we validated the hypothesis and hereby report for the first time that Piroxicam can inhibit GluN2B containing NMDARs through allosteric mode similar to the well known selective antagonist--Ifenprodil; and thus can be a therapeutic drug for the prevention of excitotoxic neurodegeneration. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Radiosynthesis of [11C]SB-705498, a selective transient receptor potential Vanilloid 1 (TRPV1) receptor antagonist

    International Nuclear Information System (INIS)

    Dolle, F.; Bramoulle, Y.; Deverre, J.R.; Bottlaender, M.; Passchier, J.

    2011-01-01

    Complete text of publication follows: Objectives: The transient receptor potential vanilloid 1 (TRPV1) receptor, previously known as the vanilloid receptor 1 (VR1), is a non-selective cation channel activated by a range of noxious stimuli and highly expressed in nociceptive fibres. TRPV1 receptor is involved in pain and sensitisation associated with tissue injury and inflammation and therefore represents a pharmacological target of choice for the development of novel therapeutic agents for the treatment of chronic pain, migraine and gastrointestinal disorders. Among a novel series of pyrrolidinyl ureas recently discovered by GSK, SB-705498 (1, namely 1-(2-bromophenyl)-3-[(R)-1-(5- trifluoromethylpyridin-2-yl)pyrrolidin-3-yl]urea) has been identified as a potent, selective and orally bioavailable TRPV1 antagonist and considered for positron emission tomography studies. SB-705498 (1) has therefore been isotopically labelled with the short-lived positron-emitter carbon-11 (t1/2: 20.38 min) at its urea site using [ 11 C]phosgene in a one-pot two-step process, via the intermediate preparation of 2-bromophenyl [ 11 C]isocyanate. Methods: Carbon-11-labeling of SB-705498 comprises: (A) Trapping of [ 11 C]phosgene (radio-synthesized from cyclotron-produced [ 11 C]methane via [ 11 C]carbon tetrachloride using minor modifications of published processes) at room temperature for 1 to 2 minutes in 250 μL of acetonitrile containing 0.6 μmole of 2-bromoaniline (2) giving 2-bromophenyl [ 11 C]isocyanate ([ 11 C]-3), followed by (B) addition of an excess of chiral (R)-1-(5- trifluoromethylpyridin-2-yl)pyrrolidin-3-ylamine (4, 40 μmoles in 500 μL of acetonitrile) as the second amine and reaction at room temperature for an additional one minute giving the desired urea derivative ([ 11 C]SB-705498 ([ 11 C]-1)), (C) dilution of the crude reaction mixture with water (500 μL) containing 4% (v:v) of DEA, injection and purification on a semi-preparative Waters Symmetry R C18 HPLC

  3. The Low-Affinity Binding of Second Generation Radiotracers Targeting TSPO is Associated with a Unique Allosteric Binding Site

    Czech Academy of Sciences Publication Activity Database

    Rojas, C.; Stathis, M.; Coughlin, J. M.; Pomper, M.; Slusher, Barbara S.

    2018-01-01

    Roč. 13, č. 1 (2018), s. 1-5 ISSN 1557-1890 Institutional support: RVO:61388963 Keywords : translocator protein 18KDa (TSPO) * allosteric modulation * residence time Subject RIV: CC - Organic Chemistry OBOR OECD: Organic chemistry Impact factor: 3.339, year: 2016

  4. Positive allosteric modulation of the human metabotropic glutamate receptor 4 (hmGluR4) by SIB-1893 and MPEP

    DEFF Research Database (Denmark)

    Mathiesen, Jesper Mosolff; Svendsen, Nannette; Bräuner-Osborne, Hans

    2003-01-01

    We have identified 2-methyl-6-(2-phenylethenyl)pyridine (SIB-1893) and 2-methyl-6-phenylethynyl pyridine hydrochloride (MPEP) as positive allosteric modulators for the hmGluR4. SIB-1893 and MPEP enhanced the potency and efficacy of L-2-amino-4-phophonobutyrate (L-AP4) in guanosine 5'-O-(3-[(35)S...

  5. A3 Adenosine Receptor Allosteric Modulator Induces an Anti-Inflammatory Effect: In Vivo Studies and Molecular Mechanism of Action

    Directory of Open Access Journals (Sweden)

    Shira Cohen

    2014-01-01

    Full Text Available The A3 adenosine receptor (A3AR is overexpressed in inflammatory cells and in the peripheral blood mononuclear cells of individuals with inflammatory conditions. Agonists to the A3AR are known to induce specific anti-inflammatory effects upon chronic treatment. LUF6000 is an allosteric compound known to modulate the A3AR and render the endogenous ligand adenosine to bind to the receptor with higher affinity. The advantage of allosteric modulators is their capability to target specifically areas where adenosine levels are increased such as inflammatory and tumor sites, whereas normal body cells and tissues are refractory to the allosteric modulators due to low adenosine levels. LUF6000 administration induced anti-inflammatory effect in 3 experimental animal models of rat adjuvant induced arthritis, monoiodoacetate induced osteoarthritis, and concanavalin A induced liver inflammation in mice. The molecular mechanism of action points to deregulation of signaling proteins including PI3K, IKK, IκB, Jak-2, and STAT-1, resulting in decreased levels of NF-κB, known to mediate inflammatory effects. Moreover, LUF6000 induced a slight stimulatory effect on the number of normal white blood cells and neutrophils. The anti-inflammatory effect of LUF6000, mechanism of action, and the differential effects on inflammatory and normal cells position this allosteric modulator as an attractive and unique drug candidate.

  6. A large-scale allosteric transition in cytochrome P450 3A4 revealed by luminescence resonance energy transfer (LRET.

    Directory of Open Access Journals (Sweden)

    Elena V Sineva

    Full Text Available Effector-induced allosteric transitions in cytochrome P450 3A4 (CYP3A4 were investigated by luminescence resonance energy transfer (LRET between two SH-reactive probes attached to various pairs of distantly located cysteine residues, namely the double-cysteine mutants CYP3A4(C64/C468, CYP3A4(C377/C468 and CYP3A4(C64/C121. Successive equimolar labeling of these proteins with the phosphorescent probe erythrosine iodoacetamide (donor and the near-infrared fluorophore DY-731 maleimide (acceptor allowed us to establish donor/acceptor pairs sensitive to conformational motions. The interactions of all three double-labeled mutants with the allosteric activators α-naphthoflavone and testosterone resulted in an increase in the distance between the probes. A similar effect was elicited by cholesterol. These changes in distance vary from 1.3 to 8.5 Å, depending on the position of the donor/acceptor pair and the nature of the effector. In contrast, the changes in the interprobe distance caused by such substrates as bromocriptine or 1-pyrenebutanol were only marginal. Our results provide a decisive support to the paradigm of allosteric modulation of CYP3A4 and indicate that the conformational transition caused by allosteric effectors increases the spatial separation between the beta-domain of the enzyme (bearing residues Cys64 and Cys377 and the alpha-domain, where Cys121 and Cys468 are located.

  7. Thermodynamics and structural analysis of positive allosteric modulation of the ionotropic glutamate receptor GluA2

    DEFF Research Database (Denmark)

    Krintel, Christian; Frydenvang, Karla; Olsen, Lars

    2012-01-01

    Positive allosteric modulators of the ionotropic glutamate receptor-2 (GluA2) are promising compounds for the treatment of cognitive disorders, e.g. Alzheimer's disease. These modulators bind within the dimer interface of the ligand-binding domain and stabilize the agonist-bound conformation slow...

  8. Surface dynamics in allosteric regulation of protein-protein interactions: modulation of calmodulin functions by Ca2+.

    Directory of Open Access Journals (Sweden)

    Yosef Y Kuttner

    2013-04-01

    Full Text Available Knowledge of the structural basis of protein-protein interactions (PPI is of fundamental importance for understanding the organization and functioning of biological networks and advancing the design of therapeutics which target PPI. Allosteric modulators play an important role in regulating such interactions by binding at site(s orthogonal to the complex interface and altering the protein's propensity for complex formation. In this work, we apply an approach recently developed by us for analyzing protein surfaces based on steered molecular dynamics simulation (SMD to the study of the dynamic properties of functionally distinct conformations of a model protein, calmodulin (CaM, whose ability to interact with target proteins is regulated by the presence of the allosteric modulator Ca(2+. Calmodulin is a regulatory protein that acts as an intracellular Ca(2+ sensor to control a wide variety of cellular processes. We demonstrate that SMD analysis is capable of pinpointing CaM surfaces implicated in the recognition of both the allosteric modulator Ca(2+ and target proteins. Our analysis of changes in the dynamic properties of the CaM backbone elicited by Ca(2+ binding yielded new insights into the molecular mechanism of allosteric regulation of CaM-target interactions.

  9. Positive allosteric modulation of GABA-A receptors reduces capsaicin-induced primary and secondary hypersensitivity in rats

    DEFF Research Database (Denmark)

    Hansen, Rikke Rie; Erichsen, Helle K; Brown, David T

    2012-01-01

    GABA-A receptor positive allosteric modulators (PAMs) mediate robust analgesia in animal models of pathological pain, in part via enhancing injury-induced loss of GABA-A-α2 and -α3 receptor function within the spinal cord. As yet, a lack of clinically suitable tool compounds has prevented this co...

  10. Allosteric inactivation of a trypsin-like serine protease by an antibody binding to the 37- and 70-loops

    DEFF Research Database (Denmark)

    Kromann-Hansen, Tobias; Lund, Ida K; Liu, Zhuo

    2013-01-01

    for elucidating fundamental allosteric mechanisms. The monoclonal antibody mU1 has previously been shown to be able to inhibit the function of murine urokinase-type plasminogen activator in vivo. We have now mapped the epitope of mU1 to the catalytic domain's 37- and 70-loops, situated about 20 Å from the S1...

  11. Analgesic effect of ADX71441, a positive allosteric modulator (PAM) of GABAB receptor in a rat model of bladder pain.

    Science.gov (United States)

    Kannampalli, Pradeep; Poli, Sonia-Maria; Boléa, Christelle; Sengupta, Jyoti N

    2017-11-01

    Therapeutic use of GABA B receptor agonists for conditions like chronic abdominal pain, overactive bladder (OAB) and gastroesophageal reflux disease (GERD) is severely affected by poor blood-brain barrier permeability and potential side effects. ADX71441 is a novel positive allosteric modulator (PAM) of the GABA B receptor that has shown encouraging results in pre-clinical models of anxiety, pain, OAB and alcohol addiction. The present study investigates the analgesic effect of ADX71441 to noxious stimulation of the urinary bladder and colon in rats. In female Sprague-Dawley rats, systemic (i.p), but not intrathecal (i.t), administration of ADX71441 produced a dose-dependent decrease in viscero-motor response (VMR) to graded urinary bladder distension (UBD) and colorectal distension (CRD). Additionally, intra-cerebroventricular (i.c.v.) administration of ADX71441 significantly decreased the VMRs to noxious UBD. In electrophysiology experiments, the drug did not attenuate the responses of UBD-sensitive pelvic nerve afferent (PNA) fibers to UBD. In contrast, ADX71441 significantly decreased the responses of UBD-responsive lumbosacral (LS) spinal neurons in spinal intact rats. However, ADX71441 did not attenuate these LS neurons in cervical (C1-C2) spinal transected rats. During cystometrogram (CMG) recordings, ADX71441 (i.p.) significantly decreased the VMR to slow infusion without affecting the number of voiding contraction. These results indicate that ADX71441 modulate bladder nociception via its effect at the supra-spinal sites without affecting the normal bladder motility and micturition reflex in naïve adult rats. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Studies of the in vitro anticancer, antimicrobial and antioxidant potentials of selected Yemeni medicinal plants from the island Soqotra

    Directory of Open Access Journals (Sweden)

    Bednarski Patrick J

    2009-03-01

    at low concentrations (more than 80% at 50 μg/ml. Conclusion Our results show once again that medicinal plants can be promising sources of natural products with potential anticancer, antimicrobial and antioxidative activity. The results will guide the selection of some plant species for further pharmacological and phytochemical investigations.

  13. Selection of lactic acid bacteria from Brazilian kefir grains for potential use as starter or probiotic cultures.

    Science.gov (United States)

    Zanirati, Débora Ferreira; Abatemarco, Mário; Sandes, Sávio Henrique de Cicco; Nicoli, Jacques Robert; Nunes, Álvaro Cantini; Neumann, Elisabeth

    2015-04-01

    Brazilian kefir is a homemade fermented beverage that is obtained by incubating milk or a brown sugar solution with kefir grains that contribute their different microbiological compositions. It is highly important to isolate and characterize microorganisms from Brazilian kefir grains to obtain starter cultures for the industrial production of a standardized commercial kefir. Thus, the present study aimed to isolate lactic acid bacteria from eight kefir grains that were propagated in milk or sugar solutions from five different locations in Brazil and to select Lactobacillus isolates based on desirable in vitro probiotic properties. One hundred eight isolates from both substrates were identified by amplified ribosomal DNA restriction analysis and/or 16S rRNA gene sequencing and were determined to belong to the following 11 species from the genera: Lactococcus, Leuconostoc, Lactobacillus (L.), and Oenococcus. Leuconostoc mesenteroides, Lactobacillus kefiri, and Lactobacillus kefiranofaciens were isolated only from milk grains, whereas Lactobacillus perolens, Lactobacillus parafarraginis, Lactobacillus diolivorans, and Oenococcus oeni were isolated exclusively from sugar water grains. When the microbial compositions of four kefir grains were evaluated with culture-independent analyses, L. kefiranofaciens was observed to predominant in milk grains, whereas Lactobacillus hilgardii was most abundant in sugar water kefir. Unfortunately, L. hilgardii was not isolated from any grain, although this bacteria was detected with a culture-independent methodology. Fifty-two isolated Lactobacilli were tested for gastric juice and bile salt tolerance, antagonism against pathogens, antimicrobial resistance, and surface hydrophobicity. Three Lactobacillus strains (L. kefiranofaciens 8U, L. diolivorans 1Z, and Lactobacillus casei 17U) could be classified as potential probiotics. In conclusion, several lactic acid bacteria that could be used in combination with yeasts as starter

  14. Site selection in global clinical trials in patients hospitalized for heart failure: perceived problems and potential solutions.

    Science.gov (United States)

    Gheorghiade, Mihai; Vaduganathan, Muthiah; Greene, Stephen J; Mentz, Robert J; Adams, Kirkwood F; Anker, Stefan D; Arnold, Malcolm; Baschiera, Fabio; Cleland, John G F; Cotter, Gadi; Fonarow, Gregg C; Giordano, Christopher; Metra, Marco; Misselwitz, Frank; Mühlhofer, Eva; Nodari, Savina; Frank Peacock, W; Pieske, Burkert M; Sabbah, Hani N; Sato, Naoki; Shah, Monica R; Stockbridge, Norman L; Teerlink, John R; van Veldhuisen, Dirk J; Zalewski, Andrew; Zannad, Faiez; Butler, Javed

    2014-03-01

    There are over 1 million hospitalizations for heart failure (HF) annually in the United States alone, and a similar number has been reported in Europe. Recent clinical trials investigating novel therapies in patients with hospitalized HF (HHF) have been negative, and the post-discharge event rate remains unacceptably high. The lack of success with HHF trials stem from problems with understanding the study drug, matching the drug to the appropriate HF subgroup, and study execution. Related to the concept of study execution is the importance of including appropriate study sites in HHF trials. Often overlooked issues include consideration of the geographic region and the number of patients enrolled at each study center. Marked differences in baseline patient co-morbidities, serum biomarkers, treatment utilization and outcomes have been demonstrated across geographic regions. Furthermore, patients from sites with low recruitment may have worse outcomes compared to sites with higher enrollment patterns. Consequently, sites with poor trial enrollment may influence key patient end points and likely do not justify the costs of site training and maintenance. Accordingly, there is an unmet need to develop strategies to identify the right study sites that have acceptable patient quantity and quality. Potential approaches include, but are not limited to, establishing a pre-trial registry, developing site performance metrics, identifying a local regionally involved leader and bolstering recruitment incentives. This manuscript summarizes the roundtable discussion hosted by the Food and Drug Administration between members of academia, the National Institutes of Health, industry partners, contract research organizations and academic research organizations on the importance of selecting optimal sites for successful trials in HHF.

  15. Evaluation of long-range transport potential of selected brominated flame retardants with measured 1-octanol-air partition coefficients

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Hyun Jeong; Kwon, Jung Hwan [Div. of Environmental Science and Ecological Engineering, Korea University, Seoul (Korea, Republic of)

    2016-10-15

    Various alternative flame retardants are used in many countries since polybrominated diphenyl ethers (PBDEs) were classified as persistent organic pollutants (POPs). However, difficulties in the evaluation of the long-range transport potential (LRTP) of the alternatives are related to the lack of information on their physicochemical properties, which govern their environmental fates and transport. Based on the simulation of LRTP using OECD P{sub OV} and LRTP Screening Tool, five alternative brominated flame retardants (BFRs) (hexabromobenzene [HBB], 2,3,4,5,6-pentabromotoluene [PBT], 2,3,4,5,6-pentabromoethylbenzene [PBEB], 2-ethylhexyl 2,3,4,5-tetrabromobenzoate [TBB], and 1,2,4,5-tetrabromo-3,6-dimethylbenzene [TBX]), and 3 PBDEs (BDE-28, BDE-47, and BDE-99) were chosen to perform a refined assessment. This was done using an experimentally measured 1-octanol–air partition coefficient (K{sub OA}) for the calculation of the air–water partition coefficient (K{sub AW}) required for the model. The four selected alternative BFRs (HBB, PBT, PBEB, TBX) have K{sub OA} values close to the in silico estimation used in the screening evaluation. On the other hand, the measured K{sub OA} value for TBB was two orders of magnitude lower than the estimated value used in the screening simulation. The refined simulation showed that characteristic travel distance (CTD) and transfer efficiency (TE) for HBB, PBT, PBEB, and TBX were greater than those for BDE-28, whereas CTD and TE for TBB were lower than those for BDE-28. This suggested that TBB has a lower LRTP than BDE-28, considering the refined partition coefficients.

  16. The Sequential Self-Selection Auction Mechanism for Selective Reenlistment Bonuses: Potential Cost Savings to the U.S. Marine Corps

    Science.gov (United States)

    2007-06-01

    information than another party, such as in the market for used cars. Mankiw , in his book, “The Principles of Economics ,” defines adverse selection as...Options,” Power Point presentation e-mailed to the author, 18 May 2007, 1-9. 37 Ibid., 2. 38 Gregory N. Mankiw , Principles of Economics , Third...the Internet.” The American Economic Review. December 1999. 89 No. 5. 1066- 1078. Mankiw , Gregory N. Principles of Economics , Third Edition (Mason

  17. Heat shock protein 70 inhibitors. 2. 2,5'-thiodipyrimidines, 5-(phenylthio)pyrimidines, 2-(pyridin-3-ylthio)pyrimidines, and 3-(phenylthio)pyridines as reversible binders to an allosteric site on heat shock protein 70.

    Science.gov (United States)

    Taldone, Tony; Kang, Yanlong; Patel, Hardik J; Patel, Maulik R; Patel, Pallav D; Rodina, Anna; Patel, Yogita; Gozman, Alexander; Maharaj, Ronnie; Clement, Cristina C; Lu, Alvin; Young, Jason C; Chiosis, Gabriela

    2014-02-27

    The discovery and development of heat shock protein 70 (Hsp70) inhibitors is currently a hot topic in cancer. In the preceding paper in this issue ( 10.1021/jm401551n ), we have described structure-activity relationship studies in the first Hsp70 inhibitor class rationally designed to bind to a novel allosteric pocket located in the N-terminal domain of the protein. These ligands contained an acrylamide to take advantage of an active cysteine embedded in the allosteric pocket and acted as covalent protein modifiers upon binding. Here, we perform chemical modifications around the irreversible inhibitor scaffold to demonstrate that covalent modification is not a requirement for activity within this class of compounds. The study identifies derivative 27c, which mimics the biological effects of the irreversible inhibitors at comparable concentrations. Collectively, the back-to-back manuscripts describe the first pharmacophores that favorably and selectively interact with a never explored pocket in Hsp70 and provide a novel blueprint for a cancer-oriented development of Hsp70-directed ligands.

  18. Potentiation of amygdala AMPA receptor activity selectively promotes escalated alcohol self-administration in a CaMKII-dependent manner.

    Science.gov (United States)

    Cannady, Reginald; Fisher, Kristen R; Graham, Caitlin; Crayle, Jesse; Besheer, Joyce; Hodge, Clyde W

    2017-05-01

    Growing evidence indicates that drugs of abuse gain control over the individual by usurping glutamate-linked mechanisms of neuroplasticity in reward-related brain regions. Accordingly, we have shown that glutamate α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) activity in the amygdala is required for the positive reinforcing effects of alcohol, which underlie the initial stages of addiction. It is unknown, however, if enhanced AMPAR activity in the amygdala facilitates alcohol self-administration, which is a kernel premise of glutamate hypotheses of addiction. Here, we show that low-dose alcohol (0.6 g/kg/30 minutes) self-administration increases phosphorylation (activation) of AMPAR subtype GluA1 S831 (pGluA1 S831) in the central amygdala (CeA), basolateral amygdala and nucleus accumbens core (AcbC) of selectively bred alcohol-preferring P-rats as compared with behavior-matched (non-drug) sucrose controls. The functional role of enhanced AMPAR activity was assessed via site-specific infusion of the AMPAR positive modulator, aniracetam, in the CeA and AcbC prior to alcohol self-administration. Intra-CeA aniracetam increased alcohol-reinforced but not sucrose-reinforced responding and was ineffective following intra-AcbC infusion. Because GluA1 S831 is a Ca2+/calmodulin-dependent protein kinase II (CaMKII) substrate, we sought to determine if AMPAR regulation of enhanced alcohol self-administration is dependent on CaMKII activity. Intra-CeA infusion of the cell-permeable CaMKII peptide inhibitor myristolated autocamtide-2-related inhibitory peptide (m-AIP) dose-dependently reduced alcohol self-administration. A subthreshold dose of m-AIP also blocked the aniracetam-induced escalation of alcohol self-administration, demonstrating that AMPAR-mediated potentiation of alcohol reinforcement requires CaMKII activity in the amygdala. Enhanced activity of plasticity-linked AMPAR-CaMKII signaling in the amygdala may promote escalated alcohol use

  19. Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol

    DEFF Research Database (Denmark)

    Manna, Moutusi; Niemelä, Miia; Tynkkynen, Joona

    2016-01-01

    ) - a prototypical G protein-coupled receptor - is modulated by cholesterol in an allosteric fashion. Extensive atomistic simulations show that cholesterol regulates b2AR by limiting its conformational variability. The mechanism of action is based on the binding of cholesterol at specific high-affinity sites located...... near the transmembrane helices 5-7 of the receptor. The alternative mechanism, where the β2AR conformation would be modulated by membrane-mediated interactions, plays only a minor role. Cholesterol analogues also bind to cholesterol binding sites and impede the structural flexibility of β2AR, however...... cholesterol generates the strongest effect. The results highlight the capacity of lipids to regulate the conformation of membrane receptors through specific interactions....

  20. Evidence for a Common Mechanism of SIRT1 Regulation by Allosteric Activators

    Science.gov (United States)

    Hubbard, Basil P.; Gomes, Ana P.; Dai, Han; Li, Jun; Case, April W.; Considine, Thomas; Riera, Thomas V.; Lee, Jessica E.; Sook Yen, E; Lamming, Dudley W.; Pentelute, Bradley L.; Schuman, Eli R.; Stevens, Linda A.; Ling, Alvin J. Y.; Armour, Sean M.; Michan, Shaday; Zhao, Huizhen; Jiang, Yong; Sweitzer, Sharon M.; Blum, Charles A.; Disch, Jeremy S.; Ng, Pui Yee; Howitz, Konrad T.; Rolo, Anabela P.; Hamuro, Yoshitomo; Moss, Joel; Perni, Robert B.; Ellis, James L.; Vlasuk, George P.; Sinclair, David A.

    2013-01-01

    A molecule that treats multiple age-related diseases would have a major impact on global health and economics. The SIRT1 deacetylase has drawn attention in this regard as a target for drug design. Yet controversy exists around the mechanism of sirtuin-activating compounds (STACs). We found that specific hydrophobic motifs found in SIRT1 substrates such as PGC-1α and FOXO3a facilitate SIRT1 activation by STACs. A single amino acid in SIRT1, Glu230, located in a structured N-terminal domain, was critical for activation by all previously reported STAC scaffolds and a new class of chemically distinct activators. In primary cells reconstituted with activation-defective SIRT1, the metabolic effects of STACs were blocked. Thus, SIRT1 can be directly activated through an allosteric mechanism common to chemically diverse STACs. PMID:23471411

  1. Molecular kinetics. Ras activation by SOS: allosteric regulation by altered fluctuation dynamics.

    Science.gov (United States)

    Iversen, Lars; Tu, Hsiung-Lin; Lin, Wan-Chen; Christensen, Sune M; Abel, Steven M; Iwig, Jeff; Wu, Hung-Jen; Gureasko, Jodi; Rhodes, Christopher; Petit, Rebecca S; Hansen, Scott D; Thill, Peter; Yu, Cheng-Han; Stamou, Dimitrios; Chakraborty, Arup K; Kuriyan, John; Groves, Jay T

    2014-07-04

    Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras-guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average. Copyright © 2014, American Association for the Advancement of Science.

  2. Gs protein peptidomimetics as allosteric modulators of the β2-adrenergic receptor

    DEFF Research Database (Denmark)

    Boyhus, Lotte Emilie; Danielsen, Mia; Bengtson, Nina Smidt

    2018-01-01

    A series of Gs protein peptidomimetics were designed and synthesised based on the published X-ray crystal structure of the active state β2-Adrenergic receptor (β2AR) in complex with the Gs protein (PDB 3SN6). We hypothesised that such peptidomimetics may function as allosteric modulators...... that target the intracellular Gs protein binding site of the β2AR. Peptidomimetics were designed to mimic the 15 residue C-Terminal α-helix of the Gs protein and were pre-organised in a helical conformation by (i, i + 4)-stapling using copper catalysed azide alkyne cycloaddition. Linear and stapled...... be able to compete with the native Gs protein for the intracellular binding site to block ISO-induced cAMP formation, but are unable to stabilise an active-like receptor conformation....

  3. A2A adenosine receptor ligand binding and signalling is allosterically modulated by adenosine deaminase.

    Science.gov (United States)

    Gracia, Eduard; Pérez-Capote, Kamil; Moreno, Estefanía; Barkešová, Jana; Mallol, Josefa; Lluís, Carme; Franco, Rafael; Cortés, Antoni; Casadó, Vicent; Canela, Enric I

    2011-05-01

    A2ARs (adenosine A2A receptors) are highly enriched in the striatum, which is the main motor control CNS (central nervous system) area. BRET (bioluminescence resonance energy transfer) assays showed that A2AR homomers may act as cell-surface ADA (adenosine deaminase; EC 3.5.4.4)-binding proteins. ADA binding affected the quaternary structure of A2ARs present on the cell surface. ADA binding to adenosine A2ARs increased both agonist and antagonist affinity on ligand binding to striatal membranes where these proteins are co-expressed. ADA also increased receptor-mediated ERK1/2 (extracellular-signal-regulated kinase 1/2) phosphorylation. Collectively, the results of the present study show that ADA, apart from regulating the concentration of extracellular adenosine, may behave as an allosteric modulator that markedly enhances ligand affinity and receptor function. This powerful regulation may have implications for the physiology and pharmacology of neuronal A2ARs.

  4. Evidence for a common mechanism of SIRT1 regulation by allosteric activators.

    Science.gov (United States)

    Hubbard, Basil P; Gomes, Ana P; Dai, Han; Li, Jun; Case, April W; Considine, Thomas; Riera, Thomas V; Lee, Jessica E; E, Sook Yen; Lamming, Dudley W; Pentelute, Bradley L; Schuman, Eli R; Stevens, Linda A; Ling, Alvin J Y; Armour, Sean M; Michan, Shaday; Zhao, Huizhen; Jiang, Yong; Sweitzer, Sharon M; Blum, Charles A; Disch, Jeremy S; Ng, Pui Yee; Howitz, Konrad T; Rolo, Anabela P; Hamuro, Yoshitomo; Moss, Joel; Perni, Robert B; Ellis, James L; Vlasuk, George P; Sinclair, David A

    2013-03-08

    A molecule that treats multiple age-related diseases would have a major impact on global health and economics. The SIRT1 deacetylase has drawn attention in this regard as a target for drug design. Yet controversy exists around the mechanism of sirtuin-activating compounds (STACs). We found that specific hydrophobic motifs found in SIRT1 substrates such as PGC-1α and FOXO3a facilitate SIRT1 activation by STACs. A single amino acid in SIRT1, Glu(230), located in a structured N-terminal domain, was critical for activation by all previously reported STAC scaffolds and a new class of chemically distinct activators. In primary cells reconstituted with activation-defective SIRT1, the metabolic effects of STACs were blocked. Thus, SIRT1 can be directly activated through an allosteric mechanism common to chemically diverse STACs.

  5. Muscarinic Acetylcholine Receptor Subtypes as Potential Drug Targets for the Treatment of Schizophrenia, Drug Abuse and Parkinson's Disease

    DEFF Research Database (Denmark)

    Dencker, Ditte; Thomsen, Morgane; Wörtwein, Gitta

    2011-01-01

    's disease and drug abuse. Dopaminergic systems are regulated by cholinergic, especially muscarinic, input. Not surprisingly, increasing evidence implicates muscarinic acetylcholine receptor-mediated pathways as potential targets for the treatment of these disorders classically viewed as "dopamine based...... site. Such agents may lead to the development of novel classes of drugs useful for the treatment of psychosis, drug abuse and Parkinson's disease. The present review highlights recent studies carried out using muscarinic receptor knock-out mice and new subtype-selective allosteric ligands to assess...... the roles of M(1), M(4), and M(5) receptors in various central processes that are under strong dopaminergic control. The outcome of these studies opens new perspectives for the use of novel muscarinic drugs for several severe disorders of the CNS....

  6. Theoretical Analysis of Allosteric and Operator Binding for Cyclic-AMP Receptor Protein Mutants

    Science.gov (United States)

    Einav, Tal; Duque, Julia; Phillips, Rob

    2018-02-01

    Allosteric transcription factors undergo binding events both at their inducer binding sites as well as at distinct DNA binding domains, and it is often difficult to disentangle the structural and functional consequences of these two classes of interactions. In this work, we compare the ability of two statistical mechanical models - the Monod-Wyman-Changeux (MWC) and the Koshland-N\\'emethy-Filmer (KNF) models of protein conformational change - to characterize the multi-step activation mechanism of the broadly acting cyclic-AMP receptor protein (CRP). We first consider the allosteric transition resulting from cyclic-AMP binding to CRP, then analyze how CRP binds to its operator, and finally investigate the ability of CRP to activate gene expression. In light of these models, we examine data from a beautiful recent experiment that created a single-chain version of the CRP homodimer, thereby enabling each subunit to be mutated separately. Using this construct, six mutants were created using all possible combinations of the wild type subunit, a D53H mutant subunit, and an S62F mutant subunit. We demonstrate that both the MWC and KNF models can explain the behavior of all six mutants using a small, self-consistent set of parameters. In comparing the results, we find that the MWC model slightly outperforms the KNF model in the quality of its fits, but more importantly the parameters inferred by the MWC model are more in line with structural knowledge of CRP. In addition, we discuss how the conceptual framework developed here for CRP enables us to not merely analyze data retrospectively, but has the predictive power to determine how combinations of mutations will interact, how double mutants will behave, and how each construct would regulate gene expression.

  7. Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions.

    Directory of Open Access Journals (Sweden)

    Massimo Lai

    2015-01-01

    Full Text Available Calmodulin is a calcium-binding protein ubiquitous in eukaryotic cells, involved in numerous calcium-regulated biological phenomena, such as synaptic plasticity, muscle contraction, cell cycle, and circadian rhythms. It exibits a characteristic dumbell shape, with two globular domains (N- and C-terminal lobe joined by a linker region. Each lobe can take alternative conformations, affected by the binding of calcium and target proteins. Calmodulin displays considerable functional flexibility due to its capability to bind different targets, often in a tissue-specific fashion. In various specific physiological environments (e.g. skeletal muscle, neuron dendritic spines several targets compete for the same calmodulin pool, regulating its availability and affinity for calcium. In this work, we sought to understand the general principles underlying calmodulin modulation by different target proteins, and to account for simultaneous effects of multiple competing targets, thus enabling a more realistic simulation of calmodulin-dependent pathways. We built a mechanistic allosteric model of calmodulin, based on an hemiconcerted framework: each calmodulin lobe can exist in two conformations in thermodynamic equilibrium, with different affinities for calcium and different affinities for each target. Each lobe was allowed to switch conformation on its own. The model was parameterised and validated against experimental data from the literature. In spite of its simplicity, a two-state allosteric model was able to satisfactorily represent several sets of experiments, in particular the binding of calcium on intact and truncated calmodulin and the effect of different skMLCK peptides on calmodulin's saturation curve. The model can also be readily extended to include multiple targets. We show that some targets stabilise the low calcium affinity T state while others stabilise the high affinity R state. Most of the effects produced by calmodulin targets can be

  8. Computational redesign reveals allosteric mutation hotspots of organophosphate hydrolase that enhance organophosphate hydrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Jacob, Reed B. [Univ. of North Carolina, Chapel Hill, NC (United States); Ding, Feng [Clemson Univ., SC (United States); Ye, Dongmei [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ackerman, Eric [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Dokholyan, Nikolay V. [Univ. of North Carolina, Chapel Hill, NC (United States)

    2015-04-01

    Organophosphates are widely used for peaceful (agriculture) and military purposes (chemical warfare agents). The extraordinary toxicity of organophosphates and the risk of deployment, make it critical to develop means for their rapid and efficient deactivation. Organophosphate hydrolase (OPH) already plays an important role in organophosphate remediation, but is insufficient for therapeutic or prophylactic purposes primarily due to low substrate affinity. Current efforts focus on directly modifying the active site to differentiate substrate specificity and increase catalytic activity. Here, we present a novel strategy for enhancing the general catalytic efficiency of OPH through computational redesign of the residues that are allosterically coupled to the active site and validated our design by mutagenesis. Specifically, we identify five such hot-spot residues for allosteric regulation and assay these mutants for hydrolysis activity against paraoxon, a chemical-weapons simulant. A high percentage of the predicted mutants exhibit enhanced activity over wild-type (kcat =16.63 s-1), such as T199I/T54I (899.5 s-1) and C227V/T199I/T54I (848 s-1), while the Km remains relatively unchanged in our high-throughput cell-free expression system. Further computational studies of protein dynamics reveal four distinct distal regions coupled to the active site that display significant changes in conformation dynamics upon these identified mutations. These results validate a computational design method that is both efficient and easily adapted as a general procedure for enzymatic enhancement.

  9. Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Yi; Qin, Ling; Ortiz Zacarías, Natalia V.; de Vries, Henk; Han, Gye Won; Gustavsson, Martin; Dabros, Marta; Zhao, Chunxia; Cherney, Robert J.; Carter, Percy; Stamos, Dean; Abagyan, Ruben; Cherezov, Vadim; Stevens, Raymond C.; IJzerman, Adriaan P.; Heitman, Laura H.; Tebben, Andrew; Kufareva, Irina; Handel , Tracy M. (Vertex Pharm); (Leiden-MC); (USC); (BMS); (UCSD)

    2016-12-07

    CC chemokine receptor 2 (CCR2) is one of 19 members of the chemokine receptor subfamily of human class A G-protein-coupled receptors. CCR2 is expressed on monocytes, immature dendritic cells, and T-cell subpopulations, and mediates their migration towards endogenous CC chemokine ligands such as CCL2 (ref. 1). CCR2 and its ligands are implicated in numerous inflammatory and neurodegenerative diseases2 including atherosclerosis, multiple sclerosis, asthma, neuropathic pain, and diabetic nephropathy, as well as cancer3. These disease associations have motivated numerous preclinical studies and clinical trials4 (see http://www.clinicaltrials.gov) in search of therapies that target the CCR2–chemokine axis. To aid drug discovery efforts5, here we solve a structure of CCR2 in a ternary complex with an orthosteric (BMS-681 (ref. 6)) and allosteric (CCR2-RA-[R]7) antagonist. BMS-681 inhibits chemokine binding by occupying the orthosteric pocket of the receptor in a previously unseen binding mode. CCR2-RA-[R] binds in a novel, highly druggable pocket that is the most intracellular allosteric site observed in class A G-protein-coupled receptors so far; this site spatially overlaps the G-protein-binding site in homologous receptors. CCR2-RA-[R] inhibits CCR2 non-competitively by blocking activation-associated conformational changes and formation of the G-protein-binding interface. The conformational signature of the conserved microswitch residues observed in double-antagonist-bound CCR2 resembles the most inactive G-protein-coupled receptor structures solved so far. Like other protein–protein interactions, receptor–chemokine complexes are considered challenging therapeutic targets for small molecules, and the present structure suggests diverse pocket epitopes that can be exploited to overcome obstacles in drug design.

  10. Signaling-sensitive amino acids surround the allosteric ligand binding site of the thyrotropin receptor.

    Science.gov (United States)

    Kleinau, Gunnar; Haas, Ann-Karin; Neumann, Susanne; Worth, Catherine L; Hoyer, Inna; Furkert, Jens; Rutz, Claudia; Gershengorn, Marvin C; Schülein, Ralf; Krause, Gerd

    2010-07-01

    The thyrotropin receptor [thyroid-stimulating hormone receptor (TSHR)], a G-protein-coupled receptor (GPCR), is endogenously activated by thyrotropin, which binds to the extra