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Sample records for facilitative nucleobase transporter

  1. Functional identification of SLC43A3 as an equilibrative nucleobase transporter involved in purine salvage in mammals.

    PubMed

    Furukawa, Junji; Inoue, Katsuhisa; Maeda, Junya; Yasujima, Tomoya; Ohta, Kinya; Kanai, Yoshikatsu; Takada, Tappei; Matsuo, Hirotaka; Yuasa, Hiroaki

    2015-01-01

    The purine salvage pathway plays a major role in the nucleotide production, relying on the supply of nucleobases and nucleosides from extracellular sources. Although specific transporters have been suggested to be involved in facilitating their transport across the plasma membrane in mammals, those which are specifically responsible for utilization of extracellular nucleobases remain unknown. Here we present the molecular and functional characterization of SLC43A3, an orphan transporter belonging to an amino acid transporter family, as a purine-selective nucleobase transporter. SLC43A3 was highly expressed in the liver, where it was localized to the sinusoidal membrane of hepatocytes, and the lung. In addition, SLC43A3 expressed in MDCKII cells mediated the uptake of purine nucleobases such as adenine, guanine, and hypoxanthine without requiring typical driving ions such as Na(+) and H(+), but it did not mediate the uptake of nucleosides. When SLC43A3 was expressed in APRT/HPRT1-deficient A9 cells, adenine uptake was found to be low. However, it was markedly enhanced by the introduction of SLC43A3 with APRT. In HeLa cells, knock-down of SLC43A3 markedly decreased adenine uptake. These data suggest that SLC43A3 is a facilitative and purine-selective nucleobase transporter that mediates the cellular uptake of extracellular purine nucleobases in cooperation with salvage enzymes. PMID:26455426

  2. Functional identification of SLC43A3 as an equilibrative nucleobase transporter involved in purine salvage in mammals

    PubMed Central

    Furukawa, Junji; Inoue, Katsuhisa; Maeda, Junya; Yasujima, Tomoya; Ohta, Kinya; Kanai, Yoshikatsu; Takada, Tappei; Matsuo, Hirotaka; Yuasa, Hiroaki

    2015-01-01

    The purine salvage pathway plays a major role in the nucleotide production, relying on the supply of nucleobases and nucleosides from extracellular sources. Although specific transporters have been suggested to be involved in facilitating their transport across the plasma membrane in mammals, those which are specifically responsible for utilization of extracellular nucleobases remain unknown. Here we present the molecular and functional characterization of SLC43A3, an orphan transporter belonging to an amino acid transporter family, as a purine-selective nucleobase transporter. SLC43A3 was highly expressed in the liver, where it was localized to the sinusoidal membrane of hepatocytes, and the lung. In addition, SLC43A3 expressed in MDCKII cells mediated the uptake of purine nucleobases such as adenine, guanine, and hypoxanthine without requiring typical driving ions such as Na+ and H+, but it did not mediate the uptake of nucleosides. When SLC43A3 was expressed in APRT/HPRT1-deficient A9 cells, adenine uptake was found to be low. However, it was markedly enhanced by the introduction of SLC43A3 with APRT. In HeLa cells, knock-down of SLC43A3 markedly decreased adenine uptake. These data suggest that SLC43A3 is a facilitative and purine-selective nucleobase transporter that mediates the cellular uptake of extracellular purine nucleobases in cooperation with salvage enzymes. PMID:26455426

  3. Nucleobase and nucleoside transport and integration into plant metabolism

    PubMed Central

    Girke, Christopher; Daumann, Manuel; Niopek-Witz, Sandra; Möhlmann, Torsten

    2014-01-01

    Nucleotide metabolism is an essential process in all living organisms. Besides newly synthesized nucleotides, the recycling (salvage) of partially degraded nucleotides, i.e., nucleosides and nucleobases serves to keep the homeostasis of the nucleotide pool. Both types of metabolites are substrates of at least six families of transport proteins in Arabidopsis thaliana (Arabidopsis) with a total of 49 members. In the last years several members of such transport proteins have been analyzed allowing to present a more detailed picture of nucleoside and nucleobase transport and the physiological function of these processes. Besides functioning in nucleotide metabolism it turned out that individual members of the before named transporters exhibit the capacity to transport a wide range of different substrates including vitamins and phytohormones. The aim of this review is to summarize the current knowledge on nucleobase and nucleoside transport processes in plants and integrate this into nucleotide metabolism in general. Thereby, we will focus on those proteins which have been characterized at the biochemical level. PMID:25250038

  4. Oxidative stress modulates nucleobase transport in microvascular endothelial cells.

    PubMed

    Bone, Derek B J; Antic, Milica; Vilas, Gonzalo; Hammond, James R

    2014-09-01

    Purine nucleosides and nucleobases play key roles in the physiological response to vascular ischemia/reperfusion events. The intra- and extracellular concentrations of these compounds are controlled, in part, by equilibrative nucleoside transporter subtype 1 (ENT1; SLC29A1) and by equilibrative nucleobase transporter subtype 1 (ENBT1). These transporters are expressed at the membranes of numerous cell types including microvascular endothelial cells. We studied the impact of reactive oxygen species on the function of ENT1 and ENBT1 in primary (CMVEC) and immortalized (HMEC-1) human microvascular endothelial cells. Both cell types displayed similar transporter expression profiles, with the majority (>90%) of 2-chloro[(3)H]adenosine (nucleoside) uptake mediated by ENT1 and [(3)H]hypoxanthine (nucleobase) uptake mediated by ENBT1. An in vitro mineral oil-overlay model of ischemia/reperfusion had no effect on ENT1 function, but significantly reduced ENBT1 Vmax in both cell types. This decrease in transport function was mimicked by the intracellular superoxide generator menadione and could be reversed by the superoxide dismutase mimetic MnTMPyP. In contrast, neither the extracellular peroxide donor TBHP nor the extracellular peroxynitrite donor 3-morpholinosydnonimine (SIN-1) affected ENBT1-mediated [(3)H]hypoxanthine uptake. SIN-1 did, however, enhance ENT1-mediated 2-chloro[(3)H]adenosine uptake. Our data establish HMEC-1 as an appropriate model for study of purine transport in CMVEC. Additionally, these data suggest that the generation of intracellular superoxide in ischemia/reperfusion leads to the down-regulation of ENBT1 function. Modification of purine transport by oxidant stress may contribute to ischemia/reperfusion induced vascular damage and should be considered in the development of therapeutic strategies. PMID:24976360

  5. Identification and Functional Characterization of the First Nucleobase Transporter in Mammals

    PubMed Central

    Yamamoto, Syunsuke; Inoue, Katsuhisa; Murata, Tomoaki; Kamigaso, Syunsuke; Yasujima, Tomoya; Maeda, Jun-ya; Yoshida, Yukihiro; Ohta, Kin-ya; Yuasa, Hiroaki

    2010-01-01

    Nucleobases are important compounds that constitute nucleosides and nucleic acids. Although it has long been suggested that specific transporters are involved in their intestinal absorption and uptake in other tissues, none of their molecular entities have been identified in mammals to date. Here we describe identification of rat Slc23a4 as the first sodium-dependent nucleobase transporter (rSNBT1). The mRNA of rSNBT1 was expressed highly and only in the small intestine. When transiently expressed in HEK293 cells, rSNBT1 could transport uracil most efficiently. The transport of uracil mediated by rSNBT1 was sodium-dependent and saturable with a Michaelis constant of 21.2 μm. Thymine, guanine, hypoxanthine, and xanthine were also transported, but adenine was not. It was also suggested by studies of the inhibitory effect on rSNBT1-mediated uracil transport that several nucleobase analogs such as 5-fluorouracil are recognized by rSNBT1, but cytosine and nucleosides are not or only poorly recognized. Furthermore, rSNBT1 fused with green fluorescent protein was mainly localized at the apical membrane, when stably expressed in polarized Madin-Darby canine kidney II cells. These characteristics of rSNBT1 were almost fully in agreement with those of the carrier-mediated transport system involved in intestinal uracil uptake. Therefore, it is likely that rSNBT1 is its molecular entity or at least in part responsible for that. It was also found that the gene orthologous to the rSNBT1 gene is genetically defective in humans. This may have a biological and evolutional meaning in the transport and metabolism of nucleobases. The present study provides novel insights into the specific transport and metabolism of nucleobases and their analogs for therapeutic use. PMID:20042597

  6. Correlation of nucleoside and nucleobase transporter gene expression with antimetabolite drug cytotoxicity.

    PubMed

    Lu, Xin; Gong, Shimei; Monks, Anne; Zaharevitz, Daniel; Moscow, Jeffrey A

    2002-01-01

    Antimetabolite drugs that inhibit nucleic acid metabolism are widely used in cancer chemotherapy. Nucleoside and nucleobase transporters are important for the cellular uptake of nucleic acids and their corresponding anticancer analogue drugs. Thus, these transporters may play a role both in antimetabolite drug sensitivity, by mediating the uptake of nucleoside analogues, and in antimetabolite drug resistance, by mediating the uptake of endogenous nucleosides that may rescue cells from toxicity. Therefore, we examined the relation of the expression of nucleoside and nucleobase transporters to antimetabolite cytotoxicity. We measured the RNA levels of all eight known nucleoside and nucleobase transporters in 50 cell lines included in the National Cancer Institute's Anticancer Drug Screen panel. RNA levels of concentrative nucleoside transporters (CNTs), equilibrative nucleoside transporters (ENTs) and nucleobase transporters (NCBTs) were determined by quantitative RT-PCR using real-time fluorescence acquisition. This method was validated by measuring the expression of the MDR1 gene, and correlating our results with independently determined measurements of MDR1 RNA levels and protein function in these cell lines. We then correlated the pattern of RNA levels to the pattern of cytotoxicity of anticancer drugs in the NCI drug screen database using the COMPARE analysis. Several hypothesized relations between transporter gene expression and cytotoxicity, based upon known interactions between certain nucleoside analogues and transporter proteins, were not observed, suggesting that expression of individual transporters may not be a significant determinant of the cytotoxicity of these drugs. The most closely correlated drug cytotoxicity patterns to transporter gene expression patterns (where increased expression corresponds to increase sensitivity) included those between CNT1 and O6-methylguanine and between ENT2 and hydroxyurea. We also observed that p53 status influenced

  7. A Transition-State Interaction Shifts Nucleobase Ionization Toward Neutrality to Facilitate Small Ribozyme Catalysis

    PubMed Central

    Liberman, Joseph A.; Guo, Man; Jenkins, Jermaine L.; Krucinska, Jolanta; Chen, Yuanyuan; Carey, Paul R.; Wedekind, Joseph E.

    2012-01-01

    One mechanism by which ribozymes can accelerate biological reactions is by adopting folds that favorably perturb nucleobase ionization. Herein we used Raman crystallography to directly measure pKa values for the Ade38 N1-imino group of a hairpin ribozyme in distinct conformational states. A transition-state analogue gave a pKa value of 6.27 ± 0.05, which agrees strikingly well with values measured by pH-rate analyses. To identify the chemical attributes that contribute to the shifted pKa we determined crystal structures of hairpin ribozyme variants containing single-atom substitutions at the active site and measured their respective Ade38 N1 pKa values. This approach led to the identification of a single interaction in the transition-state conformation that elevates the base pKa >0.8 log units relative to the precatalytic state. The agreement of the microscopic and macroscopic pKa values and the accompanying structural analysis support a mechanism in which Ade38 N1(H)+ functions as a general acid in phosphodiester bond cleavage. Overall the results quantify the contribution of a single electrostatic interaction to base ionization, which has broad relevance for understanding how RNA structure can control chemical reactivity. PMID:22989273

  8. FUN26 (Function Unknown Now 26) Protein from Saccharomyces cerevisiae Is a Broad Selectivity, High Affinity, Nucleoside and Nucleobase Transporter*

    PubMed Central

    Boswell-Casteel, Rebba C.; Johnson, Jennifer M.; Duggan, Kelli D.; Roe-Žurž, Zygy; Schmitz, Hannah; Burleson, Carter; Hays, Franklin A.

    2014-01-01

    Equilibrative nucleoside transporters (ENTs) are polytopic integral membrane proteins that transport nucleosides and, to a lesser extent, nucleobases across cell membranes. ENTs modulate efficacy for a range of human therapeutics and function in a diffusion-controlled bidirectional manner. A detailed understanding of ENT function at the molecular level has remained elusive. FUN26 (function unknown now 26) is a putative ENT homolog from S. cerevisiae that is expressed in vacuole membranes. In the present system, proteoliposome studies of purified FUN26 demonstrate robust nucleoside and nucleobase uptake into the luminal volume for a broad range of substrates. This transport activity is sensitive to nucleoside modifications in the C(2′)- and C(5′)-positions on the ribose sugar and is not stimulated by a membrane pH differential. [3H]Adenine nucleobase transport efficiency is increased ∼4-fold relative to nucleosides tested with no observed [3H]adenosine or [3H]UTP transport. FUN26 mutational studies identified residues that disrupt (G463A or G216A) or modulate (F249I or L390A) transporter function. These results demonstrate that FUN26 has a unique substrate transport profile relative to known ENT family members and that a purified ENT can be reconstituted in proteoliposomes for functional characterization in a defined system. PMID:25035431

  9. FUN26 (function unknown now 26) protein from saccharomyces cerevisiae is a broad selectivity, high affinity, nucleoside and nucleobase transporter.

    PubMed

    Boswell-Casteel, Rebba C; Johnson, Jennifer M; Duggan, Kelli D; Roe-Žurž, Zygy; Schmitz, Hannah; Burleson, Carter; Hays, Franklin A

    2014-08-29

    Equilibrative nucleoside transporters (ENTs) are polytopic integral membrane proteins that transport nucleosides and, to a lesser extent, nucleobases across cell membranes. ENTs modulate efficacy for a range of human therapeutics and function in a diffusion-controlled bidirectional manner. A detailed understanding of ENT function at the molecular level has remained elusive. FUN26 (function unknown now 26) is a putative ENT homolog from S. cerevisiae that is expressed in vacuole membranes. In the present system, proteoliposome studies of purified FUN26 demonstrate robust nucleoside and nucleobase uptake into the luminal volume for a broad range of substrates. This transport activity is sensitive to nucleoside modifications in the C(2')- and C(5')-positions on the ribose sugar and is not stimulated by a membrane pH differential. [(3)H]Adenine nucleobase transport efficiency is increased ∼4-fold relative to nucleosides tested with no observed [(3)H]adenosine or [(3)H]UTP transport. FUN26 mutational studies identified residues that disrupt (G463A or G216A) or modulate (F249I or L390A) transporter function. These results demonstrate that FUN26 has a unique substrate transport profile relative to known ENT family members and that a purified ENT can be reconstituted in proteoliposomes for functional characterization in a defined system. PMID:25035431

  10. SUPERFUND GROUNDWATER ISSUE - FACILITATED TRANSPORT

    EPA Science Inventory

    The Regional Superfund Ground Water Forum is a group of ground-water scientists representing EPA's Regional Superfund Offices, organized to exchange up to date information related to ground-water remediation at Superfund sites. Facilitated transport is an issue identified by the ...

  11. Identification of a nucleoside/nucleobase transporter from Plasmodium falciparum, a novel target for anti-malarial chemotherapy.

    PubMed Central

    Parker, M D; Hyde, R J; Yao, S Y; McRobert, L; Cass, C E; Young, J D; McConkey, G A; Baldwin, S A

    2000-01-01

    Plasmodium, the aetiologic agent of malaria, cannot synthesize purines de novo, and hence depends upon salvage from the host. Here we describe the molecular cloning and functional expression in Xenopus oocytes of the first purine transporter to be identified in this parasite. This 422-residue protein, which we designate PfENT1, is predicted to contain 11 membrane-spanning segments and is a distantly related member of the widely distributed eukaryotic protein family the equilibrative nucleoside transporters (ENTs). However, it differs profoundly at the sequence and functional levels from its homologous counterparts in the human host. The parasite protein exhibits a broad substrate specificity for natural nucleosides, but transports the purine nucleoside adenosine with a considerably higher apparent affinity (K(m) 0.32+/-0.05 mM) than the pyrimidine nucleoside uridine (K(m) 3.5+/-1.1 mM). It also efficiently transports nucleobases such as adenine (K(m) 0.32+/-0.10 mM) and hypoxanthine (K(m) 0.41+/-0.1 mM), and anti-viral 3'-deoxynucleoside analogues. Moreover, it is not sensitive to classical inhibitors of mammalian ENTs, including NBMPR [6-[(4-nitrobenzyl)thio]-9-beta-D-ribofuranosylpurine, or nitrobenzylthioinosine] and the coronary vasoactive drugs, dipyridamole, dilazep and draflazine. These unique properties suggest that PfENT1 might be a viable target for the development of novel anti-malarial drugs. PMID:10861212

  12. Structural, Dynamical and Electronic Transport Properties of Modified DNA Duplexes Containing Size-Expanded Nucleobases

    SciTech Connect

    Sumpter, Bobby G; Fuentes-Cabrera, Miguel A

    2011-01-01

    Among the distinct strategies proposed to expand the genetic alphabet, size-expanded nucleobases are promising for the development of modified DNA duplexes with improved biotechnological properties. In particular, duplexes built up by replacing canonical bases with the corresponding benzo-fused counterparts could be valuable as molecular nanowires. In this context, this study reports the results of classical molecular dynamics simulations carried out to examine the structural and dynamical features of size-expanded DNAs, including both hybrid duplexes containing mixed pairs of natural and benzo-fused bases (xDNA) and pure size-expanded (xxDNA) duplexes. Furthermore, the electronic structure of both natural and size-expanded duplexes is examined by means of density functional computations. The results confirm that the structural and flexibility properties of the canonical DNA are globally little affected by the presence of benzo-fused bases. The most relevant differences are found in the enhanced size of the grooves, and the reduction in the twist. However, the analysis also reveals subtle structural effects related to the nature and sequence of benzo-fused bases in the duplex. On the other hand, electronic structure calculations performed for xxDNAs confirm the reduction in the HOMO-LUMO gap predicted from the analysis of the natural bases and their size-expanded counterparts, which suggests that pure size-expanded DNAs can be good conductors. A more complex situation is found for xDNAs, where fluctuations in the electrostatic interaction between base pairs exerts a decisive influence on the modulation of the energy gap.

  13. Oxidation of DNA: damage to nucleobases.

    PubMed

    Kanvah, Sriram; Joseph, Joshy; Schuster, Gary B; Barnett, Robert N; Cleveland, Charles L; Landman, Uzi

    2010-02-16

    All organisms store the information necessary to maintain life in their DNA. Any process that damages DNA, causing a loss or corruption of that information, jeopardizes the viability of the organism. One-electron oxidation is such a process. In this Account, we address three of the central features of one-electron oxidation of DNA: (i) the migration of the radical cation away from the site of its formation; (ii) the electronic and structural factors that determine the nucleobases at which irreversible reactions most readily occur; (iii) the mechanism of reaction for nucleobase radical cations. The loss of an electron (ionization) from DNA generates an electron "hole" (a radical cation), located most often on its nucleobases, that migrates reversibly through duplex DNA by hopping until it is trapped in an irreversible chemical reaction. The particular sequence of nucleobases in a DNA oligomer determines both the efficiency of hopping and the specific location and nature of the damaging chemical reaction. In aqueous solution, DNA is a polyanion because of the negative charge carried by its phosphate groups. Counterions to the phosphate groups (typically Na(+)) play an important role in facilitating both hopping and the eventual reaction of the radical cation with H(2)O. Irreversible reaction of a radical cation with H(2)O in duplex DNA occurs preferentially at the most reactive site. In normal DNA, comprising the four common DNA nucleobases G, C, A, and T, reaction occurs most commonly at a guanine, resulting in its conversion primarily to 8-oxo-7,8-dihydroguanine (8-OxoG). Both electronic and steric effects control the outcome of this process. If the DNA oligomer does not contain a suitable guanine, then reaction of the radical cation occurs at the thymine of a TT step, primarily by a tandem process. The oxidative damage of DNA is a complex process, influenced by charge transport and reactions that are controlled by a combination of enthalpic, entropic, steric, and

  14. Characterization of poly(N-isopropylacrylamide)-nucleobase supramolecular complexes featuring bio-multiple hydrogen bonds.

    PubMed

    Yang, Hsiu-Wen; Lee, Ai-Wei; Huang, Chi-Hsien; Chen, Jem-Kun

    2014-11-01

    In this study we employed poly(N-isopropylacrylamide) (PNIPAAm) as a matrix that we hybridized with five different nucleobase units (adenine, thymine, uracil, guanine, cytosine) to generate PNIPAAm-nucleobase supramolecular complexes (PNSCs) stabilized through bio-multiple hydrogen bonds (BMHBs). These nucleobase units interacted with PNIPAAm through BMHBs of various strengths, leading to competition between the BMHBs and the intramolecular hydrogen bonds (HBs) of PNIPAAm. The changes in morphology, crystalline structure, and thermoresponsive behavior of PNIPAAm were related to the strength of its BMHBs with the nucleobases. The strengths of the BMHBs followed the order guanine > adenine > thymine > cytosine > uracil, as verified through analyses of Fourier transform infrared spectra, lower critical solution temperatures, and inter-association equilibrium constants. The PNSCs also exhibited remarkable improvements in conductivity upon the formation of BMHBs, which facilitated proton transport. The neat PNIPAAm film was an insulator, but it transformed into a semiconductor after hybridizing with the nucleobases. In particular, the resistivity of the PNIPAAm-guanine supramolecular complex decreased to 1.35 × 10(5) ohm cm. The resistivity of the PNIPAAm-cytosine supramolecular complex increased significantly from 5.83 × 10(6) to 3 × 10(8) ohm cm upon increasing the temperature from 40 to 50 °C, suggesting that this material might have applicability in thermo-sensing. The ability to significantly improve the conductivity of hydrogels through such a simple approach involving BMHBs might facilitate their use as novel materials in bioelectronics. PMID:25196131

  15. Modeling Facilitated Contaminant Transport by Mobile Bacteria

    NASA Astrophysics Data System (ADS)

    Corapcioglu, M. Yavuz; Kim, Seunghyun

    1995-01-01

    Introduction of exogenous biocolloids such as genetically engineered bacteria in a bioremediation operation can enhance the transport of contaminants in groundwater by reducing the retardation effects. Because of their colloidal size and favorable surface conditions, bacteria are efficient contaminant carriers. In cases where contaminants have a low mobility in porous media because of their high partition with solid matrix, facilitated contaminant transport by mobile bacteria can create high contaminant fluxes. When metabolically active mobile bacteria are present in a subsurface environment, the system can be treated as consisting of three phases: water phase, bacterial phase, and stationary solid matrix phase. In this work a mathematical model based on mass balance equations is developed to describe the facilitated transport and fate of a contaminant and bacteria in a porous medium. Bacterial partition between the bulk solution and the stationary solid matrix and contaminant partition among three phases are represented by expressions in terms of measurable quantities. Solutions were obtained to provide estimates of contaminant and bacterial concentrations. A dimensional analysis of the transport model was utilized to estimate model parameters from the experimental data and to assess the effect of several parameters on model behavior. The model results matched favorably with experimental data of Jenkins and Lion (1993). The presence of mobile bacteria enhances the contaminant transport. However, bacterial consumption of the contaminant, which serves as a bacterial nutrient, can attenuate the contaminant mobility. The work presented in this paper is the first three-phase model to include the effects of substrate metabolism on the fate of groundwater contaminants.

  16. Proton Transfer in Nucleobases is Mediated by Water

    SciTech Connect

    Khistyaev, Kirill; Golan, Amir; Bravaya, Ksenia B.; Orms, Natalie; Krylov, Anna I.; Ahmed, Musahid

    2013-08-08

    Water plays a central role in chemistry and biology by mediating the interactions between molecules, altering energy levels of solvated species, modifying potential energy proles along reaction coordinates, and facilitating ecient proton transport through ion channels and interfaces. This study investigates proton transfer in a model system comprising dry and microhydrated clusters of nucleobases. With mass spectrometry and tunable vacuum ultraviolet synchrotron radiation, we show that water shuts down ionization-induced proton transfer between nucleobases, which is very ecient in dry clusters. Instead, a new pathway opens up in which protonated nucleo bases are generated by proton transfer from the ionized water molecule and elimination of a hydroxyl radical. Electronic structure calculations reveal that the shape of the potential energy prole along the proton transfer coordinate depends strongly on the character of the molecular orbital from which the electron is removed, i.e., the proton transfer from water to nucleobases is barrierless when an ionized state localized on water is accessed. The computed energetics of proton transfer is in excellent agreement with the experimental appearance energies. Possible adiabatic passage on the ground electronic state of the ionized system, while energetically accessible at lower energies, is not ecient. Thus, proton transfer is controlled electronically, by the character of the ionized state, rather than statistically, by simple energy considerations.

  17. Structure-Function Relationship of a Plant NCS1 Member – Homology Modeling and Mutagenesis Identified Residues Critical for Substrate Specificity of PLUTO, a Nucleobase Transporter from Arabidopsis

    PubMed Central

    Witz, Sandra; Panwar, Pankaj; Schober, Markus; Deppe, Johannes; Pasha, Farhan Ahmad; Lemieux, M. Joanne; Möhlmann, Torsten

    2014-01-01

    Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members. PMID:24621654

  18. Structure-function relationship of a plant NCS1 member--homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from Arabidopsis.

    PubMed

    Witz, Sandra; Panwar, Pankaj; Schober, Markus; Deppe, Johannes; Pasha, Farhan Ahmad; Lemieux, M Joanne; Möhlmann, Torsten

    2014-01-01

    Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members. PMID:24621654

  19. Computation Of Facilitated Transport of O2 In Hemoglobin

    NASA Technical Reports Server (NTRS)

    Davis, Sanford

    1991-01-01

    Report describes computations of unsteady facilitated transport of oxygen through liquid membrane of hemoglobin. Used here, "facilitated transport" means diffusion of permeant through membrane in which that diffusion enhanced by reversible chemical reaction between permeant and membrane. In this case, reversible reactions between hemoglobin and oxygen.

  20. MACROMOLECULES FACILITATE THE TRANSPORT OF TRACE ORGANICS

    EPA Science Inventory

    Macromolecules in the pore fluid of a soil may influence the mobility of hydrophobic compounds by their partitioning to the macromolecule, which moves with, or even faster than, the water. The mobility is described mathematically by a chemical transport model. The significance of...

  1. Facilitated transport of copper with hydroxyapatite nanoparticles in saturated sand

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Saturated packed column experiments were conducted to investigate the facilitated transport of Cu with hydroxyapatite nanoparticles (nHAP) at different pore water velocities (0.22-2.2 cm min–1), solution pH (6.2-9.0), and fraction of Fe oxide coating on grain surfaces (', 0-0.36). The facilitated tr...

  2. Colloid-Facilitated Transport of Radionuclides through the Vadose Zone

    SciTech Connect

    Flury, Markus; Harsh, James B.; Zachara, John M.; McCarthy, John F.; Lichtner, Peter C.

    2006-05-31

    This project seeks to improve the basic understanding of the role of colloids in facilitating the transport of contaminants in the vadose zone. We focus on three major thrusts: (1) thermodynamic stability and mobility of colloids formed by reactions of sediments with highly alkaline tank waste solutions, (2) colloid-contaminant interactions, and (3) in-situ colloid mobilization and colloid facilitated contaminant transport occurring in both contaminated and uncontaminated Hanford sediments.

  3. Microhydration of Deprotonated Nucleobases

    NASA Astrophysics Data System (ADS)

    Wincel, Henryk

    2016-05-01

    Hydration reactions of deprotonated nucleobases (uracil, thymine, 5-fluorouracil,2-thiouracil, cytosine, adenine, and hypoxanthine) produced by electrospray have been experimentally studied in the gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔH o , ΔS o , and ΔG o , for the monohydrated systems were determined. The hydration enthalpies were found to be similar for all studied systems and varied between 39.4 and 44.8 kJ/mol. A linear correlation was found between water binding energies in the hydrated complexes and the corresponding acidities of the most acidic site of nucleobases. The structural and energetic aspects of the precursors for the hydrated complexes are discussed in conjunction with available literature data.

  4. Microhydration of Deprotonated Nucleobases

    NASA Astrophysics Data System (ADS)

    Wincel, Henryk

    2016-08-01

    Hydration reactions of deprotonated nucleobases (uracil, thymine, 5-fluorouracil,2-thiouracil, cytosine, adenine, and hypoxanthine) produced by electrospray have been experimentally studied in the gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔH o , ΔS o , and ΔG o , for the monohydrated systems were determined. The hydration enthalpies were found to be similar for all studied systems and varied between 39.4 and 44.8 kJ/mol. A linear correlation was found between water binding energies in the hydrated complexes and the corresponding acidities of the most acidic site of nucleobases. The structural and energetic aspects of the precursors for the hydrated complexes are discussed in conjunction with available literature data.

  5. Facilitative plasma membrane transporters function during ER transit

    PubMed Central

    Takanaga, Hitomi; Frommer, Wolf B.

    2010-01-01

    Although biochemical studies suggested a high permeability of the endoplasmic reticulum (ER) membrane for small molecules, proteomics identified few specialized ER transporters. To test functionality of transporters during ER passage, we tested whether glucose transporters (GLUTs, SGLTs) destined for the plasma membrane are active during ER transit. HepG2 cells were characterized by low-affinity ER transport activity, suggesting that ER uptake is protein mediated. The much-reduced capacity of HEK293T cells to take up glucose across the plasma membrane correlated with low ER transport. Ectopic expression of GLUT1, -2, -4, or -9 induced GLUT isoform-specific ER transport activity in HEK293T cells. In contrast, the Na+-glucose cotransporter SGLT1 mediated efficient plasma membrane glucose transport but no detectable ER uptake, probably because of lack of a sufficient sodium gradient across the ER membrane. In conclusion, we demonstrate that GLUTs are sufficient for mediating ER glucose transport en route to the plasma membrane. Because of the low volume of the ER, trace amounts of these uniporters contribute to ER solute import during ER transit, while uniporters and cation-coupled transporters carry out export from the ER, together potentially explaining the low selectivity of ER transport. Expression levels and residence time of transporters in the ER, as well as their coupling mechanisms, could be key determinants of ER permeability.—Takanaga, H., Frommer, W. B. Facilitative plasma membrane transporters function during ER transit. PMID:20354141

  6. No facilitator required for membrane transport of hydrogen sulfide

    PubMed Central

    Mathai, John C.; Missner, Andreas; Kügler, Philipp; Saparov, Sapar M.; Zeidel, Mark L.; Lee, John K.; Pohl, Peter

    2009-01-01

    Hydrogen sulfide (H2S) has emerged as a new and important member in the group of gaseous signaling molecules. However, the molecular transport mechanism has not yet been identified. Because of structural similarities with H2O, it was hypothesized that aquaporins may facilitate H2S transport across cell membranes. We tested this hypothesis by reconstituting the archeal aquaporin AfAQP from sulfide reducing bacteria Archaeoglobus fulgidus into planar membranes and by monitoring the resulting facilitation of osmotic water flow and H2S flux. To measure H2O and H2S fluxes, respectively, sodium ion dilution and buffer acidification by proton release (H2S ⇆ H+ + HS−) were recorded in the immediate membrane vicinity. Both sodium ion concentration and pH were measured by scanning ion-selective microelectrodes. A lower limit of lipid bilayer permeability to H2S, PM,H2S ≥ 0.5 ± 0.4 cm/s was calculated by numerically solving the complete system of differential reaction diffusion equations and fitting the theoretical pH distribution to experimental pH profiles. Even though reconstitution of AfAQP significantly increased water permeability through planar lipid bilayers, PM,H2S remained unchanged. These results indicate that lipid membranes may well act as a barrier to water transport although they do not oppose a significant resistance to H2S diffusion. The fact that cholesterol and sphingomyelin reconstitution did not turn these membranes into an H2S barrier indicates that H2S transport through epithelial barriers, endothelial barriers, and membrane rafts also occurs by simple diffusion and does not require facilitation by membrane channels. PMID:19805349

  7. Sediment control of facilitated transport and enhanced desorption

    SciTech Connect

    Johnson, W.P.

    2000-01-01

    Laboratory column experiments examined the facilitated transport and enhanced desorption of benz(a)anthracene [B(a)A] by dissolved natural organic matter (OM) in sediments of low organic carbon content. The two-component experiments examining OM-sediment interaction and B(a)A-sediment interaction were modeled to determine the value of the linear rate constants describing transfer of B(a)A and OM between water and sediment. It was found that a two-rate approach better simulated B(a)A breakthrough and elution in the sediment relative to a one-rate approach. In contrast, OM-sediment interaction was well-simulated with a one-rate approach due to low OM sorption by sediment. The three-component experiments examining facilitated transport and enhanced desorption of B(a)A by dissolved OM, showed rapid linear reversible B(a)A-OM interaction. The value, within a factor of 2, of the equilibrium distribution constant for benz(a)anthracene distribution between water and OM was {approximately}1E6 for soil humic acid and {approximately}1E5 for Suwannee River humic acid. Simulations of the three-component experiments based on the equilibrium distribution constants for B(a)A-OM interaction and the rate constants determined from the two-component experiments were performed to determine whether rate constants differed in the two-component versus three-component systems. The simulations captured the major features of the facilitated transport and enhanced desorption data; however, discrepancies indicated that either the two-rate model for solute-sediment interaction was inappropriate, or that B(a)A transfer from sediment to dissolved OM was altered in the three-component system relative to the two-component system.

  8. COLLOID-FACILITATED TRANSPORT OF RADIONUCLIDES THROUGH THE VADOSE ZONE

    SciTech Connect

    Flury, Markus

    2003-09-14

    Contaminants have leaked into the vadose zone at the USDOE Hanford reservation. It is important to understand the fate and transport of these contaminants to design remediation strategies and long-term waste management plans at the Hanford reservation. Colloids may play an important role in fate and transport of strongly sorbing contaminants, such as Cs or Pu. This project seeks to improve the basic understanding of colloid and colloid-facilitated transport of contaminants in the vadose zone. The specific objectives addressed are: (1) Determine the structure, composition, and surface charge characteristics of colloidal particles formed under conditions similar to those occurring during leakage of waste typical of Hanford tank supernatants into soils and sediments surrounding the tanks. (2) Characterize the mutual interactions between colloids, contaminant, and soil matrix in batch experiments under various ionic strength and pH conditions. We will investigate the nature of the solid-liquid interactions and the kinetics of the reactions. (3) Evaluate mobility of colloids through soil under different degrees of water saturation and solution chemistry (ionic strength and pH). (4) Determine the potential of colloids to act as carriers to transport the contaminant through the vadose zone and verify the results through comparison with field samples collected under leaking tanks. (5) Improve conceptual characterization of colloid-contaminant-soil interactions and colloid-facilitated transport for implementation into reactive chemical transport models. This project was in part supported by an NSF-IGERT grant to Washington State University. The IGERT grant provided funding for graduate student research and education, and two graduate students were involved in the EMSP project. The IGERT program also supported undergraduate internships. The project is part of a larger EMSP program to study fate and transport of contaminants under leaking Hanford waste tanks. The project has

  9. Golgi localized barley MTP8 proteins facilitate Mn transport.

    PubMed

    Pedas, Pai; Schiller Stokholm, Michaela; Hegelund, Josefine Nymark; Ladegård, Anne Hald; Schjoerring, Jan Kofod; Husted, Søren

    2014-01-01

    Many metabolic processes in plants are regulated by manganese (Mn) but limited information is available on the molecular mechanisms controlling cellular Mn homeostasis. In this study, a yeast assay was used to isolate and characterize two genes, MTP8.1 and MTP8.2, which encode membrane-bound proteins belonging to the cation diffusion facilitator (CDF) family in the cereal species barley (Hordeum vulgare). Transient expression in onion epidermal cells showed that MTP8.1 and MTP8.2 proteins fused to the green fluorescent protein (GFP) are localized to Golgi. When heterologously expressed in yeast, MTP8.1 and MTP8.2 were found to be Mn transporters catalysing Mn efflux in a similar manner as the Golgi localized endogenous yeast protein Pmr1p. The level of MTP8.1 transcripts in barley roots increased with external Mn supply ranging from deficiency to toxicity, while MTP8.2 transcripts decreased under the same conditions, indicating non-overlapping functions for the two genes. In barley leaves, the expression of both MTP8 genes declined in response to toxic Mn additions to the roots suggesting a role in ensuring proper delivery of Mn to Golgi. Based on the above we suggest that barley MTP8 proteins are involved in Mn loading to the Golgi apparatus and play a role in Mn homeostasis by delivering Mn to Mn-dependent enzymes and/or by facilitating Mn efflux via secretory vesicles. This study highlights the importance of MTP transporters in Mn homeostasis and is the first report of Golgi localized Mn2+ transport proteins in a monocot plant species. PMID:25486417

  10. Golgi Localized Barley MTP8 Proteins Facilitate Mn Transport

    PubMed Central

    Pedas, Pai; Schiller Stokholm, Michaela; Hegelund, Josefine Nymark; Ladegård, Anne Hald; Schjoerring, Jan Kofod; Husted, Søren

    2014-01-01

    Many metabolic processes in plants are regulated by manganese (Mn) but limited information is available on the molecular mechanisms controlling cellular Mn homeostasis. In this study, a yeast assay was used to isolate and characterize two genes, MTP8.1 and MTP8.2, which encode membrane-bound proteins belonging to the cation diffusion facilitator (CDF) family in the cereal species barley (Hordeum vulgare). Transient expression in onion epidermal cells showed that MTP8.1 and MTP8.2 proteins fused to the green fluorescent protein (GFP) are localized to Golgi. When heterologously expressed in yeast, MTP8.1 and MTP8.2 were found to be Mn transporters catalysing Mn efflux in a similar manner as the Golgi localized endogenous yeast protein Pmr1p. The level of MTP8.1 transcripts in barley roots increased with external Mn supply ranging from deficiency to toxicity, while MTP8.2 transcripts decreased under the same conditions, indicating non-overlapping functions for the two genes. In barley leaves, the expression of both MTP8 genes declined in response to toxic Mn additions to the roots suggesting a role in ensuring proper delivery of Mn to Golgi. Based on the above we suggest that barley MTP8 proteins are involved in Mn loading to the Golgi apparatus and play a role in Mn homeostasis by delivering Mn to Mn-dependent enzymes and/or by facilitating Mn efflux via secretory vesicles. This study highlights the importance of MTP transporters in Mn homeostasis and is the first report of Golgi localized Mn2+ transport proteins in a monocot plant species. PMID:25486417

  11. Colloid-Facilitated Transport of Radionuclides through the Vadose Zone

    SciTech Connect

    Flury, Markus; Harsh, James B.; Zachara, John M.; Jin, Yan

    2002-06-01

    This project seeks to improve the basic understanding of colloid and colloid-facilitated transport of Cs in the vadose zone. The specific objectives are: (1) Determine the structure, composition, and surface charge characteristics of colloidal particles formed under conditions similar to those occurring during leakage of waste typical of Hanford tank supernatants into soils and sediments surrounding the tanks. (2) Characterize the mutual interactions between colloids, contaminant, and soil matrix in batch experiments under various ionic strength and pH conditions. We will investigate the nature of the solid-liquid interactions and the kinetics of the reactions. (3) Evaluate mobility of colloids through soil under different degrees of water saturation and solution chemistry (ionic strength and pH). (4) Determine the potential of colloids to act as carriers to transport the contaminant through the vadose zone and verify the results through comparison with field samples collected under leaking tanks. Results of this project will help to understand the fundamental mechanisms of Cs transport under the leaking Hanford tanks, and thus contribute to the long-term clean-up strategies at the Hanford site.

  12. Colloid facilitated transport of lanthanides through discrete fractures in chalk

    NASA Astrophysics Data System (ADS)

    Tran, Emily; Klein Ben-David, Ofra; Teutsch, Nadya; Weisbrod, Noam

    2015-04-01

    Geological disposal of high-level radioactive waste is the internationally agreed-upon, long term solution for the disposal of long lived radionuclides and spent fuel. Eventually, corrosion of the waste canisters may lead to leakage of their hazardous contents, and the radionuclides can ultimately make their way into groundwater and pose a threat to the biosphere. Engineered bentonite barriers placed around nuclear waste repositories are generally considered sufficient to impede the transport of radionuclides from their storage location to the groundwater. However, colloidal-sized mobile bentonite particles eroding from these barriers have come under investigation as a potential transport vector for radionuclides sorbed to them. In addition, the presence of organic matter in groundwater has been shown to additionally facilitate the uptake of radionuclides by the clay colloids. This study aims to evaluate the transport behaviors of radionuclides in colloid-facilitated transport through a fractured chalk matrix and under geochemical conditions representative of the Negev desert, Israel. Lanthanides are considered an acceptable substitute to actinides for research on radionuclide transportation due to their similar chemical behavior. In this study, the migration of Ce both with and without colloidal particles was explored and compared to the migration of a conservative tracer (bromide). Tracer solutions containing known concentrations of Ce, bentonite colloids, humic acid and bromide were prepared in a matrix solution containing salt concentrations representative of that of the average rain water found in the Negev. These solutions were then injected into a flow system constructed around a naturally fractured chalk core. Samples were analyzed for Ce and Br using ICP-MS, and colloid concentrations were determined using spectrophotographic analysis. Breakthrough curves comparing the rates of transportation of each tracer were obtained, allowing for comparison of

  13. Colloid Facilitated Transport of Plutonium in Fractured Volcanic Tuff

    NASA Astrophysics Data System (ADS)

    Kersting, A. B.; Zhao, P.; Walensky, J. R.; Roberts, S. K.; Johnson, M. R.; Zavarin, M.; Ramon, E. C.

    2004-12-01

    The transport of low-solubility radionuclides in a colloidal- or colloidal bound state is frequently suspected or observed. Groundwater contaminated with radionuclides associated with underground nuclear tests was collected from several different well locations at the Nevada Test Site (NTS). In each case, the low-levels of plutonium detected in the groundwater were overwhelmingly (>95percent) associated with the colloidal and not the dissolved fraction of the groundwater. The colloidal fractions consisted of secondary minerals such as clays and zeolites. To better understand the mechanisms controlling the potential colloidal transport of plutonium, colloid-facilitated fracture flow laboratory experiments are being conducted. Pseudocolloids consisting of Pu(IV) sorbed to clinoptilolite were combined with a radionuclide solution cocktail consisting of Np, U, Cs, Sr, Sm and 3H and Re (analog to Tc) tracers in NTS-type synthetic groundwater (4.5mM NaHCO3-). The cocktail was injected into a smooth fracture in a volcanic tuff rock core from the NTS and the effluent analyzed. Autoradiography and secondary ion mass spectrometry will be used to understand the mineral -colloid-radionuclide interactions in the fracture volcanic tuff.

  14. Isoform-selective Inhibition of Facilitative Glucose Transporters

    PubMed Central

    Hresko, Richard C.; Kraft, Thomas E.; Tzekov, Anatoly; Wildman, Scott A.; Hruz, Paul W.

    2014-01-01

    Pharmacologic HIV protease inhibitors (PIs) and structurally related oligopeptides are known to reversibly bind and inactivate the insulin-responsive facilitative glucose transporter 4 (GLUT4). Several PIs exhibit isoform selectivity with little effect on GLUT1. The ability to target individual GLUT isoforms in an acute and reversible manner provides novel means both to investigate the contribution of individual GLUTs to health and disease and to develop targeted treatment of glucose-dependent diseases. To determine the molecular basis of transport inhibition, a series of chimeric proteins containing transmembrane and cytosolic domains from GLUT1 and GLUT4 and/or point mutations were generated and expressed in HEK293 cells. Structural integrity was confirmed via measurement of N-[2-[2-[2-[(N-biotinylcaproylamino)ethoxy)ethoxyl]-4-[2-(trifluoromethyl)-3H-diazirin-3-yl]benzoyl]-1,3-bis(mannopyranosyl-4-yloxy)-2-propylamine (ATB-BMPA) labeling of the chimeric proteins in low density microsome fractions isolated from stably transfected 293 cells. Functional integrity was assessed via measurement of zero-trans 2-deoxyglucose (2-DOG) uptake. ATB-BMPA labeling studies and 2-DOG uptake revealed that transmembrane helices 1 and 5 contain amino acid residues that influence inhibitor access to the transporter binding domain. Substitution of Thr-30 and His-160 in GLUT1 to the corresponding positions in GLUT4 is sufficient to completely transform GLUT1 into GLUT4 with respect to indinavir inhibition of 2-DOG uptake and ATB-BMPA binding. These data provide a structural basis for the selectivity of PIs toward GLUT4 over GLUT1 that can be used in ongoing novel drug design. PMID:24706759

  15. PFLOTRAN: Recent Developments Facilitating Massively-Parallel Reactive Biogeochemical Transport

    NASA Astrophysics Data System (ADS)

    Hammond, G. E.

    2015-12-01

    With the recent shift towards modeling carbon and nitrogen cycling in support of climate-related initiatives, emphasis has been placed on incorporating increasingly mechanistic biogeochemistry within Earth system models to more accurately predict the response of terrestrial processes to natural and anthropogenic climate cycles. PFLOTRAN is an open-source subsurface code that is specialized for simulating multiphase flow and multicomponent biogeochemical transport on supercomputers. The object-oriented code was designed with modularity in mind and has been coupled with several third-party simulators (e.g. CLM to simulate land surface processes and E4D for coupled hydrogeophysical inversion). Central to PFLOTRAN's capabilities is its ability to simulate tightly-coupled reactive transport processes. This presentation focuses on recent enhancements to the code that enable the solution of large parameterized biogeochemical reaction networks with numerous chemical species. PFLOTRAN's "reaction sandbox" is described, which facilitates the implementation of user-defined reaction networks without the need for a comprehensive understanding of PFLOTRAN software infrastructure. The reaction sandbox is written in modern Fortran (2003-2008) and leverages encapsulation, inheritance, and polymorphism to provide the researcher with a flexible workspace for prototyping reactions within a massively parallel flow and transport simulation framework. As these prototypical reactions mature into well-accepted implementations, they can be incorporated into PFLOTRAN as native biogeochemistry capability. Users of the reaction sandbox are encouraged to upload their source code to PFLOTRAN's main source code repository, including the addition of simple regression tests to better ensure the long-term code compatibility and validity of simulation results.

  16. Magnetic Fields Facilitate DNA-Mediated Charge Transport.

    PubMed

    Wong, Jiun Ru; Lee, Kee Jin; Shu, Jian-Jun; Shao, Fangwei

    2015-06-01

    Exaggerated radical-induced DNA damage under magnetic fields is of great concern to medical biosafety and biomolecular electronic devices. In this report, the effects of an external magnetic field (MF) on DNA electronic conductivity were investigated by studying the efficiencies of photoinduced DNA-mediated charge transport (CT) via guanine damage. Under a static MF of 300 mT, positive enhancements in the decomposition of 8-cyclopropyldeoxyguanosine ((8CP)G) were observed at both the proximal and distal guanine doublets, indicating a more efficient propagation of radical cations and higher electronic conductivity of duplex DNA. MF-assisted CT has shown sensitivity to magnetic field strength, duplex structures, and the integrity of base pair stacking. Spin evolution of charge injection and the alignment of base pairs to the CT-active conformation during radical propagation were proposed to be the two major factors that MF contributes to facilitate DNA-mediated CT. Herein, MF-assisted CT may offer a new avenue for designing DNA-based electronic devices and unraveling MF effects on redox and radical relevant biological processes. PMID:25946473

  17. Nucleocytoplasmic transport of ribosomes in a eukaryotic system: Is there a facilitated transport process

    SciTech Connect

    Khanna-Gupta, A.; Ware, V.C. )

    1989-03-01

    The authors have examined the kinetics of the process by which ribosomes are exported from the nucleus to the cytoplasm using Xenopus laevis oocytes microinjected into the germinal vesicle with radiolabeled ribosomes or ribosomal subunits from X. laevis, Tetrahymena thermophila, or Escherichia coli. Microinjected eukaryotic mature ribosomes are redistributed into the oocyte cytoplasm by an apparent carrier-mediated transport process that exhibits saturation kinetics as increasing amounts of ribosomes are injected. T. thermophila ribosomes are competent to traverse the Xenopus nuclear envelope, suggesting that the basic mechanism underlying ribosome transport is evolutionarily conserved. Microinjected E. coli ribosomes are not transported in this system, indicating that prokaryotic ribosomes lack the signals required for transport. Surprisingly, coinjected small (40S) and large (60S) subunits from T. thermophila are transported significantly faster than individual subunits. These observations support a facilitated transport model for the translocation of ribosomal subunits as separate units across the nuclear envelope whereby the transport rate of 60S or 40S subunits is enhanced by the presence of the partner subunit. Although the basic features of the transport mechanism have been preserved through evolution, other aspects of the process may be mediated through species-specific interactions. They hypothesize that a species-specific nuclear 40S-60S subunit association may expedite the transport of individual subunits across the nuclear envelope.

  18. Methanotrophic Bacteria and Facilitated Transport of Pollutants in Aquifer Material

    PubMed Central

    Jenkins, Michael B.; Chen, Jyh-Herng; Kadner, Debra J.; Lion, Leonard W.

    1994-01-01

    In situ stimulation of methanotrophic bacteria has been considered as a methodology for aquifer remediation. Chlorinated aliphatic hydrocarbons such as trichloroethylene are fortuitously oxidized by the methane monooxygenase produced by methanotrophic bacteria. Experimental results are presented that indicate that both colloidal suspensions containing methanotrophic cells and the soluble extracellular polymers produced by methanotrophic cells have the potential to enhance the transport and removal of other environmental contaminants such as polynuclear aromatic hydrocarbons and transition metals in aquifer material. Three well-characterized methanotrophic bacteria were used in the experiments: Methylomonas albus BG8 (a type I methanotroph), Methylosinus trichosporium OB3b (a type II methanotroph), and Methylocystis parvus OBBP (a type II methanotroph). Isotherms were obtained for sorption of two radiolabeled pollutants, [14C] phenanthrene and 109Cd, onto an aquifer sand in the presence and absence of washed cells and their extracellular polymer. Column transport experiments were performed with the washed methanotrophic cells and phenanthrene. The distribution coefficients for Cd with extracellular polymers were of the same order as that obtained with the aquifer sand, indicating that polymers from the methanotrophic bacteria could act to increase the transport of Cd in a porous medium. Polymer from BG8 significantly reduced the apparent distribution coefficient for Cd with an aquifer sand. [14C] phenanthrene also sorbed to extracellular polymer and to washed, suspended methanotrophic cells. The exopolymer of BG8 and OBBP significantly reduced the apparent distribution coefficient (Kd) for phenanthrene with aquifer sand. The distribution coefficients for phenanthrene with the methanotrophic cells were an order of magnitude greater than those previously reported for other heterotrophic bacteria. Cells of the methanotrophs also significantly reduced the apparent Kd

  19. Extraterrestrial Nucleobases in Carbonaceous Chondrites

    NASA Astrophysics Data System (ADS)

    Martins, Z.; Botta, O.; Fogel, M.; Sephton, M.; Glavin, D.; Watson, J.; Dworkin, J.; Schwartz, A.; Ehrenfreund, P.

    Nucleobases in Carbonaceous Chondrites Z. Martins (1), O. Botta (2), M. L. Fogel (3), M. A. Sephton (4), D. P. Glavin (2), J. S. Watson (5), J. P. Dworkin (2), A. W. Schwartz (6) and P. Ehrenfreund (1,6). (1) Astrobiology Laboratory, Leiden Institute of Chemistry, Leiden, The Netherlands, (2) NASA Goddard Space Flight Center, Goddard Center for Astrobiology, Greenbelt, MD, USA, (3) GL, Carnegie Institution of Washington, Washington DC, USA, (4) Impacts and Astromaterials Research Centre, Department of Earth Science and Engineering, South Kensington Campus, Imperial College, London, UK, (5) Planetary and Space Sciences Research Institute, The Open University, Walton Hall, Milton Keynes, UK, (6) Radboud University Nijmegen, Nijmegen, The Netherlands. E-mail: z.martins@chem.leidenuniv.nl/Phone:+31715274440 Nucleobases are crucial compounds in terrestrial biochemistry, because they are key components of DNA and RNA. Carbonaceous meteorites have been analyzed for nucleobases by different research groups [1-5]. However, significant quantitative and qualitative differences were observed, leading to the controversial about the origin of these nucleobases. In order to establish the origin of these compounds in carbonaceous chondrites and to assess the plausibility of their exogenous delivery to the early Earth, we have performed formic acid extraction of samples of the Murchison meteorite [6], followed by an extensive purification procedure, analysis and quantification by high-performance liquid chromatography with UV absorption detection and gas chromatography-mass spectrometry. Our results were qualitatively consistent with previous results [3, 4], but showed significant quantitative differences. Compound specific carbon isotope values were obtained, using gas chromatography-combustion- isotope ratio mass spectrometry. A soil sample collected in the proximity of the Murchison meteorite fall site was subjected to the same extraction, purification and analysis procedure

  20. Functionalized Solid Electrodes for Electrochemical Biosensing of Purine Nucleobases and Their Analogues: A Review

    PubMed Central

    Sharma, Vimal Kumar; Jelen, Frantisek; Trnkova, Libuse

    2015-01-01

    Interest in electrochemical analysis of purine nucleobases and few other important purine derivatives has been growing rapidly. Over the period of the past decade, the design of electrochemical biosensors has been focused on achieving high sensitivity and efficiency. The range of existing electrochemical methods with carbon electrode displays the highest rate in the development of biosensors. Moreover, modification of electrode surfaces based on nanomaterials is frequently used due to their extraordinary conductivity and surface to volume ratio. Different strategies for modifying electrode surfaces facilitate electron transport between the electrode surface and biomolecules, including DNA, oligonucleotides and their components. This review aims to summarize recent developments in the electrochemical analysis of purine derivatives, as well as discuss different applications. PMID:25594595

  1. Colloid Facilitated Transport of Radioactive Cations in the Vadose Zone: Field Experiments Oak Ridge

    SciTech Connect

    James E. Saiers

    2012-09-20

    The overarching goal of this study was to improve understanding of colloid-facilitated transport of radioactive cations through unsaturated soils and sediments. We conducted a suite of laboratory experiments and field experiments on the vadose-zone transport of colloids, organic matter, and associated contaminants of interest to the U.S. Department of Energy (DOE). The laboratory and field experiments, together with transport modeling, were designed to accomplish the following detailed objectives: 1. Evaluation of the relative importance of inorganic colloids and organic matter to the facilitation of radioactive cation transport in the vadose zone; 2. Assessment of the role of adsorption and desorption kinetics in the facilitated transport of radioactive cations in the vadose zone; 3. Examination of the effects of rainfall and infiltration dynamics and in the facilitated transport of radioactive cations through the vadose zone; 4. Exploration of the role of soil heterogeneity and preferential flow paths (e.g., macropores) on the facilitated transport of radioactive cations in the vadose zone; 5. Development of a mathematical model of facilitated transport of contaminants in the vadose zone that accurately incorporates pore-scale and column-scale processes with the practicality of predicting transport with readily available parameters.

  2. Spectroscopy of Isolated Prebiotic Nucleobases

    NASA Technical Reports Server (NTRS)

    Svadlenak, Nathan; Callahan, Michael P.; Ligare, Marshall; Gulian, Lisa; Gengeliczki, Zsolt; Nachtigallova, Dana; Hobza, Pavel; deVries, Mattanjah

    2011-01-01

    We use multiphoton ionization and double resonance spectroscopy to study the excited state dynamics of biologically relevant molecules as well as prebiotic nucleobases, isolated in the gas phase. Molecules that are biologically relevant to life today tend to exhibit short excited state lifetimes compared to similar but non-biologically relevant analogs. The mechanism is internal conversion, which may help protect the biologically active molecules from UV damage. This process is governed by conical intersections that depend very strongly on molecular structure. Therefore we have studied purines and pyrimidines with systematic variations of structure, including substitutions, tautomeric forms, and cluster structures that represent different base pair binding motifs. These structural variations also include possible alternate base pairs that may shed light on prebiotic chemistry. With this in mind we have begun to probe the ultrafast dynamics of molecules that exhibit very short excited states and search for evidence of internal conversions.

  3. Chemoenzymatic synthesis and utilization of a SAM analog with an isomorphic nucleobase.

    PubMed

    Vranken, C; Fin, A; Tufar, P; Hofkens, J; Burkart, M D; Tor, Y

    2016-07-14

    SalL, an enzyme that catalyzes the synthesis of SAM from l-methionine and 5'-chloro-5'-deoxyoadenosine, is shown to accept 5'-chloro-5'-deoxythienoadenosine as a substrate and facilitate the synthesis of a synthetic SAM analog with an unnatural nucleobase. This synthetic cofactor is demonstrated to replace SAM in the DNA methylation reaction with M.TaqI. PMID:27270873

  4. Nucleobase-functionalized ABC triblock copolymers: self-assembly of supramolecular architectures.

    PubMed

    Zhang, Keren; Fahs, Gregory B; Aiba, Motohiro; Moore, Robert B; Long, Timothy E

    2014-08-21

    RAFT polymerization afforded acrylic ABC triblock copolymers with self-complementary nucleobase-functionalized external blocks and a low-Tg soft central block. ABC triblock copolymers self-assembled into well-defined lamellar microphase-separated morphologies for potential applications as thermoplastic elastomers. Complementary hydrogen bonding within the hard phase facilitated self-assembly and enhanced mechanical performance. PMID:24984613

  5. Computation of the unsteady facilitated transport of oxygen in hemoglobin

    NASA Technical Reports Server (NTRS)

    Davis, Sanford

    1990-01-01

    The transport of a reacting permeant diffusing through a thin membrane is extended to more realistic dissociation models. A new nonlinear analysis of the reaction-diffusion equations, using implicit finite-difference methods and direct block solvers, is used to study the limits of linearized and equilibrium theories. Computed curves of molecular oxygen permeating through hemoglobin solution are used to illustrate higher-order reaction models, the effect of concentration boundary layers at the membrane interfaces, and the transient buildup of oxygen flux.

  6. Apparent genetic redundancy facilitates ecological plasticity for nitrate transport.

    PubMed

    Unkles, S E; Zhou, D; Siddiqi, M Y; Kinghorn, J R; Glass, A D

    2001-11-15

    Aspergillus nidulans possesses two high-affinity nitrate transporters, encoded by the nrtA and the nrtB genes. Mutants expressing either gene grew normally on 1-10 mM nitrate as sole nitrogen source, whereas the double mutant failed to grow on nitrate concentrations up to 200 mM. These genes appear to be regulated coordinately in all growth conditions, growth stages and regulatory genetic backgrounds studied. Flux analysis of single gene mutants using 13NO3(-) revealed that K(m) values for the NrtA and NrtB transporters were approximately 100 and approximately 10 microM, respectively, while V(max) values, though variable according to age, were approximately 600 and approximately 100 nmol/mg dry weight/h, respectively, in young mycelia. This kinetic differentiation may provide the necessary physiological and ecological plasticity to acquire sufficient nitrate despite highly variable external concentrations. Our results suggest that genes involved in nitrate assimilation may be induced by extracellular sensing of ambient nitrate without obligatory entry into the cell. PMID:11707396

  7. Transportation, integration, facilitation: Prehistoric trail networks of the Western Papagueria

    NASA Astrophysics Data System (ADS)

    White, Devin Alan

    This project used many sources of remotely sensed data, digital image analysis methods, advanced geospatial predictive modeling, and traditional archaeological survey to locate, document, contextualize, and interpret over one hundred prehistoric trails and associated networks in the Western Papagueria region of the North American Southwest in order to gain insight into how several landscapes within the region were used in the past. While a traditional culture history of the region suggests that the landscapes would have collectively been used primarily as a corridor for the transportation of exotic materials such as marine shell and salt from the Gulf of California to the Phoenix Basin and other parts of the Southwest, research has shown that the landscapes cannot be treated as a functional monolith. They exhibit a high degree of sub-regional variation motivated by strong local intra-community ties and sacred/ritual concerns in addition to energy-efficient, long distance travel motivated by exchange. This finding further strengthens current thinking related to the settlement of and regional interactions within the Western Papagueria during prehistory, one that continues to highlight its importance as a trade and transportation corridor, but also supports the idea of an indigenous semi-sedentary population that was focused inwards on fulfilling its own unique set of social, economic, and ideological needs.

  8. Transport by Collective Flagellar Beating Facilitates Evolutionary Transitions to Multicellularity

    NASA Astrophysics Data System (ADS)

    Short, Martin; Powers, Thomas

    2005-11-01

    A central problem underlying the evolution from single cells to multicellular organisms is the relationship between metabolic requirements and environmental metabolite exchange with increasing size. For organisms that form spherical colonies such as the volvocalean green algae, there is a bottleneck if diffusion alone governs nutrient uptake as they increase in size, for the diffusive flux is linear in the radius while the requirements of surface somatic cells grow quadratically. Using Volvox as a model organism, we examine experimentally and theoretically the role that advection of fluid by surface flagella plays in enhancing nutrient uptake. We show that the fluid flow driven by the coordinated beating of those flagella produces a boundary layer in the concentration of a diffusing solute which renders the metabolite exchange rate quadratic in the colony radius. This bypasses the diffusive bottleneck, facilitating evolutionary transitions to multicellularity which may be driven by other environmental factors. These results suggest that flagella may have evolved not only for motility, but also to enhance metabolite exchange.

  9. Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE

    PubMed Central

    Wisedchaisri, Goragot; Park, Min-Sun; Iadanza, Matthew G.; Zheng, Hongjin; Gonen, Tamir

    2014-01-01

    The major facilitator superfamily (MFS) is the largest collection of structurally related membrane proteins that transport a wide array of substrates. The proton-coupled sugar transporter XylE is the first member of the MFS that has been structurally characterized in multiple transporting conformations, including both the outward and inward-facing states. Here we report the crystal structure of XylE in a new inward-facing open conformation, allowing us to visualize the rocker-switch movement of the N-domain against the C-domain during the transport cycle. Using molecular dynamics simulation, and functional transport assays, we describe the movement of XylE that facilitates sugar translocation across a lipid membrane and identify the likely candidate proton-coupling residues as the conserved Asp27 and Arg133. This study addresses the structural basis for proton-coupled substrate transport and release mechanism for the sugar porter family of proteins. PMID:25088546

  10. Photoelectron Spectroscopy of Hexachloroplatinate-Nucleobase Complexes: Nucleobase Excited State Decay Observed via Delayed Electron Emission

    SciTech Connect

    Sen, Ananya; Matthews, Edward M.; Hou, Gao-Lei; Wang, Xue B.; Dessent, Caroline

    2015-11-14

    We report low-temperature photoelectron spectra of isolated gas-phase complexes of the hexachloroplatinate dianion bound to the nucleobases uracil, thymine, cytosine and adenine. The spectra display well-resolved, distinct peaks that are consistent with complexes where the hexachloroplatinate dianion is largely intact. Adiabatic electron detachment energies for the hexachloroplatinate-nucleobase complexes are measured as 2.26-2.36 eV. The magnitudes of the repulsive Coulomb barriers (RCBs) of the complexes are all ~1.7 eV, values that are lower than the RCB of the uncomplexed PtCl6 2- dianion as a result of charge solvation by the nucleobases. In addition to the resolved spectral features, broad featureless bands indicative of delayed electron detachment are observed in the 193 nm photoelectron spectra of the four clusters. The 266 nm spectra of the PtCl6 2-∙thymine and PtCl6 2-∙adenine complexes also display very prominent delayed electron emission bands. These results mirror recent results on the related Pt(CN)4 2-∙nucleobase complexes [Sen et al, J. Phys. Chem. B, 119, 11626, 2015]. The observation of delayed electron emission bands in the PtCl6 2-∙nucleobase spectra obtained in this work, as for the previously studied Pt(CN)4 2-∙nucleobase complexes, is attributed to onephoton excitation of nucleobase-centred excited states that can effectively couple to the electron detachment continuum, producing strong electron detachment. Moreover, the selective, strong excitation of the delayed emission bands in the 266 nm spectra is linked to fundamental differences in the individual nucleobase photophysics at this excitation energy. This strongly supports our previous suggestion that the dianion within these clusters can be viewed as a “dynamic tag” which has the propensity to emit electrons when the attached nucleobase decays over a timescale long enough to allow autodetachment.

  11. Active transporters as enzymes: an energetic framework applied to major facilitator superfamily and ABC importer systems.

    PubMed

    Shilton, Brian H

    2015-04-15

    Active membrane transporters are dynamic molecular machines that catalyse transport across a membrane by coupling solute movement to a source of energy such as ATP or a secondary ion gradient. A central question for many active transporters concerns the mechanism by which transport is coupled to a source of energy. The transport process and associated energetic coupling involve conformational changes in the transporter. For efficient transport, the conformational changes must be tightly regulated and they must link energy use to movement of the substrate across the membrane. The present review discusses active transport using the well-established energetic framework for enzyme-mediated catalysis. In particular, membrane transport systems can be viewed as ensembles consisting of low-energy and high-energy conformations. The transport process involves binding interactions that selectively stabilize the higher energy conformations, and in this way promote conformational changes in the system that are coupled to decreases in free energy and substrate translocation. The major facilitator superfamily of secondary active transporters is used to illustrate these ideas, which are then be expanded to primary active transport mediated by ABC (ATP-binding cassette) import systems, with a focus on the well-studied maltose transporter. PMID:25837849

  12. Decreased Salinity and Actinide Mobility: Colloid-Facilitated Transport or pH Change?

    PubMed

    Haliena, Brian; Zheng, Hangping; Melson, Nathan; Kaplan, Daniel I; Barnett, Mark O

    2016-01-19

    Colloids have been implicated in influencing the transport of actinides and other adsorbed contaminants in the subsurface, significantly increasing their mobility. Such colloid-facilitated transport can be induced by changes in groundwater chemistry that occur, for example, when high ionic strength contaminant plumes are displaced by infiltrating rainwater. We studied the transport and mobility of Th(IV), as an analogue for Pu(IV) and other tetravalent actinides [An(IV)], in saturated columns packed with a natural heterogeneous subsurface sandy sediment. As expected, decreases in ionic strength both promoted the mobilization of natural colloids and enhanced the transport of previously adsorbed Th(IV). However, colloid-facilitated transport played only a minor role in enhancing the transport of Th(IV). Instead, the enhanced transport of Th(IV) was primarily due to the pH-dependent desorption of Th(IV) caused by the change in ionic strength. In contrast, the adsorption of Th(IV) had a marked impact on the surface charge of the sandy sediment, significantly affecting the mobility of the colloids. In the absence of Th(IV), changes in ionic strength were ineffective at releasing colloids while in the presence of Th(IV), decreases in ionic strength liberated significant concentrations of colloids. Therefore, under the conditions of our experiments which mimicked acidic, high ionic strength groundwater contaminant plumes, Th(IV) had a much greater effect on colloid transport than colloids had on Th(IV) transport. PMID:26687028

  13. RNA fragment modeling with a nucleobase discrete-state model

    NASA Astrophysics Data System (ADS)

    Zhang, Jian; Bian, Yunqiang; Lin, Hui; Wang, Wei

    2012-02-01

    In this work we develop an approach for predicting the tertiary structures of RNA fragments by combining an RNA nucleobase discrete state (RNAnbds) model, a sequential Monte Carlo method, and a statistical potential. The RNAnbds model is designed for optimizing the configuration of nucleobases with respect to their preceding ones along the sequence and their spatial neighbors, in contrast to previous works that focus on RNA backbones. The tests of our approach with the fragments taken from a small RNA pseudoknot and a 23S ribosome RNA show that for short fragments (<10 nucleotides), the root mean square deviations (RMSDs) between the predicted and the experimental ones are generally smaller than 3 Å; for slightly longer fragments (10-15 nucleotides), most RMSDs are smaller than 4 Å. The comparison of our method with another physics-based predictor with a testing set containing nine loops shows that ours is superior in both accuracy and efficiency. Our approach is useful in facilitating RNA three-dimensional structure prediction as well as loop modeling. It also holds the promise of providing insight into the structural ensembles of RNA loops.

  14. Colloid facilitated transport in fractured rocks : parameter estimation and comparison with experimental data.

    SciTech Connect

    Viswanathan, H. S.; Wolfsberg, A. V.; Reimus, P. W.; Ware, S. D.; Lu, G.

    2003-01-01

    Colloid-facilitated migration of plutonium in fractured rock has been implicated in both field and laboratory studies . Other reactive radionuclides may also experience enhanced mobility due to groundwater colloids. Model prediction of this process is necessary for assessment of contaminant boundaries in systems for which radionuclides are already in the groundwater and for performance assessment of potential repositories for radioactive waste. Therefore, a reactive transport model is developed and parameterized using results from controlled laboratory fracture column experiments. Silica, montmorillonite and clinoptilolite colloids are used in the experiments along with plutonium and Tritium . . The goal of the numerical model is to identify and parameterize the physical and chemical processes that affect the colloid-facilitated transport of plutonium in the fractures. The parameters used in this model are similar in form to those that might be used in a field-scale transport model.

  15. Colloid facilitated transport in fractured rocks: parameter estimation and comparison with experimental data

    SciTech Connect

    Viswanthan, H.S.; Wolfsberg, A.V.; Reimus, P.W.; Ware, D.; Lu, G.

    2003-01-10

    Colloid-facilitated migration of plutonium in fractured rock has been implicated in both field and laboratory studies. Other reactive radionuclides may also experience enhanced mobility due to groundwater colloids. Model prediction of this process is necessary for assessment of contaminant boundaries in systems for which radionuclides are already in the groundwater and for performance assessment of potential repositories for radioactive waste. Therefore, a reactive transport model is developed and parameterized using results from controlled laboratory fracture column experiments. Silica, montmorillonite and clinoptilolite colloids are used in the experiments along with plutonium and Tritium. The goal of the numerical model is to identify and parameterize the physical and chemical processes that affect the colloid-facilitated transport of plutonium in the fractures. The parameters used in this model are similar in form to those that might be used in a field-scale transport model.

  16. Facilitating Electron Transportation in Perovskite Solar Cells via Water-Soluble Fullerenol Interlayers.

    PubMed

    Cao, Tiantian; Wang, Zhaowei; Xia, Yijun; Song, Bo; Zhou, Yi; Chen, Ning; Li, Yongfang

    2016-07-20

    TiO2 is widely used in perovskite solar cells (Pero-SCs), but its low electrical conductivity remains a drawback for application in electron transport layer (ETL). To overcome this problem, an easily accessible hydroxylated fullerene, fullerenol, was employed herein as ETL modified on ITO in n-i-p type (ITO as cathode) Pero-SCs for the first time. The results showed that the insertion of a single layer of fullerenol between perovskite and TiO2 dramatically facilitates the charge transportation and decreases the interfacial resistance. As a consequence, the device performance was greatly improved, and a higher power conversion efficiency of 14.69% was achieved, which is ∼17.5% enhancement compared with that (12.50%) of the control device without the fullerenol interlayer. This work provides a new candidate of interfacial engineering for facilitating the electron transportation in Pero-SCs. PMID:27311625

  17. Colloid-Facilitated Transport of Low-Solubility Radionuclides: A Field, Experimental, and Modeling Investigation

    SciTech Connect

    Kersting, A B; Reimus, P W; Abdel-Fattah, A; Allen, P G; Anghel, I; Benedict, F C; Esser, B K; Lu, N; Kung, K S; Nelson, J; Neu, M P; Reilly, S D; Smith, D K; Sylwester, E R; Wang, L; Ware, S D; Warren, RG; Williams, R W; Zavarin, M; Zhao, P

    2003-02-01

    For the last several years, the Underground Test Area (UGTA) program has funded a series of studies carried out by scientists to investigate the role of colloids in facilitating the transport of low-solubility radionuclides in groundwater, specifically plutonium (Pu). Although the studies were carried out independently, the overarching goals of these studies has been to determine if colloids in groundwater at the NTS can and will transport low-solubility radionuclides such as Pu, define the geochemical mechanisms under which this may or may not occur, determine the hydrologic parameters that may or may not enhance transport through fractures and provide recommendations for incorporating this information into future modeling efforts. The initial motivation for this work came from the observation in 1997 and 1998 by scientists from Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL) that low levels of Pu originally from the Benham underground nuclear test were detected in groundwater from two different aquifers collected from wells 1.3 km downgradient (Kersting et al., 1999). Greater than 90% of the Pu and other radionuclides were associated with the naturally occurring colloidal fraction (< 1 micron particles) in the groundwater. The colloids consisted mainly of zeolite (mordenite, clinoptilolite/heulandite), clays (illite, smectite) and cristobalite (SiO{sub 2}). These minerals were also identified as alteration mineral components in the host rock aquifer, a rhyolitic tuff. The observation that Pu can and has migrated in the subsurface at the NTS has forced a rethinking of our basic assumptions regarding the mechanical and geochemical transport pathways of low-solubility radionuclides. If colloid-facilitated transport is the primary mechanism for transporting low-solubility radionuclides in the subsurface, then current transport models based solely on solubility arguments and retardation estimates may underestimate the flux and

  18. Sensitivity analyses of a colloid-facilitated contaminant transport model for unsaturated heterogeneous soil conditions.

    NASA Astrophysics Data System (ADS)

    Périard, Yann; José Gumiere, Silvio; Rousseau, Alain N.; Caron, Jean

    2013-04-01

    Certain contaminants may travel faster through soils when they are sorbed to subsurface colloidal particles. Indeed, subsurface colloids may act as carriers of some contaminants accelerating their translocation through the soil into the water table. This phenomenon is known as colloid-facilitated contaminant transport. It plays a significant role in contaminant transport in soils and has been recognized as a source of groundwater contamination. From a mechanistic point of view, the attachment/detachment of the colloidal particles from the soil matrix or from the air-water interface and the straining process may modify the hydraulic properties of the porous media. Šimůnek et al. (2006) developed a model that can simulate the colloid-facilitated contaminant transport in variably saturated porous media. The model is based on the solution of a modified advection-dispersion equation that accounts for several processes, namely: straining, exclusion and attachement/detachement kinetics of colloids through the soil matrix. The solutions of these governing, partial differential equations are obtained using a standard Galerkin-type, linear finite element scheme, implemented in the HYDRUS-2D/3D software (Šimůnek et al., 2012). Modeling colloid transport through the soil and the interaction of colloids with the soil matrix and other contaminants is complex and requires the characterization of many model parameters. In practice, it is very difficult to assess actual transport parameter values, so they are often calibrated. However, before calibration, one needs to know which parameters have the greatest impact on output variables. This kind of information can be obtained through a sensitivity analysis of the model. The main objective of this work is to perform local and global sensitivity analyses of the colloid-facilitated contaminant transport module of HYDRUS. Sensitivity analysis was performed in two steps: (i) we applied a screening method based on Morris' elementary

  19. The multidrug transporters belonging to major facilitator superfamily in Mycobacterium tuberculosis.

    PubMed Central

    De Rossi, Edda; Arrigo, Patrizio; Bellinzoni, Marco; Silva, Pedro A. E.; Martín, Carlos; Aínsa, José A.; Guglierame, Paola; Riccardi, Giovanna

    2002-01-01

    BACKGROUND: Both intrinsic and acquired multidrug resistance play an important role in the insurgence of tuberculosis. Detailed knowledge of the molecular basis of drug recognition and transport by multidrug transport systems is required for the development of new antibiotics that are not extruded or of inhibitors that block the multidrug transporter and allow traditional antibiotics to be effective. MATERIALS AND METHODS: We have undertaken the inventory of the drug transporters subfamily, included in the major facilitator superfamily (MFS), encoded by the complete genome of Mycobacterium tuberculosis (MTB). These proteins were identified on the basis of their characteristic stretches of amino acids and transmembrane segments (TMS) number. CONCLUSIONS: Genome analysis and searches of homology between the identified transporters and proteins characterized in other organisms revealed 16 open reading frames encoding putative drug efflux pumps belonging to MFS. In the case of two of them, we also have demonstrated that they function as drug efflux proteins. PMID:12520088

  20. FACILITATED TRANSPORT OF INORGANIC CONTAMINANTS IN GROUNDWATER: PART II. COLLOIDAL TRANSPORT

    EPA Science Inventory

    This project consisted of both field and laboratory components. Field studies evaluated routine sampling procedures for determination of aqueous inorganicgeochemistry and assessment of contaminant transport by colloidal mobility. Research at three different metal-contaminated sit...

  1. Multifunctional, Biocompatible Supramolecular Hydrogelators Consist Only of Nucleobase, Amino Acid, and Glycoside

    PubMed Central

    Li, Xinming; Kuang, Yi; Shi, Junfeng; Gao, Yuan; Lin, Hsin-Chieh; Xu, Bing

    2011-01-01

    The integration of nucleobase, amino acid, and glycoside into a single molecule results in a novel class of supramolecular hydrogelators, which not only exhibit biocompatibility and biostability, but also facilitate the entry of nucleic acids into cytosol and nuclei of cells. This work illustrates a simple way to generate an unprecedented molecular architecture from the basic biological building blocks for the development of sophisticated soft nanomaterials, including supramolecular hydrogels. PMID:21928792

  2. Colloid-facilitated Cs transport through water-saturated Hanford sediment and Ottawa sand.

    PubMed

    Zhuang, Jie; Flury, Markus; Jin, Yan

    2003-11-01

    In this study, a series of saturated column experiments were conducted to investigate effects of colloids on Cs transport in two types of porous media (Hanford sediment characteristic of 2:1 clay minerals and silica Ottawa sand). The colloids used were obtained by reacting Hanford sediment with simulated tank waste solutions. Because of the highly nonlinear nature of Cs sorption found in batch experiments, we used two different concentrations of Cs (7.5 x 10(-5) M and 1.4 x 10(-8) M) for the transport experiments. The presence of colloids facilitated the transport of Cs through both Hanford sediment and Ottawa sand via association of Cs with mobile colloidal particles. Due to the nonlinearity of the Cs sorption, the colloid-facilitated Cs transportwas more pronounced atthe low Cs concentration (1.4 x 10(-8) M) than at the high concentration (7.5 x 10(-5) M) when expressed relative to the inflow Cs concentration. In the absence of colloids, no Cs moved through the 10-cm long columns during the experiment within about 20 pore volumes, exceptfor the high Cs concentration in the Ottawa sand where a complete Cs breakthrough was obtained. Also, it was found that colloid-associated Cs could be partially stripped off from colloids during the transport. The stripping effect was controlled by both Cs concentration and sorption capacity of the transport matrix. PMID:14620817

  3. Trehalose transporter 1, a facilitated and high-capacity trehalose transporter, allows exogenous trehalose uptake into cells

    PubMed Central

    Kikawada, Takahiro; Saito, Ayako; Kanamori, Yasushi; Nakahara, Yuichi; Iwata, Ken-ichi; Tanaka, Daisuke; Watanabe, Masahiko; Okuda, Takashi

    2007-01-01

    Trehalose is potentially a useful cryo- or anhydroprotectant molecule for cells and biomolecules such as proteins and nucleotides. A major obstacle to application is that cellular membranes are impermeable to trehalose. In this study, we isolated and characterized the functions of a facilitated trehalose transporter [trehalose transporter 1 (TRET1)] from an anhydrobiotic insect, Polypedilum vanderplanki. Tret1 cDNA encodes a 504-aa protein with 12 predicted transmembrane structures. Tret1 expression was induced by either desiccation or salinity stress. Expression was predominant in the fat body and occurred concomitantly with the accumulation of trehalose, indicating that TRET1 is involved in transporting trehalose synthesized in the fat body into the hemolymph. Functional expression of TRET1 in Xenopus oocytes showed that transport activity was stereochemically specific for trehalose and independent of extracellular pH (between 4.0 and 9.0) and electrochemical membrane potential. These results indicate that TRET1 is a trehalose-specific facilitated transporter and that the direction of transport is reversible depending on the concentration gradient of trehalose. The extraordinarily high values for apparent Km (≥100 mM) and Vmax (≥500 pmol/min per oocyte) for trehalose both indicate that TRET1 is a high-capacity transporter of trehalose. Furthermore, TRET1 was found to function in mammalian cells, suggesting that it confers trehalose permeability on cells, including those of vertebrates as well as insects. These characteristic features imply that TRET1 in combination with trehalose has high potential for basic and practical applications in vivo. PMID:17606922

  4. Photoelectron spectroscopy of hexachloroplatinate-nucleobase complexes: Nucleobase excited state decay observed via delayed electron emission

    SciTech Connect

    Sen, Ananya; Matthews, Edward M.; Dessent, Caroline E. H. E-mail: xuebin.wang@pnnl.gov; Hou, Gao-Lei; Wang, Xue-Bin E-mail: xuebin.wang@pnnl.gov

    2015-11-14

    We report low-temperature photoelectron spectra of isolated gas-phase complexes of the hexachloroplatinate dianion bound to the nucleobases uracil, thymine, cytosine, and adenine. The spectra display well-resolved, distinct peaks that are consistent with complexes where the hexachloroplatinate dianion is largely intact. Adiabatic electron detachment energies for the hexachloroplatinate-nucleobase complexes are measured as 2.26-2.36 eV. The magnitudes of the repulsive Coulomb barriers (RCBs) of the complexes are all ∼1.7 eV, values that are lower than the RCB of the uncomplexed PtCl{sub 6}{sup 2−} dianion as a result of charge solvation by the nucleobases. In addition to the resolved spectral features, broad featureless bands indicative of delayed electron detachment are observed in the 193 nm photoelectron spectra of the four clusters. The 266 nm spectra of the PtCl{sub 6}{sup 2−} ⋅ thymine and PtCl{sub 6}{sup 2−} ⋅ adenine complexes also display very prominent delayed electron emission bands. These results mirror recent results on the related Pt(CN){sub 4}{sup 2−} ⋅ nucleobase complexes [A. Sen et al., J. Phys. Chem. B 119, 11626 (2015)]. The observation of delayed electron emission bands in the PtCl{sub 6}{sup 2−} ⋅ nucleobase spectra obtained in this work, as for the previously studied Pt(CN){sub 4}{sup 2−} ⋅ nucleobase complexes, is attributed to one-photon excitation of nucleobase-centred excited states that can effectively couple to the electron detachment continuum, producing strong electron detachment. Moreover, the selective, strong excitation of the delayed emission bands in the 266 nm spectra is linked to fundamental differences in the individual nucleobase photophysics at this excitation energy. This strongly supports our previous suggestion that the dianion within these clusters can be viewed as a “dynamic tag” which has the propensity to emit electrons when the attached nucleobase decays over a time scale long enough to

  5. Synthetic ion transporters can induce apoptosis by facilitating chloride anion transport into cells

    NASA Astrophysics Data System (ADS)

    Ko, Sung-Kyun; Kim, Sung Kuk; Share, Andrew; Lynch, Vincent M.; Park, Jinhong; Namkung, Wan; van Rossom, Wim; Busschaert, Nathalie; Gale, Philip A.; Sessler, Jonathan L.; Shin, Injae

    2014-10-01

    Anion transporters based on small molecules have received attention as therapeutic agents because of their potential to disrupt cellular ion homeostasis. However, a direct correlation between a change in cellular chloride anion concentration and cytotoxicity has not been established for synthetic ion carriers. Here we show that two pyridine diamide-strapped calix[4]pyrroles induce coupled chloride anion and sodium cation transport in both liposomal models and cells, and promote cell death by increasing intracellular chloride and sodium ion concentrations. Removing either ion from the extracellular media or blocking natural sodium channels with amiloride prevents this effect. Cell experiments show that the ion transporters induce the sodium chloride influx, which leads to an increased concentration of reactive oxygen species, release of cytochrome c from the mitochondria and apoptosis via caspase activation. However, they do not activate the caspase-independent apoptotic pathway associated with the apoptosis-inducing factor. Ion transporters, therefore, represent an attractive approach for regulating cellular processes that are normally controlled tightly by homeostasis.

  6. Transportation Facilitation Education Program: A Handbook for Transportation and Distribution. Part III. Final Report.

    ERIC Educational Resources Information Center

    Oregon Univ., Eugene. Coll. of Business Administration.

    The handbook accents the nature of transportation and related domestic and international business activities. Its objective is to provide basic information for the newcomer to the field. Chapters 2 and 3 describe assistance available from public and private agencies, as well as regulatory requirements for foreign traders and a resume of the…

  7. Communication: Photoactivation of nucleobase bound platinum(II) metal complexes: probing the influence of the nucleobase.

    PubMed

    Sen, Ananya; Dessent, Caroline E H

    2014-12-28

    We present UV laser action spectra (220-300 nm) of isolated nucleobase-bound Pt(II)(CN)4(2-) complexes, i.e., Pt(CN)4(2-)⋅M, where M = uracil, thymine, cytosine, and adenine. These metal complex-nucleobase clusters represent model systems for identifying the fundamental photophysical and photochemical processes occurring in photodynamic platinum (II) drug therapies that target DNA. This is the first study to explore the specific role of the nucleobase in the photophysics of the aggregate complex. Each of the complexes studied displays a broadly similar absorption spectra, with a strong λmax ∼ 4.7 eV absorption band (nucleobase localized chromophore) and a subsequent increase in the absorption intensity towards higher spectral-energy (Pt(CN)4(2-) localized chromophore). However, strikingly different band widths are observed across the series of complexes, decreasing in the order Pt(CN)4(2-)⋅Thymine > Pt(CN)4(2-)⋅Uracil > Pt(CN)4(2-)⋅Adenine > Pt(CN)4(2-)⋅Cytosine. Changes in the bandwidth of the ∼4.7 eV band are accompanied by distinctive changes in the photofragment product ions observed following photoexcitation, with the narrower-bandwidth complexes showing a greater propensity to decay via electron detachment decay. We discuss these observations in the context of the distinctive nucleobase-dependent excited state lifetimes. PMID:25554122

  8. Facilitated diffusion of 6-deoxy-D-glucose in bakers' yeast: evidence against phosphorylation-associated transport of glucose.

    PubMed Central

    Romano, A H

    1982-01-01

    6-Deoxy-D-glucose, a structural homomorph of D-glucose which lacks a hydroxyl group at carbon 6 and thus cannot be phosphorylated, is transported by Saccharomyces cerevisiae via a facilitated diffusion system with affinity equivalent to that shown with D-glucose. This finding supports the facilitated diffusion mechanism for glucose transport and contradicts theories of transport-associated phosphorylation which hold that sugar phosphorylation is necessary for high-affinity operation of the glucose carrier. PMID:6754704

  9. Facilitated transport of anatase titanium dioxides nanoparticles in the presence of phosphate in saturated sands.

    PubMed

    Chen, Ming; Xu, Nan; Cao, Xinde; Zhou, Kairong; Chen, Zhigang; Wang, Yunlong; Liu, Cheng

    2015-08-01

    Soil and water environments are inevitably contaminated by the excess of artificial nanoparticles (NPs) and phosphorus (P) fertilizers. There is a possibility of phosphate facilitating or inhibiting the transport of nanoparticles titanium dioxides (nTiO2). It is a great urgency and high priority to investigate the nTiO2 retention mechanisms and accurately describe the transport of nTiO2 in the presence of phosphate. Anatase nTiO2 with two sizes of 20 and 50nm through the saturated porous sand columns were observed under the conditions (0-50mM NaNO3 electrolyte, influent P concentrations of 0.10mM and 2.0mM, pH 6.5 and 7.5). The experimental results show the phosphate favor the dispersion of nTiO2, and consequently improve their transport patterns. The likely mechanism is that phosphate adsorption increasing the negative charge on the surface promotes the transportability of nTiO2 resulting from the low deposition rate and attachment efficiency of NPs. In particular, the facilitated transport of nTiO2 (50nm) is greater than those relative smaller as 20nm. In addition, this enhancement of nTiO2 transportability by phosphate at pH 6.5 is increased at higher pH of 7.5 due to the more negative zeta potential of surface, which indicates the potential risks to groundwater systems. PMID:25897849

  10. Carbonaceous Meteorites Contain a Wide Range of Extraterrestrial Nucleobases

    NASA Technical Reports Server (NTRS)

    Callahan, Michael P.; Smith, Karen E.; Cleaves, H. James, II; Ruzicka, Josef; Stern, Jennifer C.; Glavin, Daniel P.; House, Christopher H.; Dworkin, Jason P.

    2011-01-01

    All terrestrial organisms depend on nucleic acids (RNA and DNA), which use pyrimidine and purine nucleobases to encode genetic information. Carbon-rich meteorites may have been important sources of organic compounds required for the emergence of life on the early Earth; however, the origin and formation of nuc1eobases in meteorites has been debated for over 50 y. So far, the few nuc1eobases reported in meteorites are biologically common and lacked the structural diversity typical of other indigenous meteoritic organics. Here, we investigated the abundance and distribution of nucleobases and nucleobase analogs in formic acid extracts of 12 different meteorites by liquid chromatography-mass spectrometry. The Murchison and Lonewolf Nunataks 94102 meteorites contained a diverse suite of nucleobases, which included three unusual and terrestrially rare nucleobase analogs; purine, 2,6-diminopurine, and 6,8-diaminopurine. In a parallel experiment, we found an identical suite of nucleobases and nucleobase analogs generated in reactions of ammonium cyanide. Additionally, these nucleobase analoge were not detected above our parts-per-billion detection limits in any of the procedural blanks, control samples, a terrestrial soil sample, and an Antarctic ice sample. Our results demonstrate that the purines detected in meteorites are consistent with products of ammonium cyanide chemistry, which provides a plausible mechanism for their synthesis in the asteroid parent bodies, and strongly supports an extraterrestrial origin. The discovery of new nucleobase analogs in meteorites also expands the prebiotic molecular inventory available for constructing the first genetic molecules.

  11. Facilitated transport ceramic membranes for high-temperature gas cleanup. Final report, February 1990--April 1994

    SciTech Connect

    Quinn, R.; Minford, E.; Damle, A.S.; Gangwal, S.K.; Hart, B.A.

    1994-04-01

    The objective of this program was to demonstrate the feasibility of developing high temperature, high pressure, facilitated transport ceramic membranes to control gaseous contaminants in Integrated Gasification Combined Cycle (IGCC) power generation systems. Meeting this objective requires that the contaminant gas H{sub 2}S be removed from an IGCC gas mixture without a substantial loss of the other gaseous components, specifically H{sub 2} and CH{sub 4}. As described above this requires consideration of other, nonconventional types of membranes. The solution evaluated in this program involved the use of facilitated transport membranes consisting of molten mixtures of alkali and alkaline earth carbonate salts immobilized in a microporous ceramic support. To accomplish this objective, Air Products and Chemicals, Inc., Golden Technologies Company Inc., and Research Triangle Institute worked together to develop and test high temperature facilitated membranes for the removal of H{sub 2}S from IGCC gas mixtures. Three basic experimental activities were pursued: (1) evaluation of the H{sub 2}S chemistry of a variety of alkali and alkaline earth carbonate salt mixtures; (2) development of microporous ceramic materials which were chemically and physically compatible with molten carbonate salt mixtures under IGCC conditions and which could function as a host to support a molten carbonate mixture and; (3) fabrication of molten carbonate/ceramic immobilized liquid membranes and evaluation of these membranes under conditions approximating those found in the intended application. Results of these activities are presented.

  12. Members of the Francisella tularensis Phagosomal Transporter Subfamily of Major Facilitator Superfamily Transporters Are Critical for Pathogenesis

    PubMed Central

    Marohn, Mark E.; Santiago, Araceli E.; Shirey, Kari Ann; Lipsky, Michael; Vogel, Stefanie N.

    2012-01-01

    Francisella tularensis is the causative agent of tularemia. Due to its aerosolizable nature and low infectious dose, F. tularensis is classified as a category A select agent and, therefore, is a priority for vaccine development. Survival and replication in macrophages and other cell types are critical to F. tularensis pathogenesis, and impaired intracellular survival has been linked to a reduction in virulence. The F. tularensis genome is predicted to encode 31 major facilitator superfamily (MFS) transporters, and the nine-member Francisella phagosomal transporter (Fpt) subfamily possesses homology with virulence factors in other intracellular pathogens. We hypothesized that these MFS transporters may play an important role in F. tularensis pathogenesis and serve as good targets for attenuation and vaccine development. Here we show altered intracellular replication kinetics and attenuation of virulence in mice infected with three of the nine Fpt mutant strains compared with wild-type (WT) F. tularensis LVS. The vaccination of mice with these mutant strains was protective against a lethal intraperitoneal challenge. Additionally, we observed pronounced differences in cytokine profiles in the livers of mutant-infected mice, suggesting that alterations in in vivo cytokine responses are a major contributor to the attenuation observed for these mutant strains. These results confirm that this subset of MFS transporters plays an important role in the pathogenesis of F. tularensis and suggest that a focus on the development of attenuated Fpt subfamily MFS transporter mutants is a viable strategy toward the development of an efficacious vaccine. PMID:22508856

  13. Protonation of Glu135 Facilitates the Outward-to-Inward Structural Transition of Fucose Transporter

    PubMed Central

    Liu, Yufeng; Ke, Meng; Gong, Haipeng

    2015-01-01

    Major facilitator superfamily (MFS) transporters typically need to alternatingly sample the outward-facing and inward-facing conformations, in order to transport the substrate across membrane. To understand the mechanism, in this work, we focused on one MFS member, the L-fucose/H+ symporter (FucP), whose crystal structure exhibits an outward-open conformation. Previous experiments imply several residues critical to the substrate/proton binding and structural transition of FucP, among which Glu135, located in the periplasm-accessible vestibule, is supposed as being involved in both proton translocation and conformational change of the protein. Here, the structural transition of FucP in presence of substrate was investigated using molecular-dynamics simulations. By combining the equilibrium and accelerated simulations as well as thermodynamic calculations, not only was the large-scale conformational change from the outward-facing to inward-facing state directly observed, but also the free energy change during the structural transition was calculated. The simulations confirm the critical role of Glu135, whose protonation facilitates the outward-to-inward structural transition both by energetically favoring the inward-facing conformation in thermodynamics and by reducing the free energy barrier along the reaction pathway in kinetics. Our results may help the mechanistic studies of both FucP and other MFS transporters. PMID:26244736

  14. Facilitation of axon regeneration by enhancing mitochondrial transport and rescuing energy deficits.

    PubMed

    Zhou, Bing; Yu, Panpan; Lin, Mei-Yao; Sun, Tao; Chen, Yanmin; Sheng, Zu-Hang

    2016-07-01

    Although neuronal regeneration is a highly energy-demanding process, axonal mitochondrial transport progressively declines with maturation. Mature neurons typically fail to regenerate after injury, thus raising a fundamental question as to whether mitochondrial transport is necessary to meet enhanced metabolic requirements during regeneration. Here, we reveal that reduced mitochondrial motility and energy deficits in injured axons are intrinsic mechanisms controlling regrowth in mature neurons. Axotomy induces acute mitochondrial depolarization and ATP depletion in injured axons. Thus, mature neuron-associated increases in mitochondria-anchoring protein syntaphilin (SNPH) and decreases in mitochondrial transport cause local energy deficits. Strikingly, enhancing mitochondrial transport via genetic manipulation facilitates regenerative capacity by replenishing healthy mitochondria in injured axons, thereby rescuing energy deficits. An in vivo sciatic nerve crush study further shows that enhanced mitochondrial transport in snph knockout mice accelerates axon regeneration. Understanding deficits in mitochondrial trafficking and energy supply in injured axons of mature neurons benefits development of new strategies to stimulate axon regeneration. PMID:27268498

  15. The Sodium Glucose Cotransporter SGLT1 Is an Extremely Efficient Facilitator of Passive Water Transport.

    PubMed

    Erokhova, Liudmila; Horner, Andreas; Ollinger, Nicole; Siligan, Christine; Pohl, Peter

    2016-04-29

    The small intestine is void of aquaporins adept at facilitating vectorial water transport, and yet it reabsorbs ∼8 liters of fluid daily. Implications of the sodium glucose cotransporter SGLT1 in either pumping water or passively channeling water contrast with its reported water transporting capacity, which lags behind that of aquaporin-1 by 3 orders of magnitude. Here we overexpressed SGLT1 in MDCK cell monolayers and reconstituted the purified transporter into proteoliposomes. We observed the rate of osmotic proteoliposome deflation by light scattering. Fluorescence correlation spectroscopy served to assess (i) SGLT1 abundance in both vesicles and plasma membranes and (ii) flow-mediated dilution of an aqueous dye adjacent to the cell monolayer. Calculation of the unitary water channel permeability, pf, yielded similar values for cell and proteoliposome experiments. Neither the absence of glucose or Na(+), nor the lack of membrane voltage in vesicles, nor the directionality of water flow grossly altered pf Such weak dependence on protein conformation indicates that a water-impermeable occluded state (glucose and Na(+) in their binding pockets) lasts for only a minor fraction of the transport cycle or, alternatively, that occlusion of the substrate does not render the transporter water-impermeable as was suggested by computational studies of the bacterial homologue vSGLT. Although the similarity between the pf values of SGLT1 and aquaporin-1 makes a transcellular pathway plausible, it renders water pumping physiologically negligible because the passive flux would be orders of magnitude larger. PMID:26945065

  16. SWEET17, a Facilitative Transporter, Mediates Fructose Transport across the Tonoplast of Arabidopsis Roots and Leaves1[W][OPEN

    PubMed Central

    Guo, Woei-Jiun; Nagy, Reka; Chen, Hsin-Yi; Pfrunder, Stefanie; Yu, Ya-Chi; Santelia, Diana; Frommer, Wolf B.; Martinoia, Enrico

    2014-01-01

    Fructose (Fru) is a major storage form of sugars found in vacuoles, yet the molecular regulation of vacuolar Fru transport is poorly studied. Although SWEET17 (for SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTERS17) has been characterized as a vacuolar Fru exporter in leaves, its expression in leaves is low. Here, RNA analysis and SWEET17-β-glucuronidase/-GREEN FLUORESCENT PROTEIN fusions expressed in Arabidopsis (Arabidopsis thaliana) reveal that SWEET17 is highly expressed in the cortex of roots and localizes to the tonoplast of root cells. Expression of SWEET17 in roots was inducible by Fru and darkness, treatments that activate accumulation and release of vacuolar Fru, respectively. Mutation and ectopic expression of SWEET17 led to increased and decreased root growth in the presence of Fru, respectively. Overexpression of SWEET17 specifically reduced the Fru content in leaves by 80% during cold stress. These results intimate that SWEET17 functions as a Fru-specific uniporter on the root tonoplast. Vacuoles overexpressing SWEET17 showed increased [14C]Fru uptake compared with the wild type. SWEET17-mediated Fru uptake was insensitive to ATP or treatment with NH4Cl or carbonyl cyanide m-chlorophenyl hydrazone, indicating that SWEET17 functions as an energy-independent facilitative carrier. The Arabidopsis genome contains a close paralog of SWEET17 in clade IV, SWEET16. The predominant expression of SWEET16 in root vacuoles and reduced root growth of mutants under Fru excess indicate that SWEET16 also functions as a vacuolar transporter in roots. We propose that in addition to a role in leaves, SWEET17 plays a key role in facilitating bidirectional Fru transport across the tonoplast of roots in response to metabolic demand to maintain cytosolic Fru homeostasis. PMID:24381066

  17. The influence of non-linear sorption on colloid facilitated radionuclide transport through fractured media

    SciTech Connect

    Smith, P.A.

    1993-12-31

    In the safety assessment of nuclear waste repositories, sorption of radionuclides on the surfaces of colloids may significantly modify transport behavior where colloid concentration is sufficiently high. In the case of fractured geological media, colloids may be excluded from matrix pores, in which case radionuclides bound to them are not subject to the retarding effects of matrix diffusion and sorption onto matrix pore surfaces. A model is presented describing colloid facilitated transport through fractured media with non-linear sorption. A simple criterion is developed to predict when the presence of colloids will have a significant influence on transport and effects resulting from non-linearity of sorption are described. However, lack of comprehensive sorption data, as well as computational efficiency, mean that the use of a simplified transport model, with linear sorption both on pore surfaces and colloids, is desirable if it can be demonstrated to be conservative. A further criterion is developed to predict where such a model, with linear sorption calculated for the highest concentration encountered along the flow path, would be expected to yield conservative results.

  18. Facilitated transport of heavy metals by bacterial colloids in sand columns

    NASA Astrophysics Data System (ADS)

    Guiné, V.; Martins, J.; Gaudet, J. P.

    2003-05-01

    The aim of this work is to evaluate the ability of biotic collois (e.g. bacterial cells) to facilitate the transport of heavy metals in soils. and to identify the main factors influencing colloid transport in order to detelmine the geo-chemical conditions where this secondary transport process may become dominant. The model colloids studied here are living cells of Escherichia coli and Ralstonia metallidurans. We studied the transport of mercury zinc, and cadmium in columns of Fontainebleau sand. The properties (i.e. optical and morphological properties, charge (zeta potential, zeta) and hydrophobia (water/hexadecane distribution parameter, K_{hw})) of the bacterial cells surface were characterised, as well as their potential for heavy metals sorption (kinetic and isotherm). Both surface charge (zeta=-54 and -14 mV) and hydrophobia (K_{hw} = 0.25 and 0.05) differ strongly for the two bacteria. Column studies were conducted with bacteria and heavy metals separately or simultaneously. The cell surface differences led to different transport behaviour of the two bacteria, although the retardation factor is close to 1 for both. We observed that colloid mobility increases when increasing bacterial cells concentration and when decreasing the ionic strength. We also observed that bacterial colloids appeared as excellent vectors for Hg, Zn and Cd. Indeed, heavy metals adsorbed on the Fontainebleau sand when injected alone in columns (retardation factors of 1.4 ; 2.9 and 3.8 for Hg, Zn and Cd, respectively); whereas no retardation (R≈1) is observed when injected in the presence of both bacteria. Moreover, transport of bio-sorbed metal appears to be 4 to 6 times higher than dissolved heavy-metal.

  19. De novo pyrimidine nucleotide synthesis mainly occurs outside of plastids, but a previously undiscovered nucleobase importer provides substrates for the essential salvage pathway in Arabidopsis.

    PubMed

    Witz, Sandra; Jung, Benjamin; Fürst, Sarah; Möhlmann, Torsten

    2012-04-01

    Nucleotide de novo synthesis is highly conserved among organisms and represents an essential biochemical pathway. In plants, the two initial enzymatic reactions of de novo pyrimidine synthesis occur in the plastids. By use of green fluorescent protein fusions, clear support is provided for a localization of the remaining reactions in the cytosol and mitochondria. This implies that carbamoyl aspartate, an intermediate of this pathway, must be exported and precursors of pyrimidine salvage (i.e., nucleobases or nucleosides) are imported into plastids. A corresponding uracil transport activity could be measured in intact plastids isolated from cauliflower (Brassica oleracea) buds. PLUTO (for plastidic nucleobase transporter) was identified as a member of the Nucleobase:Cation-Symporter1 protein family from Arabidopsis thaliana, capable of transporting purine and pyrimidine nucleobases. A PLUTO green fluorescent protein fusion was shown to reside in the plastid envelope after expression in Arabidopsis protoplasts. Heterologous expression of PLUTO in an Escherichia coli mutant lacking the bacterial uracil permease uraA allowed a detailed biochemical characterization. PLUTO transports uracil, adenine, and guanine with apparent affinities of 16.4, 0.4, and 6.3 μM, respectively. Transport was markedly inhibited by low concentrations of a proton uncoupler, indicating that PLUTO functions as a proton-substrate symporter. Thus, a protein for the absolutely required import of pyrimidine nucleobases into plastids was identified. PMID:22474184

  20. Pultonium Colloid-Facilitated Transport in the Environment - Experimental and Transport Modeling Evidence for Plutonium Migration Mechanisms

    SciTech Connect

    Zavarin, M; Maxwell, R M; Kersting, A B; Zhao, P; Sylwester, E R; Allen, P G; Williams, R W

    2003-02-19

    Natural inorganic colloids (< 1 micron particles) found in groundwater can sorb low-solubility actinides and may provide a pathway for transport in the subsurface. For example, Kerting et al found that Pu, associated with colloids fraction of the groundwater, was detected over 1 km away from the underground nuclear test at the Nevada Test Site (NTS) where it was originally deposited 28 years earlier. However, laboratory experiments have not identified the mechanisms by which Pu may sorb to colloids or exist as its own colloid and travel relatively unimpeded in the subsurface. Some data suggest that Pu sorption to colloids is a very fast process while desorption is very slow or simply does not occur. Slow desorption of Pu from colloids could allow Pu sorbed to a colloid to travel much farther than if sorption were an equilibrium process. However, PU sorption (and particularly desorption) data in the literature are scant and sometimes contradictory. In some cases, Pu desorption is rather fast, with rates dependent on colloid mineralogy. Moreover, the effect of sorption and desorption kinetics (as well as other mechanisms) on colloid-facilitated transport at the field scale has not been thoroughly evaluated. This is, in part, due to limitations in colloid transport as well as sorption/desorption models.

  1. Functional characterization of the human facilitative glucose transporter 12 (GLUT12) by electrophysiological methods.

    PubMed

    Pujol-Giménez, Jonai; Pérez, Alejandra; Reyes, Alejandro M; Loo, Donald D F; Lostao, Maria Pilar

    2015-06-15

    GLUT12 is a member of the facilitative family of glucose transporters. The goal of this study was to characterize the functional properties of GLUT12, expressed in Xenopus laevis oocytes, using radiotracer and electrophysiological methods. Our results showed that GLUT12 is a facilitative sugar transporter with substrate selectivity: d-glucose ≥ α-methyl-d-glucopyranoside (α-MG) > 2-deoxy-d-glucose(2-DOG) > d-fructose = d-galactose. α-MG is a characteristic substrate of the Na(+)/glucose (SGLT) family and has not been shown to be a substrate of any of the GLUTs. In the absence of sugar, (22)Na(+) was transported through GLUT12 at a higher rate (40%) than noninjected oocytes, indicating that there is a Na(+) leak through GLUT12. Genistein, an inhibitor of GLUT1, also inhibited sugar uptake by GLUT12. Glucose uptake was increased by the PKA activator 8-bromoadenosine 3',5'-cyclic monophosphate (8-Br-cAMP) but not by the PKC activator phorbol-12-myristate-13-acetate (PMA). In high K(+) concentrations, glucose uptake was blocked. Addition of glucose to the external solution induced an inward current with a reversal potential of approximately -15 mV and was blocked by Cl(-) channel blockers, indicating the current was carried by Cl(-) ions. The sugar-activated Cl(-) currents were unaffected by genistein. In high external K(+) concentrations, sugar-activated Cl(-) currents were also blocked, indicating that GLUT12 activity is voltage dependent. Furthermore, glucose-induced current was increased by the PKA activator 8-Br-cAMP but not by the PKC activator PMA. These new features of GLUT12 are very different from those described for other GLUTs, indicating that GLUT12 must have a specific physiological role within glucose homeostasis, still to be discovered. PMID:25855082

  2. Colloid-facilitated Pb transport in two shooting-range soils in Florida.

    PubMed

    Yin, Xianqiang; Gao, Bin; Ma, Lena Q; Saha, Uttam Kumar; Sun, Huimin; Wang, Guodong

    2010-05-15

    Shooting range soils with elevated Pb contents are of environmental concern due to their adverse impacts on human and animals. In Florida, the problem merits special attention because of Florida's sandy soil, high rainfall, and shallow groundwater level, which tend to favor Pb migration. This study used large intact soil column to examine colloid-facilitated Pb transport in two Florida shooting-range soils with different physicochemical properties (e.g., organic carbon content, pH, and clay content). Simulated rainwater (SRW) was pumped through the intact soil columns under different ionic strengths (0.07 and 5 mmol L(-1)) and flow rates (2.67, 5.30 and 10.6 cm h(-1)) to mobilize Pb and soil colloids. Our results showed that colloids dominated Pb transport in both soils and there was a significant correlation between colloids and Pb in the leachates. Decreases in ionic strength and increases in flow rate enhanced the release of both colloids and Pb in the soils. Size fraction analyses showed that in OCR soils (sandy soils with low organic carbon), most of the Pb (87%) was associated with coarse colloid fraction (0.45-8 microm). However, high Pb level (66%) was found in the dissolved and nano-sized colloid fraction (<0.1 microm) in the MPR soils (sandy soils with high organic carbon). This suggests that soil properties are important to Pb migration in soils and groundwater. Our study indicated that colloids play an important role in facilitating Pb transport in shooting range soils. PMID:20079969

  3. Intrinsic and Carrier Colloid-facilitated transport of lanthanides through discrete fractures in chalk

    NASA Astrophysics Data System (ADS)

    Weisbrod, N.; Tran, E. L.; Klein-BenDavid, O.; Teutsch, N.

    2015-12-01

    Geological disposal of high-level radioactive waste is the long term solution for the disposal of long lived radionuclides and spent fuel. However, some radionuclides might be released from these repositories into the subsurface as a result of leakage, which ultimately make their way into groundwater. Engineered bentonite barriers around nuclear waste repositories are generally considered sufficient to impede the transport of radionuclides from their source to the groundwater. However, colloidal-sized mobile bentonite particles ("carrier" colloids) originating from these barriers have come under investigation as a potential transport vector for radionuclides sorbed to them. As lanthanides are generally accepted to have the same chemical behaviors as their more toxic actinide counterparts, lanthanides are considered an acceptable substitute for research on radionuclide transportation. This study aims to evaluate the transport behaviors of lanthanides in colloid-facilitated transport through a fractured chalk matrix and under geochemical conditions representative the Negev desert, Israel. The migration of Ce both with and without colloidal particles was explored and compared to the migration of a conservative tracer (bromide) using a flow system constructed around a naturally fractured chalk core. Results suggest that mobility of Ce as a solute is negligible. In experiments conducted without bentonite colloids, the 1% of the Ce that was recovered migrated as "intrinsic" colloids in the form of carbonate precipitates. However, the total recovery of the Ce increased to 9% when it was injected into the core in the presence of bentonite colloids and 13% when both bentonite and precipitate colloids were injected. This indicates that lanthanides are essentially immobile in chalk as a solute but may be mobile as carbonate precipitates. Bentonite colloids, however, markedly increase the mobility of lanthanides through fractured chalk matrices.

  4. Colloid-facilitated transport of cesium in variably saturated Hanford sediments.

    PubMed

    Chen, Gang; Flury, Markus; Harsh, James B; Lichtner, Peter C

    2005-05-15

    Radioactive 137Cs has leaked from underground waste tanks into the vadose zone at the Hanford Reservation in south-central Washington State. There is concern that 137Cs, currently located in the vadose zone, can reach the groundwater. In this study, we investigated whether, and to what extent, colloidal particles can facilitate the transport of 137Cs at Hanford. We used colloidal materials isolated from Hanford sediments. Transport experiments were conducted under variably saturated, steady-state flow conditions in repacked, 20 cm long Hanford sediment columns, with effective water saturations ranging from 0.2 to 1.0. Cesium, pre-associated with colloids, was stripped off during transport through the sediments. The higher the flow rates, the less Cs was stripped off, indicating in part that Cs desorption from carrying colloids was a residence-time-dependent process. Depending on the flow rate, up to 70% of the initially sorbed Cs desorbed from colloidal carriers and was captured in the stationary sediments. Less Cs was stripped off colloids under unsaturated than under saturated flow conditions at similar flow rates. This phenomenon was likely due to the reduced availability of sorption sites for Cs on the sediments as the water content decreased and water flow was divided between mobile and immobile regions. PMID:15952347

  5. Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone

    PubMed Central

    Sheng, Jia; Zhang, Wen; Hassan, Abdalla E. A.; Gan, Jianhua; Soares, Alexei S.; Geng, Song; Ren, Yi; Huang, Zhen

    2012-01-01

    Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, >76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH3) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH3 and its 5′-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH3 is replaced with a larger atom (selenium or sulfur). The 5-O-CH3 modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH3 modification, which might potentially rigidify the local conformation and facilitates translation. PMID:22641848

  6. Colloid facilitated transport in fractured rock : parameter estimation and comparison with experimental data

    SciTech Connect

    Viswanathan, H. S.; Wolfsberg, A. V.

    2002-01-01

    Many contaminants in groundwater strongly interact with the immobile porous matrix, which retards their movement relative to groundwater flow. Colloidal particles, which are often present in groundwater, have a relatively small size and large specific surface area which makes it possible for them to also adsorb pollutants. The sorption of tracers to colloids may enhance their mobility in groundwater, relative to the case where colloids are not present. A class of pollutants for which colloid-facilitated transport may be of particular significance are radioactive isotopes. A major reason for why geologic repositories are considered suitable for the disposal of spent nuclear fuel is the strong affinity of many radionuclides to adsorb onto the porous matrix. Therefore, radionuclides accidentally released, would be contained in the geological media by adsorption or filtration until sufficient decay takes place. However, the presence of colloids may enhance radionuclide mobility in the groundwater, and reduce the efficiency of geologic media to act as a natural barrier.

  7. Do anthropogenic transports facilitate stored-product pest moth dispersal? A molecular approach

    NASA Astrophysics Data System (ADS)

    Ryne, Camilla; Bensch, Staffan

    2008-02-01

    Stored-product moths cause large economic damage in food processing industries and storage facilities. Control of indoor pests is currently dealt with locally, and control strategies seldom include different mills or cooperative industries in joint efforts to reduce infestations. In colder climates where conditions hinder flight dispersal of stored-product moths, we hypothesize that human transport between mills will facilitate dispersal. Albeit considered intuitive, this hypothesis has so far never been tested. Male moths from three mills (populations) in southern Sweden and Denmark were collected and by using amplified fragment length polymorphism (AFLP) pair-wise F st values were calculated. Cluster (population) origins of the genotypes were computed by using a model-based method, structure. The results suggest that known transportation of flour between two mills generate genetically more similar populations of the economically important stored-product moth, Ephestia kuehniella (Zell.) (Lepidoptera; Pyralidae), compared to the third mill, with another distribution area, but situated geographically in between the other mills. The structure model placed the sampled genotypes to belong to either two or five original populations, with a higher probability of two original populations. The third mill was consistently different from the other two mills independent of the models’ calculated number of populations. Although the study was restricted to three mills and one transportation route, it highlights the possibility that transportation of food products promotes genetic mixing (i.e. dispersal) of insect pest populations. Including cooperating mills in control (or monitor) strategy schemes against stored-product pest insects would therefore be a more effective action, rather than to treat each mill separately.

  8. Colloid-Facilitated Transport of Cations in an Unsaturated Fractured Soil Under Transient Conditions

    SciTech Connect

    Ryan, Joseph

    2015-01-31

    Rainfall experiments were conducted using intact soil cores and an instrumented soil pedon to examine the effect of physical heterogeneity and rainfall characteristics on the mobilization of colloids, organic matter, cesium, and strontium in a fractured soil. To measure the spatial variability of infiltration of colloids and contaminants, samples were collected through a 19-port grid placed below the soil core in laboratory study and in 27 samplers at multiple depths in the soil pedon in the field study. Cesium and strontium were applied to the soil cores and the soil pedon prior to mobilization experiments. Rainwater solutions of multiple ionic strengths and organic matter concentrations were applied to the soil cores and soil pedon to mobilize in situ colloids, cesium, and strontium. The mobilization of colloids and metal cations occurred through preferential flow paths in the soil cores. Compared to steady rainfall, greater amounts of colloids were mobilized during rainfall interrupted by pauses, which indicates that the supply of colloids to be mobilized was replenished during the pauses. A maximum in the amount of mobilized colloids were mobilized during a rainfall following a pause of 2.5 d. Pauses of shorter or longer duration resulted in less colloid mobilization. Freeze-thaw cycles, a transient condition in winter, enhanced colloid mobilization and colloid-facilitated transport of cesium and strontium in the soil cores. The exchange of solutes between the soil matrix and macropores caused a hysteretic mobilization of colloids, cesium, and strontium during changes in ionic strength. Colloid-facilitated mobilization of cesium and strontium was important at low ionic strength in fractures where slow flow allowed greater exchange of flow between the fractures and the surrounding matrix. The release of cesium and strontium by cation exchange occurred at high ionic strength in fractures where there is a little exchange of pore water with the surrounding matrix

  9. ‘Transient’ Genetic Suppression Facilitates Generation of Hexose Transporter Null Mutants in Leishmania mexicana

    PubMed Central

    Feng, Xiuhong; Rodriguez-Contreras, Dayana; Polley, Tamsen; Lye, Lon-Fye; Scott, David; Burchmore, Richard J.S.; Beverley, Stephen M.; Landfear, Scott M.

    2012-01-01

    Summary The genome of Leishmania mexicana encompasses a cluster of three glucose transporter genes designated LmxGT1, LmxGT2, and LmxGT3. Functional and genetic studies of a cluster null mutant (Δlmxgt1-3) have dissected the roles of these proteins in Leishmania metabolism and virulence. However, null mutants were recovered at very low frequency, and comparative genome hybridizations revealed that Δlmxgt1-3 mutants contained a linear extrachromosomal 40 kb amplification of a region on chromosome 29 not amplified in WT parasites. These data suggested a model where this 29–40k amplicon encoded a second site suppressor contributing to parasite survival in the absence of GT1-3 function. To test this, we quantified the frequency of recovery of knockouts in the presence of individual overexpressed ORFs covering the 29–40k amplicon. The data mapped the suppressor activity to PIFTC3, encoding a component of the intraflagellar transport pathway. We discuss possible models by which PIFTC3 might act to facilitate loss of GTs specifically. Surprisingly, by plasmid segregation we showed that continued PIFTC3 overexpression was not required for Δlmxgt1-3 viability. These studies provide the first evidence that genetic suppression can occur by providing critical biological functions transiently. This novel form of genetic suppression may extend to other genes, pathways and organisms. PMID:23170981

  10. Self-organized transient facilitated atomic transport in Pt /Al(111)

    NASA Astrophysics Data System (ADS)

    Süle, P.

    2008-04-01

    During the course of atomic transport in a host material, impurity atoms need to surmount an energy barrier driven by thermodynamic bias or at ultralow temperatures by quantum tunneling. In the present article, we demonstrate using atomistic simulations that at ultralow temperature, transient interlayer atomic transport is also possible without tunneling when the Pt /Al(111) impurity/host system self-organizes itself spontaneously into an intermixed configuration. No such extremely fast athermal concerted process has been reported before at ultralow temperatures. The outlined novel transient atomic exchange mechanism could be of general validity. We find that the source of ultralow temperature heavy particle barrier crossing is intrinsic and no external bias is necessary for atomic intermixing and surface alloying in Pt /Al, although the dynamic barrier height is a few eV. The mechanism is driven by the local thermalization of the Al(111) surface in a self-organized manner arranged spontaneously by the system without any external stimulus. The core of the short lived thermalized region reaches the local temperature of ˜1000K (including a few tens of Al atoms), while the average temperature of the simulation cell is ˜3K. The transient facilitated intermixing process also takes place with repulsive impurity-host interaction potential leading to negative atomic mobility; hence, the atomic injection is largely independent of the strength of the impurity-surface interaction. We predict that similar exotic behavior is possible in other materials as well.

  11. Colloid-Facilitated Radionuclide Transport at the Potential Yucca Mountain Repository

    NASA Astrophysics Data System (ADS)

    Alcorn, S. R.; Mertz, C. J.

    2001-12-01

    In a geologic repository for nuclear waste, transport of radionuclides on or within colloids may be important for radionuclides of concern that have low solubility and can be entrained in, or sorbed onto, colloidal particles generated within the repository system. It is anticipated that colloids will be formed and mobilized at the potential Yucca Mountain repository as a result of alteration of high-level radioactive waste (HLW) and spent nuclear fuel (SNF) waste forms, as well as corrosion of engineered barrier system (EBS) components. The abundance of colloids leaving a breached waste package and entering the repository drift will depend on the extent of waste form and EBS component alteration and the alteration products formed. Further, colloid abundance and stability will depend on such environmental factors as the ionic strength, pH, cation concentrations, natural colloid content, and organic acid and microbe content of groundwater entering the waste package from the drift. Colloids may flocculate and settle, be chemically retarded, mechanically filtered, or dissolve. In addition, colloids may sorb readily at the interfaces between air and water in rocks and engineered barriers and, depending upon the characteristics and degree of saturation of the porous medium, may be immobilized, retarded, or transported. A methodology for modeling colloid-facilitated radionuclide transport in the potential repository at Yucca Mountain was developed for use in Total System Performance Assessment calculations. The model incorporates several colloid sources and addresses factors affecting colloid stability and concentration as well as distribution and attachment of radionuclides onto colloids. Waste form corrosion tests performed at Argonne National Laboratory (ANL) have focused on determination of colloid composition, stability, concentration, size distribution, and associated radionuclide concentration. Data from these experiments were used as model inputs.

  12. Transport of vitamin A across blood-tissue barriers is facilitated by STRA6.

    PubMed

    Kelly, Mary; Widjaja-Adhi, M Airanthi K; Palczewski, Grzegorz; von Lintig, Johannes

    2016-08-01

    Vitamin A bound to retinol binding protein 4 (RBP4) constitutes the major transport mode for retinoids in fasting circulation. Emerging evidence suggests that membrane protein, STRA6 (stimulated by retinoic acid 6), is the RBP4 receptor and vitamin A channel; however, the role of STRA6 in vitamin A homeostasis remains to be defined in vivo We subjected Stra6-knockout mice to diets sufficient and insufficient for vitamin A and used heterozygous siblings as controls. We determined vitamin A levels of the eyes, brain, and testis, which highly express Stra6, as well as of tissues with low expression, such as lung and fat. We also studied the consequence of STRA6 deficiency on retinoid-dependent processes in tissues. Furthermore, we examined how STRA6 deficiency affected retinoid homeostasis of the aging mouse. The picture that emerged indicates a critical role for STRA6 in the transport of vitamin A across blood-tissue barriers in the eyes, brain, and testis. Concurrently, fat and lung rely on dietary vitamin A. In testis and brain, Stra6 expression was regulated by vitamin A. In controls, this regulation reduced vitamin A consumption when the dietary supply was limited, sequestering it for the eye. Thus, STRA6 is critical for vitamin A homeostasis and the adaption of this process to the fluctuating supply of the vitamin.-Kelly, M., Widjaja-Adhi, M. A. K., Palczewski, G., von Lintig, J. Transport of vitamin A across blood-tissue barriers is facilitated by STRA6. PMID:27189978

  13. Atrazine adsorption and colloid-facilitated transport through the unsaturated zone

    USGS Publications Warehouse

    Sprague, L.A.; Herman, J.S.; Hornberger, G.M.; Mills, A.L.

    2000-01-01

    One explanation for unexpectedly widespread ground water contamination from atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine) may be the occurence of colloid-facilitated transport, whereby the dissolved herbicide becomes adsorbed to mobile colloids that migrate through preferential flow-paths in the soil zone and into the ground water. The objectives of this study were to determine the extent of adsorpton of atrazine to bulk soil and to soil colloids and to determine the extent of colloid-facilitated transport of atrazine at a field site in Virginia during simulated rainfall events. Equilibrium batch adsorption experiments were performed over a concentration range of 0.05 to 10.0 mg atrazine L-1 on bulk soil samples and on colloidal suspensions of 75 mg L-1, a concentration comparable with those observed at the field site. Linear partition coefficients ranged from 0.496 to 2.48 L kg-1 for the bulk soil and from 70.8 to 832 L kg-1 for the soil colloids. In the field, gravity lysimeters were insured at a depth of 25 cm below the surface of six 0.25-m2 undisturbed plots. Mass recovery of surface-applied atrazine in the lysimeters was not significantly affected by rainfall rate and was, on average, 2.7% for plots receiving 25 mm h-1 simulated rainfall and 3.6% for plots receiving 50 mm h-1 simulated rainfall. Of the total atrazine collected in the lysimeters, the fraction that was colloid-associated ranged from 4.9 to 30% (mean of 15%), indicating that a measurable portion of mobile atrazine is transported via association with colloids.One explanation for unexpectedly widespread ground water contamination from atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine) may be the occurrence of colloid-facilitated transport, whereby the dissolved herbicide becomes adsorbed to mobile colloids that migrate through preferential flow-paths in the soil zone and into the ground water. The objectives of this study were to determine the extent of adsorption of

  14. Latest advances in biomaterials: from deoxyribonucleic acid to nucleobases

    NASA Astrophysics Data System (ADS)

    Ouchen, Fahima; Gomez, Eliot; Joyce, Donna; Williams, Adrienne; Kim, Steve; Heckman, Emily; Johnson, Lewis; Yaney, Perry; Venkat, Narayanan; Steckl, Andrew; Kajzar, François; Rau, Ileana; Pawlicka, Agnieszka; Prasad, Paras; Grote, James

    2014-03-01

    This paper is a review of the recent research in bio-based materials for photonics and electronics applications. Materials that we have been working with include: deoxyribonucleic acid (DNA)-based biopolymers and nucleobases. We will highlight work on increasing the ionic conductivity of DNA-based membranes, enhancing the direct (DC) current and photoconductivity of DNA-based biopolymers, crosslinking of DNA-based biopolymers and promising applications for DNA nucleobases. Key

  15. Mass transfer model of nanoparticle-facilitated contaminant transport in saturated porous media.

    PubMed

    Johari, Wan Lutfi Wan; Diamessis, Peter J; Lion, Leonard W

    2010-02-01

    A one-dimensional model has been evaluated for transport of hydrophobic contaminants, such as polycyclic aromatic hydrocarbon (PAH) compounds, facilitated by synthetic amphiphilic polyurethane (APU) nanoparticles in porous media. APU particles synthesized from poly(ethylene glycol)-modified urethane acrylate (PMUA) precursor chains have been shown to enhance the desorption rate and mobility of phenanthrene (PHEN) in soil. A reversible process governed by attachment and detachment rates was considered to describe the PMUA binding in soil in addition to PMUA transport through advection and dispersion. Ultimately, an irreversible second-order PMUA attachment rate in which the fractional soil saturation capacity with PMUA was a rate control was found to be adequate to describe the retention of PMUA particles. A gamma-distributed site model (GS) was used to describe the spectrum of physical/chemical constraints for PHEN transfer from solid to aqueous phases. Instantaneous equilibrium was assumed for PMUA-PHEN interactions. The coupled model for PMUA and PHEN behavior successfully described the enhanced elution profile of PHEN by PMUA. Sensitivity analysis was performed to analyze the significance of model parameters on model predictions. The adjustable parameter alpha in the gamma-distribution shapes the contaminant desorption distribution profile as well as elution and breakthrough curves. Model simulations show the use of PMUA can be also expected to improve the release rate of PHEN in soils with higher organic carbon content. The percentage removal of PHEN mass over time is shown to be influenced by the concentration of PMUA added and this information can be used to optimize cost and time require to accomplish a desired remediation goal. PMID:19406449

  16. Expression, purification, and functional characterization of the insulin-responsive facilitative glucose transporter GLUT4.

    PubMed

    Kraft, Thomas E; Hresko, Richard C; Hruz, Paul W

    2015-12-01

    The insulin-responsive facilitative glucose transporter GLUT4 is of fundamental importance for maintenance of glucose homeostasis. Despite intensive effort, the ability to express and purify sufficient quantities of structurally and functionally intact protein for biophysical analysis has previously been exceedingly difficult. We report here the development of novel methods to express, purify, and functionally reconstitute GLUT4 into detergent micelles and proteoliposomes. Rat GLUT4 containing FLAG and His tags at the amino and carboxy termini, respectively, was engineered and stably transfected into HEK-293 cells. Overexpression in suspension culture yielded over 1.5 mg of protein per liter of culture. Systematic screening of detergent solubilized GLUT4-GFP fusion protein via fluorescent-detection size exclusion chromatography identified lauryl maltose neopentyl glycol (LMNG) as highly effective for isolating monomeric GLUT4 micelles. Preservation of structural integrity and ligand binding was demonstrated via quenching of tryptophan fluorescence and competition of ATB-BMPA photolabeling by cytochalasin B. GLUT4 was reconstituted into lipid nanodiscs and proper folding was confirmed. Reconstitution of purified GLUT4 with amphipol A8-35 stabilized the transporter at elevated temperatures for extended periods of time. Functional activity of purified GLUT4 was confirmed by reconstitution of LMNG-purified GLUT4 into proteoliposomes and measurement of saturable uptake of D-glucose over L-glucose. Taken together, these data validate the development of an efficient means to generate milligram quantities of stable and functionally intact GLUT4 that is suitable for a wide array of biochemical and biophysical analyses. PMID:26402434

  17. Carbon dioxide capture using a CO{sub 2}-selective facilitated transport membrane

    SciTech Connect

    Huang, J.; Zou, J.; Ho, W.S.W.

    2008-02-15

    A novel CO{sub 2}-selective membrane with the facilitated transport mechanism has been synthesized to capture CO{sub 2} from the industrial gas mixtures, including flue gas. Both mobile and fixed amine carriers were incorporated into the cross-linked poly(vinyl alcohol) (PVA) during the membrane synthesis. The membrane showed desirable CO{sub 2} permeability (with a suitable effective thickness) and CO{sub 2}/N{sub 2} selectivity up to 170{sup o} C. In the CO{sub 2} capture experiments from a gas mixture with N{sub 2} and H{sub 2}, a permeate CO{sub 2} dry concentration of {gt}98% was obtained, using steam as the sweep gas. The effects of the feed flow rate and the sweep:feed molar ratio on the membrane separation performance were investigated. A one-dimensional isothermal model was established to examine the performance of a hollow-fiber membrane module composed of the described CO{sub 2}-selective membrane. The modeling results show that a CO{sub 2} recovery of {gt}95% and a permeate CO{sub 2} dry concentration of {gt}98% are achievable from a 1000 standard cubic feet per minute (SCFM) (or 21.06 mol/s) flue gas stream with a 2 ft (0.61 m) hollow-fiber module that contained 980 000 fibers.

  18. Fatty Acid-Binding Protein 5 Facilitates the Blood-Brain Barrier Transport of Docosahexaenoic Acid.

    PubMed

    Pan, Yijun; Scanlon, Martin J; Owada, Yuji; Yamamoto, Yui; Porter, Christopher J H; Nicolazzo, Joseph A

    2015-12-01

    The brain has a limited ability to synthesize the essential polyunsaturated fatty acid (PUFA) docosahexaenoic acid (DHA) from its omega-3 fatty acid precursors. Therefore, to maintain brain concentrations of this PUFA at physiological levels, plasma-derived DHA must be transported across the blood-brain barrier (BBB). While DHA is able to partition into the luminal membrane of brain endothelial cells, its low aqueous solubility likely limits its cytosolic transfer to the abluminal membrane, necessitating the requirement of an intracellular carrier protein to facilitate trafficking of this PUFA across the BBB. As the intracellular carrier protein fatty acid-binding protein 5 (FABP5) is expressed at the human BBB, the current study assessed the putative role of FABP5 in the brain endothelial cell uptake and BBB transport of DHA in vitro and in vivo, respectively. hFAPB5 was recombinantly expressed and purified from Escherichia coli C41(DE3) cells and the binding affinity of DHA to hFABP5 assessed using isothermal titration calorimetry. The impact of FABP5 siRNA on uptake of (14)C-DHA into immortalized human brain microvascular endothelial (hCMEC/D3) cells was assessed. An in situ transcardiac perfusion method was optimized in C57BL/6 mice and subsequently used to compare the BBB influx rate (Kin) of (14)C-DHA between FABP5-deficient (FABP5(-/-)) and wild-type (FABP5(+/+)) C57BL/6 mice. DHA bound to hFABP5 with an equilibrium dissociation constant of 155 ± 8 nM (mean ± SEM). FABP5 siRNA transfection decreased hCMEC/D3 mRNA and protein expression of FABP5 by 53.2 ± 5.5% and 44.8 ± 13.7%, respectively, which was associated with a 14.1 ± 2.7% reduction in (14)C-DHA cellular uptake. By using optimized conditions for the in situ transcardiac perfusion (a 1 min preperfusion (10 mL/min) followed by perfusion of (14)C-DHA (1 min)), the Kin of (14)C-DHA was 0.04 ± 0.01 mL/g/s. Relative to FABP5(+/+) mice, the Kin of (14)C-DHA decreased 36.7 ± 12.4% in FABP5(-/-) mice

  19. Structure and evolution of the plant cation diffusion facilitator family of ion transporters

    PubMed Central

    2011-01-01

    Background Members of the cation diffusion facilitator (CDF) family are integral membrane divalent cation transporters that transport metal ions out of the cytoplasm either into the extracellular space or into internal compartments such as the vacuole. The spectrum of cations known to be transported by proteins of the CDF family include Zn, Fe, Co, Cd, and Mn. Members of this family have been identified in prokaryotes, eukaryotes, and archaea, and in sequenced plant genomes. CDF families range in size from nine members in Selaginella moellendorffii to 19 members in Populus trichocarpa. Phylogenetic analysis suggests that the CDF family has expanded within plants, but a definitive plant CDF family phylogeny has not been constructed. Results Representative CDF members were annotated from diverse genomes across the Viridiplantae and Rhodophyta lineages and used to identify phylogenetic relationships within the CDF family. Bayesian phylogenetic analysis of CDF amino acid sequence data supports organizing land plant CDF family sequences into 7 groups. The origin of the 7 groups predates the emergence of land plants. Among these, 5 of the 7 groups are likely to have originated at the base of the tree of life, and 2 of 7 groups appear to be derived from a duplication event prior to or coincident with land plant evolution. Within land plants, local expansion continues within select groups, while several groups are strictly maintained as one gene copy per genome. Conclusions Defining the CDF gene family phylogeny contributes to our understanding of this family in several ways. First, when embarking upon functional studies of the members, defining primary groups improves the predictive power of functional assignment of orthologous/paralogous genes and aids in hypothesis generation. Second, defining groups will allow a group-specific sequence motif to be generated that will help define future CDF family sequences and aid in functional motif identification, which currently is

  20. Facilitated transport of Cu with hydroxyapatite nanoparticles in saturated sand: Effects of solution ionic strength and composition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Column experiments were conducted to investigate the facilitated transport of Cu in association with hydroxyapatite nanoparticles (nHAP) in water-saturated quartz sand at different solution concentrations of NaCl (0 to 100 mM) or CaCl2 (0.1 to 1.0 mM). The experimental breakthrough curves and retent...

  1. Role of Desorption Kinetics and Porous Medium Heterogeneity in Colloid-Facilitated Transport of Cesium and Strontium: Preliminary Results

    NASA Astrophysics Data System (ADS)

    Dittrich, T. M.; Ryan, J. N.

    2008-12-01

    The presence of mobile colloids (particles between 1 nm and 1 μm in size) in natural soil and groundwater systems has been well established. Colloids generally have a high sorptive capacity resulting from their high surface area to mass ratio, which makes them effective sorbents of low solubility, strongly sorbing contaminants. Mobile colloids that sorb contaminants can increase the apparent solubility and rate of transport of the contaminants when desorption from the colloids is slow relative to the rate of flow. This process is known as colloid-facilitated transport (CFT). The additional transport of contaminants associated with mobile colloids should be accounted for to accurately predict transport rates of strongly-sorbing contaminants in the environment. Some examples of contaminants that have the potential for CFT are hydrophobic pesticides, polycyclic aromatic hydrocarbons (PAHs), actinide cations (e.g., Th, U, Pu, Am), and many metals (e.g, Pb, Cu, Hg). Many low solubility contaminants that have the potential for CFT are also harmful or toxic to humans, underscoring the importance of accurate modeling techniques to protect water sources from contamination. Contaminated Department of Energy (DOE) sites have been particularly valuable research opportunities for studying the transport of radionuclides in the natural environment. The DOE has conducted energy and weapons research and development in thirty-one states and Puerto Rico and has introduced many toxic and radioactive chemicals into surface waters, soils, and groundwater. Field experiments on DOE sites including the Nevada Test Site, the Hanford 200 Area tank farm, Rocky Flats CO, and Oak Ridge TN, have confirmed that metals and radionuclides have moved further than expected due to colloid-facilitated transport. The major goal of this research project is to identify and quantify the effects of sorption kinetics on colloid- facilitated transport in unsaturated porous media. This information will be used

  2. Evidence for expression of the facilitated glucose transporter in rat hepatocytes.

    PubMed Central

    Rhoads, D B; Takano, M; Gattoni-Celli, S; Chen, C C; Isselbacher, K J

    1988-01-01

    The eukaryotic facilitated glucose transporter (GT) is expressed by many cell types, with the notable exception of hepatocytes; however, GT is expressed by several hepatoma cell lines, including the well-differentiated lines Fao, Hep3B, and HepG2. We report on studies carried out to determine the aspect(s) of the transformed phenotype that might be responsible for activating GT expression. Using RNA blot analysis with probes derived from rat GT cDNA, we found that GT was expressed by rat hepatocytes under two conditions (i) in vitro, when isolated hepatocytes were placed in cell culture, and (ii) in vivo, when rats were subjected to starvation for greater than or equal to 2 days. However, GT expression was not an obligatory feature of hepatomas, since two primary hepatocellular carcinomas did not express any GT mRNA. GT expression in hepatocytes was reduced by addition of dimethyl sulfoxide or sodium butyrate to the culture medium. Since these reagents are known to promote differentiation in some cell culture systems, their effect on hepatocytes may be to maintain the GT repression normally observed in vivo. Inclusion or exclusion in the culture medium of several other agents that enhance hepatocyte viability (serum, insulin, corticosteroids, epidermal growth factor, or triiodothyronine) did not affect GT expression. It is unclear whether the two conditions that led to GT expression in hepatocytes are related by a common signaling mechanism. Possibly, both cases involve a "stress" response: in vivo, a normal physiological response to starvation; in vitro, a response to a major alteration in the cellular environment. Images PMID:3194405

  3. Excitation of nucleobases from a computational perspective I: reaction paths.

    PubMed

    Giussani, Angelo; Segarra-Martí, Javier; Roca-Sanjuán, Daniel; Merchán, Manuela

    2015-01-01

    The main intrinsic photochemical events in nucleobases can be described on theoretical grounds within the realm of non-adiabatic computational photochemistry. From a static standpoint, the photochemical reaction path approach (PRPA), through the computation of the respective minimum energy path (MEP), can be regarded as the most suitable strategy in order to explore the electronically excited isolated nucleobases. Unfortunately, the PRPA does not appear widely in the studies reported in the last decade. The main ultrafast decay observed experimentally for the gas-phase excited nucleobases is related to the computed barrierless MEPs from the bright excited state connecting the initial Franck-Condon region and a conical intersection involving the ground state. At the highest level of theory currently available (CASPT2//CASPT2), the lowest excited (1)(ππ*) hypersurface for cytosine has a shallow minimum along the MEP deactivation pathway. In any case, the internal conversion processes in all the natural nucleobases are attained by means of interstate crossings, a self-protection mechanism that prevents the occurrence of photoinduced damage of nucleobases by ultraviolet radiation. Many alternative and secondary paths have been proposed in the literature, which ultimately provide a rich and constructive interplay between experimentally and theoretically oriented research. PMID:24264958

  4. Microbially Produced Organic Matter and Its Role in Facilitating Pu Transport in the Deep Vadose Zone

    NASA Astrophysics Data System (ADS)

    Fisher, J. C.; Tinnacher, R. M.; Zavarin, M.; Kersting, A. B.; Czerwinski, K.; Moser, D. P.

    2010-12-01

    Microorganisms have the potential to affect the fate and mobility of actinides in the deep vadose zone (DVZ) by metabolism (direct oxidation/reduction and changes to ecosystem redox potential), production of colloids and ligands, or by sorption (biofilms). The role of microbial communities in colloid-facilitated Pu transport is currently under investigation at the Nevada Test Site (NTS). Our experimental objective is to obtain both qualitative and quantitative data on the in situ role of biological organic material (DOM, POC, and EPS) on the (de)sorption of Pu at environmentally relevant concentrations. Groundwater samples were collected through vertical ventilation holes from a flooded post-test tunnel at the (NTS), where SSU rRNA gene libraries revealed a range of potential microbial physiotypes. Microbial enrichments were set up with the aim of isolating numerically significant representatives of major relevant physiotypes (e.g. aerobic heterotrophs, Mn/Fe reducers, EPS producers). NTS isolates, a well-characterized Shewanella sp.(str. CN-32), and an EPS-mutant of this strain were screened for their reactivity with Pu(IV). Organisms with both high and low (relative) Kd’s were used in sorption and cell lysis experiments. Viability experiments were conducted for all isolates in NaCl or NaCl/NaHCO3 solutions (I=0.01) for pH = 3, 5, 7, and 9. Products from cell lysis were filtered (0.22 um) or dialyzed (MW cutoff = 20,000 kD). These fractions were normalized by TOC and equilibrated with Pu to determine if Pu sorbs more strongly to either viable cells, EPS, cell membranes, or cell exudates. In our experiments, Pu(IV) sorbed most strongly to cells or cell fractions with EPS (expolysaccharide, the major biofilm component). However, cell fractions and exudates, which may become mobile when released from lysed or senescing cells, also strongly sorbed to Pu(IV). Therefore, changes in groundwater chemistry (e.g., pH or ionic strength) may have both direct chemical

  5. LONG-TERM COLLOID MOBILIZATION AND COLLOID-FACILITATED TRANSPORT OF RADIONUCLIDES IN A SEMI-ARID VADOSE ZONE

    SciTech Connect

    Markus Flury; James B. Harsh; Fred Zhang; Glendon W. Gee; Earl D. Mattson; Peter C. L

    2012-08-01

    The main purpose of this project was to improve the fundamental mechanistic understanding and quantification of long-term colloid mobilization and colloid-facilitated transport of radionuclides in the vadose zone, with special emphasis on the semi-arid Hanford site. While we focused some of the experiments on hydrogeological and geochemical conditions of the Hanford site, many of our results apply to colloid and colloid-facilitated transport in general. Specific objectives were (1) to determine the mechanisms of colloid mobilization and colloid-facilitated radionuclide transport in undisturbed Hanford sediments under unsaturated flow, (2) to quantify in situ colloid mobilization and colloid-facilitated radionuclidetransport from Hanford sediments under field conditions, and (3) to develop a field-scale conceptual and numerical model for colloid mobilization and transport at the Hanford vadose zone, and use that model to predict long-term colloid and colloid- facilitated radionuclide transport. To achieve these goals and objectives, we have used a combination of experimental, theoretical, and numerical methods at different spatial scales, ranging from microscopic investigationsof single particle attachment and detachment to larger-scale field experiments using outdoor lysimeters at the Hanford site. Microscopic and single particle investigations provided fundamental insight into mechanisms of colloid interactions with the air-water interface. We could show that a moving air water interface (such as a moving water front during infiltration and drainage) is very effective in removing and mobilizing particles from a stationary surface. We further demonstrated that it is particularly the advancing air-water interface which is mainly responsible for colloid mobilization. Forces acting on the colloids calculated from theory corroborated our experimental results, and confirm that the detachment forces (surface tension forces) during the advancing air-water interface

  6. Facilitated transport of amino acids across organic phases and the human erythrocyte membrane.

    PubMed Central

    Hider, R C; McCormack, W

    1980-01-01

    1. An artificial facilitated amino-acid-transfer process operating across a chloroform phase is reported. 2. This process utilizes a family of bis(salicylamidato)copper(II) complexes. 3. A mechanism is proposed for this process and for its sensitivity towards cyanide and bathophenanthroline sulphonate. 4. Facilitated transfer of L-leucine in human erythrocytes has been shown to be inhibited by bathophenanthroline sulphonate. PMID:7396879

  7. Recognition of DNA sequencing through binding of nucleobases to graphene

    NASA Astrophysics Data System (ADS)

    Zaffino, Valentina

    Graphene is one of the most promising materials in nanotechnology. Its large surface to volume ratio, high conductivity and electron mobility at room temperature are outstanding properties for use in DNA sensors. For this study, we used Density Functional Theory (DFT), ?with and without the inclusion of van der Waals (vdW) interactions, ?to investigate the adsorption of nucleobases (cytosine, guanine, adenine, thymine, and uracil) on pristine graphene and graphene with defects (Divacancy and Stone-Wales). We investigated the performance of two types of vdW-DF functional (optB86b-vdW and rPW86-vdW), as well as the PBE functional, and their description of the adsorption geometry and electronic structure of the nucleobase-graphene systems.The inclusion of defects results in an increase in binding energy, closer adsorption of the molecule to graphene and greater buckling in both the graphene structure and nucleobase.

  8. A Major Facilitator Superfamily Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis[W

    PubMed Central

    Remy, Estelle; Cabrito, Tânia R.; Baster, Pawel; Batista, Rita A.; Teixeira, Miguel C.; Friml, Jiri; Sá-Correia, Isabel; Duque, Paula

    2013-01-01

    Many key aspects of plant development are regulated by the polarized transport of the phytohormone auxin. Cellular auxin efflux, the rate-limiting step in this process, has been shown to rely on the coordinated action of PIN-formed (PIN) and B-type ATP binding cassette (ABCB) carriers. Here, we report that polar auxin transport in the Arabidopsis thaliana root also requires the action of a Major Facilitator Superfamily (MFS) transporter, Zinc-Induced Facilitator-Like 1 (ZIFL1). Sequencing, promoter-reporter, and fluorescent protein fusion experiments indicate that the full-length ZIFL1.1 protein and a truncated splice isoform, ZIFL1.3, localize to the tonoplast of root cells and the plasma membrane of leaf stomatal guard cells, respectively. Using reverse genetics, we show that the ZIFL1.1 transporter regulates various root auxin-related processes, while the ZIFL1.3 isoform mediates drought tolerance by regulating stomatal closure. Auxin transport and immunolocalization assays demonstrate that ZIFL1.1 indirectly modulates cellular auxin efflux during shootward auxin transport at the root tip, likely by regulating plasma membrane PIN2 abundance. Finally, heterologous expression in yeast revealed that ZIFL1.1 and ZIFL1.3 share H+-coupled K+ transport activity. Thus, by determining the subcellular and tissue distribution of two isoforms, alternative splicing dictates a dual function for the ZIFL1 transporter. We propose that this MFS carrier regulates stomatal movements and polar auxin transport by modulating potassium and proton fluxes in Arabidopsis cells. PMID:23524662

  9. “Molecular trinity” for soft nanomaterials: Integrating nucleobases, amino acids, and glycosides to construct multifunctional hydrogelators

    PubMed Central

    Li, Xinming; Kuang, Yi

    2013-01-01

    This highlight introduces the development of hydrogelators consisting of nucleobases, amino acids, and glycosides (i.e., molecular trinity), or nucleobases and amino acids (i.e., nucleopeptides). These novel small molecule hydrogelators self-assemble in water to form stable supramolecular nanofibers/hydrogels and exhibit useful biological properties (e.g., biocompatibility, biostability, and the ability to bind and transport DNA into live cells). The approach discussed here not only provides a new strategy to develop soft biomaterials as a form of nanomedicines, but also contributes to the understanding of molecular self-assembly in water by modulating the non-covalent interactions derived from the three basic building blocks used in living organisms. PMID:24368929

  10. ESTIMATING THE POTENTIAL FOR FACILITATED TRANSPORT OF NAPROPAMIDE BY DISSOLVED ORGANIC MATTER

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dissolved organic matter (DOM) has been found to significantly affect the soil sorption/desorption of napropamide [2-(a-naphthoxy-N, N-diethylpropionamide] and to enhance its transport through soil columns. A method to qualitatively predict if DOM will enhance the transport of napropamide based on e...

  11. Zero-tension lysimeters: An improved design to monitor colloid-facilitated contaminant transport in the vadose zone

    SciTech Connect

    Thompson, M.L.; Scharf, R.L.; Shang, C.

    1995-04-24

    There is increasing evidence that mobile colloids facilitate the long-distance transport of contaminants. The mobility of fine particles and macromolecules has been linked to the movement of actinides, organic contaminants, and heavy metals through soil. Direct evidence for colloid mobility includes the presence of humic materials in deep aquifers as well as coatings of accumulated clay, organic matter, or sesquioxides on particle or aggregate surfaces in subsoil horizons of many soils. The potential for colloid-facilitated transport of contaminants from hazardous-waste sites requires adequate monitoring before, during, and after in-situ remediation treatments. Zero-tension lysimeters (ZTLs) are especially appropriate for sampling water as it moves through saturated soil, although some unsaturated flow events may be sampled as well. Because no ceramic barrier or fiberglass wick is involved to maintain tension on the water (as is the case with other lysimeters), particles suspended in the water as well as dissolved species may be sampled with ZTLs. In this report, a ZTL design is proposed that is more suitable for monitoring colloid-facilitated contaminant migration. The improved design consists of a cylinder made of polycarbonate or polytetrafluoroethylene (PTFE) that is placed below undisturbed soil material. In many soils, a hydraulically powered tube may be used to extract an undisturbed core of soil before placement of the lysimeter. In those cases, the design has significant advantages over conventional designs with respect to simplicity and speed of installation. Therefore, it will allow colloid-facilitated transport of contaminants to be monitored at more locations at a given site.

  12. Extraction and carrier-facilitated transport of amino acids using synthetic non-cyclic receptors through bulk liquid membrane.

    PubMed

    Joshi, Pratibha; Joshi, Nidhi; Sharma, Uma

    2006-10-01

    The extraction and carrier-facilitated transport of amino acids (leucine, valine and glycine) was studied through chloroform bulk liquid membrane system using a series of non-cyclic receptors such as diethylene glycol (1), diethylene glycol dimethyl ether (2), diethylene glycol dibutyl ether (3), diethylene glycol dibenzoate (4), triethylene glycol (5) and tetraethylene glycol (6). The amount of amino acid extracted and transported depends mainly upon the structure and the concentration of the receptors and also on the concentration of amino acid. The receptors 1 to 4, having small chain length and flexible end groups, formed stable complexes with amino acids, and the flexibility of receptors in different conformational forms was responsible for their carrier ability, while the receptors 5 and 6, having larger chain length showed poor carrier ability. Hydrophobicity of amino acids also play an important role in the extraction as well as transport process. PMID:17133741

  13. Connective Auxin Transport in the Shoot Facilitates Communication between Shoot Apices.

    PubMed

    Bennett, Tom; Hines, Geneviève; van Rongen, Martin; Waldie, Tanya; Sawchuk, Megan G; Scarpella, Enrico; Ljung, Karin; Leyser, Ottoline

    2016-04-01

    The bulk polar movement of the plant signaling molecule auxin through the stem is a long-recognized but poorly understood phenomenon. Here we show that the highly polar, high conductance polar auxin transport stream (PATS) is only part of a multimodal auxin transport network in the stem. The dynamics of auxin movement through stems are inconsistent with a single polar transport regime and instead suggest widespread low conductance, less polar auxin transport in the stem, which we term connective auxin transport (CAT). The bidirectional movement of auxin between the PATS and the surrounding tissues, mediated by CAT, can explain the complex auxin transport kinetics we observe. We show that the auxin efflux carriers PIN3, PIN4, and PIN7 are major contributors to this auxin transport connectivity and that their activity is important for communication between shoot apices in the regulation of shoot branching. We propose that the PATS provides a long-range, consolidated stream of information throughout the plant, while CAT acts locally, allowing tissues to modulate and be modulated by information in the PATS. PMID:27119525

  14. Connective Auxin Transport in the Shoot Facilitates Communication between Shoot Apices

    PubMed Central

    Bennett, Tom; Hines, Geneviève; van Rongen, Martin; Sawchuk, Megan G.; Scarpella, Enrico; Ljung, Karin

    2016-01-01

    The bulk polar movement of the plant signaling molecule auxin through the stem is a long-recognized but poorly understood phenomenon. Here we show that the highly polar, high conductance polar auxin transport stream (PATS) is only part of a multimodal auxin transport network in the stem. The dynamics of auxin movement through stems are inconsistent with a single polar transport regime and instead suggest widespread low conductance, less polar auxin transport in the stem, which we term connective auxin transport (CAT). The bidirectional movement of auxin between the PATS and the surrounding tissues, mediated by CAT, can explain the complex auxin transport kinetics we observe. We show that the auxin efflux carriers PIN3, PIN4, and PIN7 are major contributors to this auxin transport connectivity and that their activity is important for communication between shoot apices in the regulation of shoot branching. We propose that the PATS provides a long-range, consolidated stream of information throughout the plant, while CAT acts locally, allowing tissues to modulate and be modulated by information in the PATS. PMID:27119525

  15. Convective transport of highly plasma protein bound drugs facilitates direct penetration into deep tissues after topical application

    PubMed Central

    Dancik, Yuri; Anissimov, Yuri G; Jepps, Owen G; Roberts, Michael S

    2012-01-01

    AIMS To relate the varying dermal, subcutaneous and muscle microdialysate concentrations found in man after topical application to the nature of the drug applied and to the underlying physiology. METHODS We developed a physiologically based pharmacokinetic model in which transport to deeper tissues was determined by tissue diffusion, blood, lymphatic and intersitial flow transport and drug properties. The model was applied to interpret published human microdialysis data, estimated in vitro dermal diffusion and protein binding affinity of drugs that have been previously applied topically in vivo and measured in deep cutaneous tissues over time. RESULTS Deeper tissue microdialysis concentrations for various drugs in vivo vary widely. Here, we show that carriage by the blood to the deeper tissues below topical application sites facilitates the transport of highly plasma protein bound drugs that penetrate the skin, leading to rapid and significant concentrations in those tissues. Hence, the fractional concentration for the highly plasma protein bound diclofenac in deeper tissues is 0.79 times that in a probe 4.5 mm below a superficial probe whereas the corresponding fractional concentration for the poorly protein bound nicotine is 0.02. Their corresponding estimated in vivo lag times for appearance of the drugs in the deeper probes were 1.1 min for diclofenac and 30 min for nicotine. CONCLUSIONS Poorly plasma protein bound drugs are mainly transported to deeper tissues after topical application by tissue diffusion whereas the transport of highly plasma protein bound drugs is additionally facilitated by convective blood, lymphatic and interstitial transport to deep tissues. PMID:21999217

  16. COLLOIDAL-FACILITATED TRANSPORT OF INORGANIC CONTAMINANTS IN GROUND WATER: PART I. SAMPLING CONSIDERATIONS

    EPA Science Inventory

    Investigations at Pinal Creek, Arizona, evaluated routine sampling procedures for determination of aqueous inorganic geochemistry and assessment of contaminant transport by colloidal mobility. Sampling variables included pump type and flow rate, collection under air or nitrogen,...

  17. Isolation of Human Genomic DNA Sequences with Expanded Nucleobase Selectivity.

    PubMed

    Rathi, Preeti; Maurer, Sara; Kubik, Grzegorz; Summerer, Daniel

    2016-08-10

    We report the direct isolation of user-defined DNA sequences from the human genome with programmable selectivity for both canonical and epigenetic nucleobases. This is enabled by the use of engineered transcription-activator-like effectors (TALEs) as DNA major groove-binding probes in affinity enrichment. The approach provides the direct quantification of 5-methylcytosine (5mC) levels at single genomic nucleotide positions in a strand-specific manner. We demonstrate the simple, multiplexed typing of a variety of epigenetic cancer biomarker 5mC with custom TALE mixes. Compared to antibodies as the most widely used affinity probes for 5mC analysis, i.e., employed in the methylated DNA immunoprecipitation (MeDIP) protocol, TALEs provide superior sensitivity, resolution and technical ease. We engineer a range of size-reduced TALE repeats and establish full selectivity profiles for their binding to all five human cytosine nucleobases. These provide insights into their nucleobase recognition mechanisms and reveal the ability of TALEs to isolate genomic target sequences with selectivity for single 5-hydroxymethylcytosine and, in combination with sodium borohydride reduction, single 5-formylcytosine nucleobases. PMID:27429302

  18. Photochemical etiology of promising ancestors of the RNA nucleobases.

    PubMed

    Brister, M M; Pollum, M; Crespo-Hernández, C E

    2016-07-27

    RNA is a product of chemical and biological evolution and the identification of its heterocyclic ancestors is essential for understanding the molecular origins of life. Among a diverse array of selection pressures thought to have shaped the composition of the nucleobases on prebiotic Earth, protection against intense ultraviolet radiation must have been essential. In this contribution, a detailed spectroscopic and photophysical investigation of barbituric acid and 2,4,6-triaminopyrimidine, two promising candidates for the prebiotic ancestors of RNA nucleobases, is presented in aqueous solution. It is shown that although these pyrimidine derivatives absorb ultraviolet radiation strongly, both compounds possess efficient electronic relaxation mechanisms for dissipating most of the absorbed ultraviolet energy to their aqueous environment as heat within hundreds of femtoseconds, thus safeguarding their chemical integrity. In fact, these two heterocyclic compounds rival the photostability observed in the canonical nucleobases in aqueous solution, thus supporting the recent proposal that both barbituric acid and 2,4,6-triaminopyrimidine are promising ancestors of the RNA nucleobases. PMID:26898746

  19. Directed evolution of xylose specific transporters to facilitate glucose-xylose co-utilization.

    PubMed

    Wang, Meng; Yu, Chenzhao; Zhao, Huimin

    2016-03-01

    A highly active xylose specific transporter without glucose inhibition is highly desirable in cost-effective production of biofuels from lignocellulosic biomass. However, currently available xylose specific transporters suffer from low overall activity and most are inhibited by glucose. In this study, we applied a directed evolution strategy to engineer the xylose specific transporter AN25 from Neurospora crassa with improved xylose transportation capacity. After four rounds of directed evolution using two different strategies, we obtained an AN25 mutant AN25-R4.18 with 43-fold improvement in terms of xylose transportation capacity while maintaining its high xylose specificity. In addition, glucose inhibition was almost completely eliminated in the final evolved mutant. We demonstrated that improved xylose transportation of AN25 mutants in the exponential growth phase led to significant improvement of xylose consumption in high cell-density fermentation. Finally, we showed that AN25 mutant AN25-R4.18 can enable relatively efficient glucose-xylose co-utilization in high concentrations of mixed sugars. PMID:26284760

  20. The Renaissance of Metal-Pyrimidine Nucleobase Coordination Chemistry.

    PubMed

    Lippert, Bernhard; Sanz Miguel, Pablo J

    2016-08-16

    The significance of metal ions for the function and properties of DNA and RNA, long seen primarily under biological aspects and medicinal uses, has recently gained a renewed momentum. This is a consequence of the advent of novel applications in the fields of materials science, biotechnology, and analytical sensor chemistry that relate to the designed incorporation of transition metal ions into nucleic acid base pairs. Ag(+) and Hg(2+) ions, binding to pyrimidine (pym) nucleobases, represent major players in this development. Interestingly, these metal ions were the ones that some 60 years ago started the field! At the same time, the mentioned metal ions had demonstrated a "special relationship" with the pym nucleobases cytosine, thymine, and uracil! Parallel work conducted with oligonucleotides and model nucleobases fostered numerous significant details of these interactions, in particular when X-ray crystallography was involved, correcting earlier views occasionally. Our own activities during the past three to four decades have focused on, among others, the coordination chemistry of transition and main-group metal ions with pym model nucleobases, with an emphasis on Pt(II) and Pd(II). It has always been our goal to deduce, if possible, the potential relevance of our findings for biological processes. It is interesting to put our data, in particular for trans-a2Pt(II) (a = NH3 or amine), into perspective with those of other metal ions, notably Ag(+) and Hg(2+). Irrespective of major differences in kinetics and lability/inertness between d(8) and d(10) metal ions, there is also a lot of similarity in structural aspects as a result of the preferred linear coordination geometry of these species. Moreover, the apparent clustering of metal ions to the pym nucleobases, which is presumably essential for the formation of nanoclusters on oligonucleotide scaffolds, is impressively reflected in model systems, as are reasons for inter-nucleobase cross-links containing more

  1. Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter.

    PubMed

    Lee, Yongchan; Nishizawa, Tomohiro; Yamashita, Keitaro; Ishitani, Ryuichiro; Nureki, Osamu

    2015-01-01

    SWEET family proteins mediate sugar transport across biological membranes and play crucial roles in plants and animals. The SWEETs and their bacterial homologues, the SemiSWEETs, are related to the PQ-loop family, which is characterized by highly conserved proline and glutamine residues (PQ-loop motif). Although the structures of the bacterial SemiSWEETs were recently reported, the conformational transition and the significance of the conserved motif in the transport cycle have remained elusive. Here we report crystal structures of SemiSWEET from Escherichia coli, in the both inward-open and outward-open states. A structural comparison revealed that SemiSWEET undergoes an intramolecular conformational change in each protomer. The conserved PQ-loop motif serves as a molecular hinge that enables the 'binder clip-like' motion of SemiSWEET. The present work provides the framework for understanding the overall transport cycles of SWEET and PQ-loop family proteins. PMID:25598322

  2. Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter

    NASA Astrophysics Data System (ADS)

    Lee, Yongchan; Nishizawa, Tomohiro; Yamashita, Keitaro; Ishitani, Ryuichiro; Nureki, Osamu

    2015-01-01

    SWEET family proteins mediate sugar transport across biological membranes and play crucial roles in plants and animals. The SWEETs and their bacterial homologues, the SemiSWEETs, are related to the PQ-loop family, which is characterized by highly conserved proline and glutamine residues (PQ-loop motif). Although the structures of the bacterial SemiSWEETs were recently reported, the conformational transition and the significance of the conserved motif in the transport cycle have remained elusive. Here we report crystal structures of SemiSWEET from Escherichia coli, in the both inward-open and outward-open states. A structural comparison revealed that SemiSWEET undergoes an intramolecular conformational change in each protomer. The conserved PQ-loop motif serves as a molecular hinge that enables the ‘binder clip-like’ motion of SemiSWEET. The present work provides the framework for understanding the overall transport cycles of SWEET and PQ-loop family proteins.

  3. Heterologous production and functional and thermodynamic characterization of cation diffusion facilitator (CDF) transporters of mesophilic and hyperthermophilic origin.

    PubMed

    Goswami, Devrishi; Kaur, Jagdeep; Surade, Sachin; Grell, Ernst; Michel, Hartmut

    2012-07-01

    The members of the cation diffusion facilitator (CDF) family transport heavy metal ions and play an important function in zinc ion homeostasis of the cell. A recent structure of an Escherichia coli CDF transporter protein YiiP has revealed its dimeric nature and autoregulatory zinc transport mechanism. Here, we report the cloning and heterologous production of four different CDF transporters, two each from the pathogenic mesophilic bacterium Salmonella typhimurium and from the hyperthermophilic bacterium Aquifex aeolicus, in E. coli host cells. STM0758 of S. typhimurium was able to restore resistance to zinc ions when tested by complementation assays in the zinc-sensitive GG48 strain. Furthermore, copurification of bicistronically produced STM0758 and cross-linking experiments with the purified protein have revealed its possible oligomeric nature. The interaction between heavy metal ions and Aq_2073 of A. aeolicus was investigated by titration calorimetry. The entropy-driven, high-affinity binding of two Cd2+ and two Zn2+ per protein monomer with Kd values of around 100 nm and 1 μm, respectively, was observed. In addition, at least one more Zn2+ can be bound per monomer with low affinity. This low-affinity site is likely to possess a functional role contributing to Zn2+ transport across membranes. PMID:22944666

  4. Proteome scale census of major facilitator superfamily transporters in Trichoderma reesei using protein sequence and structure based classification enhanced ranking.

    PubMed

    Chaudhary, Nitika; Kumari, Indu; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf

    2016-07-01

    Trichoderma spp. have been acknowledged as potent bio-control agents against microbial pathogens and also as plant growth promoters. Various secondary metabolites are attributed for these beneficial activities. Major facilitator superfamily (MFS) includes the large proportion of efflux-pumps which are linked with membrane transport of these secondary metabolites. We have carried out a proteome-wide identification of MFS transporters using protein sequence and structure based hierarchical method in Trichoderma reesei. 448 proteins out of 9115 were detected to carry transmembrane helices. MFS specific intragenic gene duplication and its context with transport function have been presented. Finally, using homology based techniques, domains and motifs of MFS families have been identified and utilized to classify them. From query dataset of 448 transmembrane proteins, 148 proteins are identified as potential MFS transporters. Sugar porter, drug: H(+) antiporter-1, monocarboxylate porter and anion: cation symporter emerged as major MFS families with 51, 35, 17 and 11 members respectively. Representative protein tertiary structures of these families are homology modeled for structure-function analysis. This study may help to understand the molecular basis of secretion and transport of agriculturally valuable secondary metabolites produced by these bio-control fungal agents which may be exploited in future for enhancing its biotechnological applications in eco-friendly sustainable development. PMID:27041239

  5. Electrically facilitated molecular transport. Analysis of the relative contributions of diffusion, migration, and electroosmosis to solute transport in an ion-exchange membrane.

    PubMed

    Bath, B D; White, H S; Scott, E R

    2000-02-01

    Electrically facilitated molecular transport in an ion-exchange membrane (Nafion, 1100 equiv wt) has been studied using a scanning electrochemical microscope. The transport rates of ferrocenylmethyltrimethylammonium (a cation), acetaminophen (a neutral molecule), and ascorbate (an anion) through approximately 120-micron-thick membranes were measured as a function of the iontophoretic current passed across the membrane (-1.0 to +1.0 A/cm2). Transport rates were analyzed by employing the Nernst-Planck equation, modified to account for electric field-driven convective transport. Excellent agreement between experimental and theoretical values of the molecular flux was obtained using a single fitting parameter for each molecule (electroosmotic drag coefficient). The electroosmotic velocity of the neutral molecule, acetaminophen, was shown to be a factor of approximately 500 larger than that of the cation ferrocenylmethyltrimethylammonium, a consequence of the electrostatic interaction of the cation with the negatively charged pore walls of the ion-exchange membrane. Electroosmotic transport of ascorbate occurred at a negligible rate due to repulsion of the anion by the cation-selective membrane. These results suggest that electroosmotic velocities of solute molecules are determined by specific chemical interactions of the permeant and membrane and may be very different from the average solution velocity. The efficiency of electroosmotic transport was also shown to be a function of the membrane thickness, in addition to membrane/solute interactions. PMID:10695125

  6. Undergraduate Laboratory Experiment Facilitating Active Learning of Concepts in Transport Phenomena: Experiment with a Subliming Solid

    ERIC Educational Resources Information Center

    Utgikar, Vivek P.

    2015-01-01

    An experiment based on the sublimation of a solid was introduced in the undergraduate Transport Phenomena course. The experiment required the students to devise their own apparatus and measurement techniques. The theoretical basis, assignment of the experiment, experimental results, and student/instructor observations are described in this paper.…

  7. New HYDRUS Modules for Simulating Preferential Flow, Colloid-Facilitated Contaminant Transport, and Various Biogeochemical Processes in Soils

    NASA Astrophysics Data System (ADS)

    Simunek, J.; Sejna, M.; Jacques, D.; Langergraber, G.; Bradford, S. A.; van Genuchten, M. Th.

    2012-04-01

    We have dramatically expanded the capabilities of the HYDRUS (2D/3D) software package by developing new modules to account for processes not available in the standard HYDRUS version. These new modules include the DualPerm, C-Hitch, HP2/3, Wetland, and Unsatchem modules. The dual-permeability modeling approach of Gerke and van Genuchten [1993] simulating preferential flow and transport is implemented into the DualPerm module. Colloid transport and colloid-facilitated solute transport, the latter often observed for many contaminants, such as heavy metals, radionuclides, pharmaceuticals, pesticides, and explosives [Šimůnek et al., 2006] are implemented into the C-Hitch module. HP2 and HP3 are the two and three-dimensional alternatives of the HP1 module, currently available with HYDRUS-1D [Jacques and Šimůnek, 2005], that couple HYDRUS flow and transport routines with the generic geochemical model PHREEQC of Parkhurst and Appelo [1999]. The Wetland module includes two alternative approaches (CW2D of Langergraber and Šimůnek [2005] and CWM1 of Langergraber et al. [2009]) for modeling aerobic, anaerobic, and anoxic biogeochemical processes in natural and constructed wetlands. Finally, the Unsatchem module simulates the transport and reactions of major ions in a soil profile. Brief descriptions and an application of each module will be presented. Except for HP3, all modules simulate flow and transport processes in two-dimensional transport domains. All modules are fully supported by the HYDRUS graphical user interface. Further development of these modules, as well as of several other new modules (such as Overland), is still envisioned. Continued feedback from the research community is encouraged.

  8. Modeling of Colloid Transport Mechanisms Facilitating Migration of Radionuclides in Fractured Media

    SciTech Connect

    Li Shihhai; Yang, H.-T.; Jen, C.-P.

    2004-12-15

    Performance assessments of high-level radioactive waste disposal have emphasized the role of colloids in the migration of radionuclides in the geosphere. The transport of colloids often brings them in contact with fracture surfaces or porous rock matrix. Colloids that attach to these surfaces are treated as being immobile and are called filtered colloids. The filtered colloids could be released into the fracture again; that is, the attachment of colloids may be reversible. Also, the colloids in the fracture could diffuse into the porous matrix rock. A methodology is proposed to evaluate a predictive model to assess transport within the fractured rock as well as various phenomenological coefficients employed in the different mechanisms, such as filtration, remobilization, and matrix diffusion of colloids. The governing equations of colloids considering mechanisms of the colloidal transport in the fractured media, including filtration, remobilization, and matrix diffusion, have been modeled and solved analytically in previous studies. In the present study, transport equations of colloids and radionuclides that consider the combination of the aforementioned transport mechanisms have also been solved numerically and investigated. The total concentration of mobile radionuclides in the fracture becomes lower because the concentration of mobile colloids in the fracture decreases when the filtration coefficient for colloids increases. Additionally, the concentration of mobile radionuclides was increased at any given time step due to the higher sorption partition coefficient of radionuclides associated with colloids. The results also show that the concentration of radionuclides in the fracture zone decreases when the remobilization coefficient of colloids or the percentages of the matrix diffusion flux of colloids increase.

  9. Communication: Photoactivation of nucleobase bound platinum{sup II} metal complexes: Probing the influence of the nucleobase

    SciTech Connect

    Sen, Ananya; Dessent, Caroline E. H.

    2014-12-28

    We present UV laser action spectra (220-300 nm) of isolated nucleobase-bound Pt{sup II}(CN){sub 4}{sup 2−} complexes, i.e., Pt(CN){sub 4}{sup 2−}⋅M, where M = uracil, thymine, cytosine, and adenine. These metal complex-nucleobase clusters represent model systems for identifying the fundamental photophysical and photochemical processes occurring in photodynamic platinum (II) drug therapies that target DNA. This is the first study to explore the specific role of the nucleobase in the photophysics of the aggregate complex. Each of the complexes studied displays a broadly similar absorption spectra, with a strong λ{sub max} ∼ 4.7 eV absorption band (nucleobase localized chromophore) and a subsequent increase in the absorption intensity towards higher spectral-energy (Pt(CN){sub 4}{sup 2−} localized chromophore). However, strikingly different band widths are observed across the series of complexes, decreasing in the order Pt(CN){sub 4}{sup 2−}⋅Thymine > Pt(CN){sub 4}{sup 2−}⋅Uracil > Pt(CN){sub 4}{sup 2−}⋅Adenine > Pt(CN){sub 4}{sup 2−}⋅Cytosine. Changes in the bandwidth of the ∼4.7 eV band are accompanied by distinctive changes in the photofragment product ions observed following photoexcitation, with the narrower-bandwidth complexes showing a greater propensity to decay via electron detachment decay. We discuss these observations in the context of the distinctive nucleobase-dependent excited state lifetimes.

  10. Tunneling holes in microparticles to facilitate the transport of lithium ions for high volumetric density batteries.

    PubMed

    Zhu, Jian; Ng, K Y Simon; Deng, Da

    2015-09-14

    Microscale materials generally have a higher tap density than that of random nanoparticles. Therefore, microparticles have been attracting much attention for application as high volumetric density electrodes for lithium ion batteries. However, microparticles have much longer electrolyte diffusion and Li-ion migration length and less accessibility to the electrolyte than that of nanoparticles. Therefore, it will be interesting to tunnel-holes in the high volumetric density microparticles to facilitate the reversible storage of lithium ions. Here, tunnel-like holes were generated in microparticles to dramatically increase the accessibility of the active materials to facilitate the lithium ion transfer. A plausible formation mechanism to explain the generation of tunnel-like holes was proposed based on time-course experiments and intensive characterization. Impressively, the as-prepared microbeads with tunnels demonstrated dramatically improved performance compared to the solid microbeads without tunnels in lithium ion storage. The microparticles with tunnels could achieve comparable electrochemical performances to those nanoparticles reported in the literature, suggesting that microparticles, properly tuned, could be promising candidates as negative electrodes for lithium-ion batteries and worthy of further studies. We also directly measured the volumetric density of the microparticles. We would like to highlight that a superior volumetric capacity of 514 mA h cm(-3) has been achieved. We hope to promote more frequent use of the unit mA h cm(-3) in addition to the conventional unit mA h g(-1) in the battery community. PMID:26247159

  11. Content variations of triterpenic acid, nucleoside, nucleobase, and sugar in jujube (Ziziphus jujuba) fruit during ripening.

    PubMed

    Guo, Sheng; Duan, Jin-Ao; Qian, Dawei; Tang, Yuping; Wu, Dawei; Su, Shulan; Wang, Hanqing; Zhao, Yunan

    2015-01-15

    Jujube (Ziziphus jujuba) fruit is widely consumed as food and traditional Chinese medicine in Asian countries due to its potential effects for human health. To facilitate selection of the maturity stage providing optimum health benefits, jujube fruits were analysed at six stages of growth (S1-6) for triterpenic acids, nucleosides, nucleobases, and sugars by UHPLC-MS/MS or HPLC-ELSD methods. The content levels of most triterpenic acids and sugars increased with ripening, and reached the highest at S5 and S6, respectively. The accumulation of the cyclic nucleotides (cAMP and cGMP) was mainly in the later stage of ripening (S5-6). Therefore, if taking triterpenic acids as the major quality indicator, S5 should be the ideal time to harvest jujube fruit, and the full ripen stage (S6) maybe the best choice when taking sugars and cyclic nucleotides as the most important components. PMID:25149013

  12. Tunneling holes in microparticles to facilitate the transport of lithium ions for high volumetric density batteries

    NASA Astrophysics Data System (ADS)

    Zhu, Jian; Ng, K. Y. Simon; Deng, Da

    2015-08-01

    Microscale materials generally have a higher tap density than that of random nanoparticles. Therefore, microparticles have been attracting much attention for application as high volumetric density electrodes for lithium ion batteries. However, microparticles have much longer electrolyte diffusion and Li-ion migration length and less accessibility to the electrolyte than that of nanoparticles. Therefore, it will be interesting to tunnel-holes in the high volumetric density microparticles to facilitate the reversible storage of lithium ions. Here, tunnel-like holes were generated in microparticles to dramatically increase the accessibility of the active materials to facilitate the lithium ion transfer. A plausible formation mechanism to explain the generation of tunnel-like holes was proposed based on time-course experiments and intensive characterization. Impressively, the as-prepared microbeads with tunnels demonstrated dramatically improved performance compared to the solid microbeads without tunnels in lithium ion storage. The microparticles with tunnels could achieve comparable electrochemical performances to those nanoparticles reported in the literature, suggesting that microparticles, properly tuned, could be promising candidates as negative electrodes for lithium-ion batteries and worthy of further studies. We also directly measured the volumetric density of the microparticles. We would like to highlight that a superior volumetric capacity of 514 mA h cm-3 has been achieved. We hope to promote more frequent use of the unit mA h cm-3 in addition to the conventional unit mA h g-1 in the battery community.Microscale materials generally have a higher tap density than that of random nanoparticles. Therefore, microparticles have been attracting much attention for application as high volumetric density electrodes for lithium ion batteries. However, microparticles have much longer electrolyte diffusion and Li-ion migration length and less accessibility to the

  13. Bacillus cereus efflux protein BC3310 – a multidrug transporter of the unknown major facilitator family, UMF-2

    PubMed Central

    Kroeger, Jasmin K.; Hassan, Karl; Vörös, Aniko; Simm, Roger; Saidijam, Massoud; Bettaney, Kim E.; Bechthold, Andreas; Paulsen, Ian T.; Henderson, Peter J. F.; Kolstø, Anne-Brit

    2015-01-01

    Phylogenetic classification divides the major facilitator superfamily (MFS) into 82 families, including 25 families that are comprised of transporters with no characterized functions. This study describes functional data for BC3310 from Bacillus cereus ATCC 14579, a member of the “unknown major facilitator family-2” (UMF-2). BC3310 was shown to be a multidrug efflux pump conferring resistance to ethidium bromide, SDS and silver nitrate when heterologously expressed in Escherichia coli DH5α ΔacrAB. A conserved aspartate residue (D105) in putative transmembrane helix 4 was identified, which was essential for the energy dependent ethidium bromide efflux by BC3310. Transport proteins of the MFS comprise specific sequence motifs. Sequence analysis of UMF-2 proteins revealed that they carry a variant of the MFS motif A, which may be used as a marker to distinguish easily between this family and other MFS proteins. Genes orthologous to bc3310 are highly conserved within the B. cereus group of organisms and thus belong to the core genome, suggesting an important conserved functional role in the normal physiology of these bacteria. PMID:26528249

  14. Nitrate facilitates cadmium uptake, transport and accumulation in the hyperaccumulator Sedum plumbizincicola.

    PubMed

    Hu, Pengjie; Yin, Yong-Gen; Ishikawa, Satoru; Suzui, Nobuo; Kawachi, Naoki; Fujimaki, Shu; Igura, Masato; Yuan, Cheng; Huang, Jiexue; Li, Zhu; Makino, Tomoyuki; Luo, Yongming; Christie, Peter; Wu, Longhua

    2013-09-01

    The aims of this study are to investigate whether and how the nitrogen form (nitrate (NO3 (-)) versus ammonium (NH4 (+))) influences cadmium (Cd) uptake and translocation and subsequent Cd phytoextraction by the hyperaccumulator species Sedum plumbizincicola. Plants were grown hydroponically with N supplied as either NO3 (-) or NH4 (+). Short-term (36 h) Cd uptake and translocation were determined innovatively and quantitatively using a positron-emitting (107)Cd tracer and positron-emitting tracer imaging system. The results show that the rates of Cd uptake by roots and transport to the shoots in the NO3 (-) treatment were more rapid than in the NH4 (+) treatment. After uptake for 36 h, 5.6 (0.056 μM) and 29.0 % (0.290 μM) of total Cd in the solution was non-absorbable in the NO3 (-) and NH4 (+) treatments, respectively. The local velocity of Cd transport was approximately 1.5-fold higher in roots (3.30 cm h(-1)) and 3.7-fold higher in shoots (10.10 cm h(-1)) of NO3 (-)- than NH4 (+)-fed plants. Autoradiographic analysis of (109)Cd reveals that NO3 (-) nutrition enhanced Cd transportation from the main stem to branches and young leaves. Moreover, NO3 (-) treatment increased Cd, Ca and K concentrations but inhibited Fe and P in the xylem sap. In a 21-day hydroponic culture, shoot biomass and Cd concentration were 1.51 and 2.63 times higher in NO3 (-)- than in NH4 (+)-fed plants. We conclude that compared with NH4 (+), NO3 (-) promoted the major steps in the transport route followed by Cd from solution to shoots in S. plumbizincicola, namely its uptake by roots, xylem loading, root-to-shoot translocation in the xylem and uploading to the leaves. S. plumbizincicola prefers NO3 (-) nutrition to NH4 (+) for Cd phytoextraction. PMID:23589260

  15. DNA Stains as Surrogate Nucleobases in Fluorogenic Hybridization Probes.

    PubMed

    Hövelmann, Felix; Seitz, Oliver

    2016-04-19

    The increasing importance assigned to RNA dynamics in cells and tissues calls for probe molecules that enable fluorescence microscopy imaging in live cells. To achieve this goal, fluorescence dyes are conjugated with oligonucleotides so as to provide strong emission upon hybridization with the target molecule. The impressive 10(3)-fold fluorescence intensification observed when DNA stains such as thiazole orange (TO) interact with double-stranded DNA is intriguing and prompted the exploration of oligonucleotide conjugates. However, nonspecific interactions of DNA stains with polynucleotides tend to increase background, which would affect the contrast achievable in live-cell imaging. This Account describes the development of DNA-stain-labeled hybridization probes that provide high signal-to-background. We focus on our contributions in context with related advances from other laboratories. The emphasis will be on the requirements of RNA imaging in live cells. To reduce background, intercalator dyes such as TO were appended to peptide nucleic acid (PNA), which is less avidly recognized by DNA stains than DNA/RNA. Constraining the TO dye as a nucleobase surrogate in "forced intercalation (FIT) probes" improved the target specificity, presumably by helping to prevent unspecific interactions. The enforcement of TO intercalation between predetermined base pairs upon formation of the probe-target duplex provided for high brightness and enabled match/mismatch selectivity beyond stringency of hybridization. We show examples that highlight the use of PNA FIT probes in the imaging of mRNA, miRNA, and lncRNA in living cells. The "FIT approach" was recently extended to DNA probes. Signal brightness can become limiting when low-abundance targets ought to be visualized over cellular autofluorescence. We discuss strategies that further the brightness of signaling by FIT probes. Multilabeling with identical dyes does not solve the brightness issue. To avoid self-quenching, we

  16. Bacterial Peptide Recognition and Immune Activation Facilitated by Human Peptide Transporter PEPT2

    PubMed Central

    Swaan, Peter W.; Bensman, Timothy; Bahadduri, Praveen M.; Hall, Mark W.; Sarkar, Anasuya; Bao, Shengying; Khantwal, Chandra M.; Ekins, Sean; Knoell, Daren L.

    2008-01-01

    Microbial detection requires the recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs) that are distributed on the cell surface and within the cytosol. The nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) family functions as an intracellular PRR that triggers the innate immune response. The mechanism by which PAMPs enter the cytosol to interact with NLRs, particularly muropeptides derived from the bacterial proteoglycan cell wall, is poorly understood. PEPT2 is a proton-dependent transporter that mediates the active translocation of di- and tripeptides across epithelial tissues, including the lung. Using computational tools, we initially established that bacterial dipeptides, particularly γ-D-glutamyl-meso-diaminopimelic acid (γ-iE-DAP), are suitable substrates for PEPT2. We then determined in primary cultures of human upper airway epithelia and transiently transfected CHO-PEPT2 cell lines that γ-iE-DAP uptake was mediated by PEPT2 with an affinity constant of approximately 193 μM, whereas muramyl dipeptide was not transported. Exposure to γ-iE-DAP at the apical surface of differentiated, polarized cultures resulted in activation of the innate immune response in an NOD1- and RIP2-dependent manner, resulting in release of IL-6 and IL-8. Based on these findings we report that PEPT2 plays a vital role in microbial recognition by NLR proteins, particularly with regard to airborne pathogens, thereby participating in host defense in the lung. PMID:18474668

  17. Facilitation of Drug Transport across the Blood–Brain Barrier with Ultrasound and Microbubbles

    PubMed Central

    Meairs, Stephen

    2015-01-01

    Medical treatment options for central nervous system (CNS) diseases are limited due to the inability of most therapeutic agents to penetrate the blood–brain barrier (BBB). Although a variety of approaches have been investigated to open the BBB for facilitation of drug delivery, none has achieved clinical applicability. Mounting evidence suggests that ultrasound in combination with microbubbles might be useful for delivery of drugs to the brain through transient opening of the BBB. This technique offers a unique non-invasive avenue to deliver a wide range of drugs to the brain and promises to provide treatments for CNS disorders with the advantage of being able to target specific brain regions without unnecessary drug exposure. If this method could be applied for a range of different drugs, new CNS therapeutic strategies could emerge at an accelerated pace that is not currently possible in the field of drug discovery and development. This article reviews both the merits and potential risks of this new approach. It assesses methods used to verify disruption of the BBB with MRI and examines the results of studies aimed at elucidating the mechanisms of opening the BBB with ultrasound and microbubbles. Possible interactions of this novel delivery method with brain disease, as well as safety aspects of BBB disruption with ultrasound and microbubbles are addressed. Initial translational research for treatment of brain tumors and Alzheimer’s disease is presented. PMID:26404357

  18. Local piezoresponse and polarization switching in nucleobase thymine microcrystals

    NASA Astrophysics Data System (ADS)

    Bdikin, Igor; Heredia, Alejandro; Neumayer, Sabine M.; Bystrov, Vladimir S.; Gracio, José; Rodriguez, Brian J.; Kholkin, Andrei L.

    2015-08-01

    Thymine (2-oxy-4-oxy-5 methyl pyrimidine) is one of the four nucleobases of deoxyribonucleic acid (DNA). In the DNA molecule, thymine binds to adenine via two hydrogen bonds, thus stabilizing the nucleic acid structure and is involved in pairing and replication. Here, we show that synthetic thymine microcrystals grown from the solution exhibit local piezoelectricity and apparent ferroelectricity, as evidenced by nanoscale electromechanical measurements via Piezoresponse Force Microscopy. Our experimental results demonstrate significant electromechanical activity and polarization switchability of thymine, thus opening a pathway for piezoelectric and ferroelectric-based applications of thymine and, perhaps, of other DNA nucleobase materials. The results are supported by molecular modeling of polarization switching under an external electric field.

  19. Glucose-Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA.

    PubMed

    Vengut-Climent, Empar; Gómez-Pinto, Irene; Lucas, Ricardo; Peñalver, Pablo; Aviñó, Anna; Fonseca Guerra, Célia; Bickelhaupt, F Matthias; Eritja, Ramón; González, Carlos; Morales, Juan C

    2016-07-18

    Noncovalent forces rule the interactions between biomolecules. Inspired by a biomolecular interaction found in aminoglycoside-RNA recognition, glucose-nucleobase pairs have been examined. Deoxyoligonucleotides with a 6-deoxyglucose insertion are able to hybridize with their complementary strand, thus exhibiting a preference for purine nucleobases. Although the resulting double helices are less stable than natural ones, they present only minor local distortions. 6-Deoxyglucose stays fully integrated in the double helix and its OH groups form two hydrogen bonds with the opposing guanine. This 6-deoxyglucose-guanine pair closely resembles a purine-pyrimidine geometry. Quantum chemical calculations indicate that glucose-purine pairs are as stable as a natural T-A pair. PMID:27328804

  20. Nucleobase appended viologens: Building blocks for new optoelectronic materials

    NASA Astrophysics Data System (ADS)

    Ciobanu, Marius; Asaftei, Simona

    2015-04-01

    We describe here the fabrication, characterization and possible applications of a new type of optical material - consisting of 4,4‧-bipyridinium core ("viologen") and nucleobases i.e. adenine and/or thymine made by H-bonding. The viologen-nucleobase derivatives were used to construct supramolecular structures in a "biomimetic way" with complementary oligonucleotides (ssDNA) and peptide nucleic acids (ssPNA) as templates. The new nanostructured materials are expected to exhibit enhanced optical and optoelectronic properties with application in the field of supramolecular electronics. Such viologen derivatives could be significant in the design of new 2D and 3D materials with potentially application in optoelectronics, molecular electronics or sensoric.

  1. Supramolecular gels made from nucleobase, nucleoside and nucleotide analogs.

    PubMed

    Peters, Gretchen Marie; Davis, Jeffery T

    2016-06-01

    Supramolecular or molecular gels are attractive for various applications, including diagnostics, tissue scaffolding and targeted drug release. Gelators derived from natural products are of particular interest for biomedical purposes, as they are generally biocompatible and stimuli-responsive. The building blocks of nucleic acids (i.e. nucleobases, nucleosides, and nucleotides) are desirable candidates for supramolecular gelation as they readily engage in reversible, noncovalent interactions. In this review, we describe a number of organo- and hydrogels formed through the assembly of nucleosides, nucleotides, and their derivatives. While natural nucleosides and nucleotides generally require derivatization to induce gelation, guanosine and its corresponding nucleotides are well known gelators. This unique gelating ability is due to propensity of the guanine nucleobase to self-associate into stable higher-order assemblies, such as G-ribbons, G4-quartets, and G-quadruplexes. PMID:27146863

  2. Facilitating guest transport in clathrate hydrates by tuning guest-host interactions.

    PubMed

    Moudrakovski, Igor L; Udachin, Konstantin A; Alavi, Saman; Ratcliffe, Christopher I; Ripmeester, John A

    2015-02-21

    The understanding and eventual control of guest molecule transport in gas hydrates is of central importance for the efficient synthesis and processing of these materials for applications in the storage, separation, and sequestration of gases and natural gas production. Previously, some links have been established between dynamics of the host water molecules and guest-host hydrogen bonding interactions, but direct observation of transport in the form of cage-to-cage guest diffusion is still lacking. Recent calculations have suggested that pairs of different guest molecules in neighboring cages can affect guest-host hydrogen bonding and, therefore, defect injection and water lattice motions. We have chosen two sets of hydrate guest pairs, tetrahydrofuran (THF)-CO2 and isobutane-CO2, that are predicted to enhance or to diminish guest-host hydrogen bonding interactions as compared to those in pure CO2 hydrate and we have studied guest dynamics in each using (13)C nuclear magnetic resonance (NMR) methods. In addition, we have obtained the crystal structure of the THF-CO2 sII hydrate using the combined single crystal X-ray diffraction and (13)C NMR powder pattern data and have performed molecular dynamics-simulation of the CO2 dynamics. The NMR powder line shape studies confirm the enhanced and delayed dynamics for the THF and isobutane containing hydrates, respectively, as compared to those in the CO2 hydrate. In addition, from line shape studies and 2D exchange spectroscopy NMR, we observe cage-to-cage exchange of CO2 molecules in the THF-CO2 hydrate, but not in the other hydrates studied. We conclude that the relatively rapid intercage guest dynamics are the result of synergistic guest A-host water-guest B interactions, thus allowing tuning of the guest transport properties in the hydrates by choice of the appropriate guest molecules. Our experimental value for inter-cage hopping is slower by a factor of 10(6) than a published calculated value. PMID:25702022

  3. Facilitating guest transport in clathrate hydrates by tuning guest-host interactions

    SciTech Connect

    Moudrakovski, Igor L.; Udachin, Konstantin A.; Ratcliffe, Christopher I.; Alavi, Saman; Ripmeester, John A.

    2015-02-21

    The understanding and eventual control of guest molecule transport in gas hydrates is of central importance for the efficient synthesis and processing of these materials for applications in the storage, separation, and sequestration of gases and natural gas production. Previously, some links have been established between dynamics of the host water molecules and guest-host hydrogen bonding interactions, but direct observation of transport in the form of cage-to-cage guest diffusion is still lacking. Recent calculations have suggested that pairs of different guest molecules in neighboring cages can affect guest-host hydrogen bonding and, therefore, defect injection and water lattice motions. We have chosen two sets of hydrate guest pairs, tetrahydrofuran (THF)-CO{sub 2} and isobutane-CO{sub 2}, that are predicted to enhance or to diminish guest–host hydrogen bonding interactions as compared to those in pure CO{sub 2} hydrate and we have studied guest dynamics in each using {sup 13}C nuclear magnetic resonance (NMR) methods. In addition, we have obtained the crystal structure of the THF-CO{sub 2} sII hydrate using the combined single crystal X-ray diffraction and {sup 13}C NMR powder pattern data and have performed molecular dynamics-simulation of the CO{sub 2} dynamics. The NMR powder line shape studies confirm the enhanced and delayed dynamics for the THF and isobutane containing hydrates, respectively, as compared to those in the CO{sub 2} hydrate. In addition, from line shape studies and 2D exchange spectroscopy NMR, we observe cage-to-cage exchange of CO{sub 2} molecules in the THF-CO{sub 2} hydrate, but not in the other hydrates studied. We conclude that the relatively rapid intercage guest dynamics are the result of synergistic guest A–host water–guest B interactions, thus allowing tuning of the guest transport properties in the hydrates by choice of the appropriate guest molecules. Our experimental value for inter-cage hopping is slower by a factor of 10

  4. Facilitating guest transport in clathrate hydrates by tuning guest-host interactions

    NASA Astrophysics Data System (ADS)

    Moudrakovski, Igor L.; Udachin, Konstantin A.; Alavi, Saman; Ratcliffe, Christopher I.; Ripmeester, John A.

    2015-02-01

    The understanding and eventual control of guest molecule transport in gas hydrates is of central importance for the efficient synthesis and processing of these materials for applications in the storage, separation, and sequestration of gases and natural gas production. Previously, some links have been established between dynamics of the host water molecules and guest-host hydrogen bonding interactions, but direct observation of transport in the form of cage-to-cage guest diffusion is still lacking. Recent calculations have suggested that pairs of different guest molecules in neighboring cages can affect guest-host hydrogen bonding and, therefore, defect injection and water lattice motions. We have chosen two sets of hydrate guest pairs, tetrahydrofuran (THF)-CO2 and isobutane-CO2, that are predicted to enhance or to diminish guest-host hydrogen bonding interactions as compared to those in pure CO2 hydrate and we have studied guest dynamics in each using 13C nuclear magnetic resonance (NMR) methods. In addition, we have obtained the crystal structure of the THF-CO2 sII hydrate using the combined single crystal X-ray diffraction and 13C NMR powder pattern data and have performed molecular dynamics-simulation of the CO2 dynamics. The NMR powder line shape studies confirm the enhanced and delayed dynamics for the THF and isobutane containing hydrates, respectively, as compared to those in the CO2 hydrate. In addition, from line shape studies and 2D exchange spectroscopy NMR, we observe cage-to-cage exchange of CO2 molecules in the THF-CO2 hydrate, but not in the other hydrates studied. We conclude that the relatively rapid intercage guest dynamics are the result of synergistic guest A-host water-guest B interactions, thus allowing tuning of the guest transport properties in the hydrates by choice of the appropriate guest molecules. Our experimental value for inter-cage hopping is slower by a factor of 106 than a published calculated value.

  5. The role of organic complexants and microparticulates in the facilitated transport of radionuclides

    SciTech Connect

    Schilk, A.J.; Robertson, D.E.; Abel, K.H.; Thomas, C.W.

    1996-12-01

    This progress report describes the results of ongoing radiological and geochemical investigations of the mechanisms of radionuclide transport in groundwater at two low-level waste (LLW) disposal sites within the waste management area of the Chalk River Laboratories (CRL), Ontario, Canada. These sites, the Chemical Pit liquid disposal facility and the Waste Management Area C solid LLW disposal site, have provided valuable 30- to 40-year-old field locations for characterizing the migration of radionuclides and evaluating a number of recent site performance objectives for LLW disposal facilities. This information will aid the NRC and other federal, state, and local regulators, as well as LLW disposal site developers and waste generators, in maximizing the effectiveness of existing or projected LLW disposal facilities for isolating radionuclides from the general public and thereby improving the health and safety aspects of LLW disposal.

  6. Augmenting an observation network to facilitate flow and transport model discrimination

    NASA Astrophysics Data System (ADS)

    Pachepsky, Y. A.; Kuznetsov, M.; Guber, A.; Yakirevich, A.; Martinez Garcia, G.; Gish, T. J.; Cady, R.; Nicholson, T. J.

    2011-12-01

    Improving understanding of subsurface conditions includes performance comparison for competing models, independently developed or obtained via model abstraction. The model comparison and discrimination can be improved if additional observations will be included. The objective of this work was to implement and to test a Bayesian method for the sequential design of the network augmentation. The method is based on (1) generalization of Kullback's discriminant function and "weights of evidence" for the case of available prior probabilities, (2) ensemble modeling to estimate variance of the predicted values. The method was tested with the data from the tracer experiment at the USDA-ARS OPE3 integrated research site. A pulse of KCL solution was applied to an irrigation plot, and chloride concentrations were measured in the groundwater at three sampling depths in 12 observations wells. The spatial distribution of soil materials was obtained from cores taken from depths of 0-200 cm with 20 cm increment during installation of observation wells. A three-dimension flow and transport model was developed to simulate the flow and chloride transport for the tracer experiment at the OPE3 site. The manual calibration of hydraulic conductivities and dispersivities was performed, and pedotransfer functions were conditioned to calibration results to build ensemble of models. The search of the optimal location of the augmentation wells was done on a 2D grid. Models of different complexity were compared. Both single and multiple responses were used to discriminate models. The outcome of this study can provide the information for the future data collection and monitoring efforts to further reduce the uncertainty

  7. DNA-nucleobases: gate dielectric/passivation layer for flexible GFET-based sensor applications

    NASA Astrophysics Data System (ADS)

    Williams, Adrienne D.; Ouchen, Fahima; Kim, Steve S.; Elhamri, Said; Naik, Rajesh R.; Grote, James

    2015-09-01

    The main goal of this research was to maintain the bulk charge carrier mobility of graphene, after deposition of the gate dielectric layer used for making transistor devices. The approach was introducing a thin film of deoxyribonucleic acid (DNA) nucleobase purine guanine, deposited by physical vapor deposition (PVD), onto layers of graphene that were transferred onto various flexible substrates. Several test platforms were fabricated with guanine as a standalone gate dielectric, as the control, and guanine as a passivation layer between the graphene and PMMA. It was found that the bulk charge carrier mobility of graphene was best maintained and most stable using guanine as a passivation layer between the graphene and PMMA. Other transport properties, such as charge carrier concentration, conductivity type and electrical resistivity were investigated as well. This is an important first step to realizing high performance graphene-based transistors that have potential use in bio and environmental sensors, computer-processing and electronics.

  8. A Physical Interaction between the Dopamine Transporter and DJ-1 Facilitates Increased Dopamine Reuptake

    PubMed Central

    Luk, Beryl; Mohammed, Mohinuddin; Liu, Fang; Lee, Frank J. S.

    2015-01-01

    The regulation of the dopamine transporter (DAT) impacts extracellular dopamine levels after release from dopaminergic neurons. Furthermore, a variety of protein partners have been identified that can interact with and modulate DAT function. In this study we show that DJ-1 can potentially modulate DAT function. Co-expression of DAT and DJ-1 in HEK-293T cells leads to an increase in [3H] dopamine uptake that does not appear to be mediated by increased total DAT expression but rather through an increase in DAT cell surface localization. In addition, through a series of GST affinity purifications and co-immunoprecipitations, we provide evidence that the DAT can be found in a complex with DJ-1, which involve distinct regions within both DAT and DJ-1. Using in vitro binding experiments we also show that this complex can be formed in part by a direct interaction between DAT and DJ-1. Co-expression of a mini-gene that can disrupt the DAT/DJ-1 complex appears to block the increase in [3H] dopamine uptake by DJ-1. Mutations in DJ-1 have been linked to familial forms of Parkinson’s disease, yet the normal physiological function of DJ-1 remains unclear. Our study suggests that DJ-1 may also play a role in regulating dopamine levels by modifying DAT activity. PMID:26305376

  9. Colloid facilitated transport of humic substances in soil: laboratory experiment and modeling calculation.

    NASA Astrophysics Data System (ADS)

    Dinu, Marina; Moiseenko, Tatyana

    2016-04-01

    An understanding of ability to predict the fate and transport of colloids in soil systems are of great importance in many environmental and industrial applications. Especially, in the case study sizes and zeta potentials of lignin and humus components (as a parameter reflecting the mobility and tread of organic substances). The objects of investigation were water extracts of gleepodzolic soil of European territory of Russia and Western Siberia, as well as humus substances extracted from this soil. In this study, evaluation of size, molecular weight distribution and zeta potential were used to predict the mobility of the organic component fractions of the soil. Fractionation was performed using multistage filtration plant (100 Da) and measuring physic-chemical parameters measured with the Malvern Zetasizer Nano ZSP. Significant differences in the distribution of organic matter on the molecular weight, charge (sign) of the zeta potential and the size of the sample of European Russia in comparison with samples of Western Siberia have been found. Also, laboratory studies have demonstrated of any differences in physicochemical parameters as infrared spectra, ultraviolet spectra, complexing ability of samples of the same soil type but different areas of Russia. The results can be used in the prediction of the migration ability of fractions humus substances and their stability at change physic-chemical conditions (the coefficient of mobility of the organic components by calculated in MathCad). This work was supported by the grant № 14-17-00460 RSF from 07.11.2014

  10. Facilitated Strontium Transport by Remobilization of Strontium-Containing Secondary Precipitates in Hanford Site Subsurface

    SciTech Connect

    Wang, Guohui; Um, Wooyong

    2013-03-15

    Significantly enhanced immobilization of radionuclides (such as 90Sr and 137Cs) due to adsorption and coprecipitation with neo-formed colloid-sized secondary precipitates has been reported at the U.S. Department of Energy’s Hanford Site. However, the stability of these secondary precipitates containing radionuclides in the subsurface under changeable field conditions is not clear. Here, the authors tested the remobilization possibility of Sr containing secondary precipitates (nitrate-cancrinite) in the subsurface using saturated column experiments under different geochemical and flow conditions. The columns were packed with quartz sand that contained secondary precipitates (nitrate-cancrinite containing Sr), and leached using colloid-free solutions under different flow rates, varying pH, and ionic strength conditions. The results indicate remobilization of the neo-formed secondary precipitates could be possible given a change of background conditions. The remobility of the neo formed precipitates increased with the rise in the leaching solution flow rate and pH (in a range of pH 4 to 11), as well as with decreasing solution ionic strength. The increased mobility of Sr-containing secondary precipitates with changing background conditions can be a potential source for additional radionuclide transport in Hanford Site subsurface environments.

  11. Colloidal-facilitated transport of inorganic contaminants in ground water: part 1, sampling considerations

    USGS Publications Warehouse

    Puls, Robert W.; Eychaner, James H.; Powell, Robert M.

    1996-01-01

    Investigations at Pinal Creek, Arizona, evaluated routine sampling procedures for determination of aqueous inorganic geochemistry and assessment of contaminant transport by colloidal mobility. Sampling variables included pump type and flow rate, collection under air or nitrogen, and filter pore diameter. During well purging and sample collection, suspended particle size and number as well as dissolved oxygen, temperature, specific conductance, pH, and redox potential were monitored. Laboratory analyses of both unfiltered samples and the filtrates were performed by inductively coupled argon plasma, atomic absorption with graphite furnace, and ion chromatography. Scanning electron microscopy with Energy Dispersive X-ray was also used for analysis of filter particulates. Suspended particle counts consistently required approximately twice as long as the other field-monitored indicators to stabilize. High-flow-rate pumps entrained normally nonmobile particles. Difference in elemental concentrations using different filter-pore sizes were generally not large with only two wells having differences greater than 10 percent in most wells. Similar differences (>10%) were observed for some wells when samples were collected under nitrogen rather than in air. Fe2+/Fe3+ ratios for air-collected samples were smaller than for samples collected under a nitrogen atmosphere, reflecting sampling-induced oxidation.

  12. Multiple Surface Regions on the Niemann-Pick C2 Protein Facilitate Intracellular Cholesterol Transport.

    PubMed

    McCauliff, Leslie A; Xu, Zhi; Li, Ran; Kodukula, Sarala; Ko, Dennis C; Scott, Matthew P; Kahn, Peter C; Storch, Judith

    2015-11-01

    The cholesterol storage disorder Niemann-Pick type C (NPC) disease is caused by defects in either of two late endosomal/lysosomal proteins, NPC1 and NPC2. NPC2 is a 16-kDa soluble protein that binds cholesterol in a 1:1 stoichiometry and can transfer cholesterol between membranes by a mechanism that involves protein-membrane interactions. To examine the structural basis of NPC2 function in cholesterol trafficking, a series of point mutations were generated across the surface of the protein. Several NPC2 mutants exhibited deficient sterol transport properties in a set of fluorescence-based assays. Notably, these mutants were also unable to promote egress of accumulated intracellular cholesterol from npc2(-/-) fibroblasts. The mutations mapped to several regions on the protein surface, suggesting that NPC2 can bind to more than one membrane simultaneously. Indeed, we have previously demonstrated that WT NPC2 promotes vesicle-vesicle interactions. These interactions were abrogated, however, by mutations causing defective sterol transfer properties. Molecular modeling shows that NPC2 is highly plastic, with several intense positively charged regions across the surface that could interact favorably with negatively charged membrane phospholipids. The point mutations generated in this study caused changes in NPC2 surface charge distribution with minimal conformational changes. The plasticity, coupled with membrane flexibility, probably allows for multiple cholesterol transfer routes. Thus, we hypothesize that, in part, NPC2 rapidly traffics cholesterol between closely appositioned membranes within the multilamellar interior of late endosomal/lysosomal proteins, ultimately effecting cholesterol egress from this compartment. PMID:26296895

  13. Phosphoregulatory protein 14-3-3 facilitates SAC1 transport from the endoplasmic reticulum

    PubMed Central

    Bajaj Pahuja, Kanika; Wang, Jinzhi; Blagoveshchenskaya, Anastasia; Lim, Lillian; Madhusudhan, M. S.; Mayinger, Peter; Schekman, Randy

    2015-01-01

    Most secretory cargo proteins in eukaryotes are synthesized in the endoplasmic reticulum and actively exported in membrane-bound vesicles that are formed by the cytosolic coat protein complex II (COPII). COPII proteins are assisted by a variety of cargo-specific adaptor proteins required for the concentration and export of secretory proteins from the endoplasmic reticulum (ER). Adaptor proteins are key regulators of cargo export, and defects in their function may result in disease phenotypes in mammals. Here we report the role of 14-3-3 proteins as a cytosolic adaptor in mediating SAC1 transport in COPII-coated vesicles. Sac1 is a phosphatidyl inositol-4 phosphate (PI4P) lipid phosphatase that undergoes serum dependent translocation between the endoplasmic reticulum and Golgi complex and controls cellular PI4P lipid levels. We developed a cell-free COPII vesicle budding reaction to examine SAC1 exit from the ER that requires COPII and at least one additional cytosolic factor, the 14-3-3 protein. Recombinant 14-3-3 protein stimulates the packaging of SAC1 into COPII vesicles and the sorting subunit of COPII, Sec24, interacts with 14-3-3. We identified a minimal sorting motif of SAC1 that is important for 14-3-3 binding and which controls SAC1 export from the ER. This LS motif is part of a 7-aa stretch, RLSNTSP, which is similar to the consensus 14-3-3 binding sequence. Homology models, based on the SAC1 structure from yeast, predict this region to be in the exposed exterior of the protein. Our data suggest a model in which the 14-3-3 protein mediates SAC1 traffic from the ER through direct interaction with a sorting signal and COPII. PMID:26056309

  14. Biosorption of dichlorodiphenyltrichloroethane and hexachlorobenzene in groundwater and its implications for facilitated transport.

    PubMed

    Lindqvist, R; Enfield, C G

    1992-07-01

    The potential for enhanced mobility of hydrophobic pollutants by cotransport with bacteria in saturated soils was evaluated from measurements of biosorption of 14C-labeled hexachlorobenzene and dichlorodiphenyltrichloroethane (DDT) to five strains of soil and sewage bacteria. The sorption process could be described by a linear partition equation and appeared to be reversible, but desorption kinetics were slow and/or partly irreversible. The DDT partition coefficients varied with equilibration time, possibly reflecting DDT-induced changes in the physiology of the bacteria. The partition coefficients, normalized to the masses of the bacteria, ranged from 250 to 14,000 for live cells, but the largest coefficients were associated with autoclaved cells of a Pseudomonas sp. The sorptive capacity of the bacterial biomass was greater for DDT than for hexachlorobenzene but was not correlated to overall bacterial hydrophobicity, measured by hydrophobic interaction chromatography. In a column study, 1.2 x 10(9) cells of a Bacillus sp. strain per ml enhanced DDT transport about 8-fold, whereas an advective-dispersive-sorptive equilibrium model for two mobile phases, water and free-living bacteria, suggested a 14-fold enhancement, based on the DDT partition coefficient. The disagreement was in part due to a retarded nonequilibrium movement of the bacteria. Model calculations based on literature data covering a wide range of organisms and compounds suggested that 10(6) cells ml-1 would increase the mobility of very hydrophobic compounds (log octanol-water partition coefficient [K(ow) of greater than or equal to 6), whereas higher densities of bacteria (10(8) cells ml-1) would have a significant impact on compounds with a log K(ow) of greater than or equal to 4.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1637158

  15. Intracellular cholesterol transport proteins enhance hydrolysis of HDL-CEs and facilitate elimination of cholesterol into bile.

    PubMed

    Wang, Jing; Bie, Jinghua; Ghosh, Shobha

    2016-09-01

    While HDL-associated unesterified or free cholesterol (FC) is thought to be rapidly secreted into the bile, the fate of HDL-associated cholesteryl esters (HDL-CEs) that represent >80% of HDL-cholesterol, is only beginning to be understood. In the present study, we examined the hypothesis that intracellular cholesterol transport proteins [sterol carrier protein 2 (SCP2) and fatty acid binding protein-1 (FABP1)] not only facilitate CE hydrolase-mediated hydrolysis of HDL-CEs, but also enhance elimination of cholesterol into bile. Adenovirus-mediated overexpression of FABP1 or SCP2 in primary hepatocytes significantly increased hydrolysis of HDL-[(3)H]CE, reduced resecretion of HDL-CE-derived FC as nascent HDL, and increased its secretion as bile acids. Consistently, the flux of [(3)H]cholesterol from HDL-[(3)H]CE to biliary bile acids was increased by overexpression of SCP2 or FABP1 in vivo and reduced in SCP2(-/-) mice. Increased flux of HDL-[(3)H]CE to biliary FC was noted with FABP1 overexpression and in SCP2(-/-) mice that have increased FABP1 expression. Lack of a significant decrease in the flux of HDL-[(3)H]CE to biliary FC or bile acids in FABP1(-/-) mice indicates the likely compensation of its function by an as yet unidentified mechanism. Taken together, these studies demonstrate that FABP1 and SCP2 facilitate the preferential movement of HDL-CEs to bile for final elimination. PMID:27381048

  16. Stomatal Spacing Safeguards Stomatal Dynamics by Facilitating Guard Cell Ion Transport Independent of the Epidermal Solute Reservoir.

    PubMed

    Papanatsiou, Maria; Amtmann, Anna; Blatt, Michael R

    2016-09-01

    Stomata enable gaseous exchange between the interior of the leaf and the atmosphere through the stomatal pore. Control of the pore aperture depends on osmotic solute accumulation by, and its loss from the guard cells surrounding the pore. Stomata in most plants are separated by at least one epidermal cell, and this spacing is thought to enhance stomatal function, although there are several genera that exhibit stomata in clusters. We made use of Arabidopsis (Arabidopsis thaliana) stomatal patterning mutants to explore the impact of clustering on guard cell dynamics, gas exchange, and ion transport of guard cells. These studies showed that stomatal clustering in the Arabidopsis too many mouths (tmm1) mutant suppressed stomatal movements and affected CO2 assimilation and transpiration differentially between dark and light conditions and were associated with alterations in K(+) channel gating. These changes were consistent with the impaired dynamics of tmm1 stomata and were accompanied by a reduced accumulation of K(+) ions in the guard cells. Our findings underline the significance of spacing for stomatal dynamics. While stomatal spacing may be important as a reservoir for K(+) and other ions to facilitate stomatal movements, the effects on channel gating, and by inference on K(+) accumulation, cannot be explained on the basis of a reduced number of epidermal cells facilitating ion supply to the guard cells. PMID:27406168

  17. Expression and Regulation of Facilitative Glucose Transporters in Equine Insulin-Sensitive Tissue: From Physiology to Pathology

    PubMed Central

    Lacombe, Véronique A.

    2014-01-01

    Glucose uptake is the rate-limiting step in glucose utilization in mammalians and is tightly regulated by a family of specialized proteins, called the facilitated glucose transporters (GLUTs/SLC2). GLUT4, the major isoform in insulin-responsive tissue, translocates from an intracellular pool to the cell surface and as such determines insulin-stimulated glucose uptake. However, despite intensive research over 50 years, the insulin-dependent and -independent pathways that mediate GLUT4 translocation are not fully elucidated in any species. Insulin resistance (IR) is one of the hallmarks of equine metabolic syndrome and is the most common metabolic predisposition for laminitis in horses. IR is characterized by the impaired ability of insulin to stimulate glucose disposal into insulin-sensitive tissues. Similar to other species, the functional capability of the insulin-responsive GLUTs is impaired in muscle and adipose tissue during IR in horses. However, the molecular mechanisms of altered glucose transport remain elusive in all species, and there is still much to learn about the physiological and pathophysiological functions of the GLUT family members, especially in regard to class III. Since GLUTs are key regulators of whole-body glucose homeostasis, they have received considerable attention as potential therapeutic targets to treat metabolic disorders in human and equine patients. PMID:24977043

  18. Cation Diffusion Facilitators Transport Initiation and Regulation Is Mediated by Cation Induced Conformational Changes of the Cytoplasmic Domain

    PubMed Central

    Maes, Michal; Davidov, Geula; Baram, Michal; Raschdorf, Oliver; Nadav-Tsubery, Merav; Kolusheva, Sofiya; Bitton, Ronit; Goobes, Gil; Friedler, Assaf; Miller, Yifat; Schüler, Dirk; Zarivach, Raz

    2014-01-01

    Cation diffusion facilitators (CDF) are part of a highly conserved protein family that maintains cellular divalent cation homeostasis in all domains of life. CDF's were shown to be involved in several human diseases, such as Type-II diabetes and neurodegenerative diseases. In this work, we employed a multi-disciplinary approach to study the activation mechanism of the CDF protein family. For this we used MamM, one of the main ion transporters of magnetosomes – bacterial organelles that enable magnetotactic bacteria to orientate along geomagnetic fields. Our results reveal that the cytosolic domain of MamM forms a stable dimer that undergoes distinct conformational changes upon divalent cation binding. MamM conformational change is associated with three metal binding sites that were identified and characterized. Altogether, our results provide a novel auto-regulation mode of action model in which the cytosolic domain's conformational changes upon ligand binding allows the priming of the CDF into its transport mode. PMID:24658343

  19. Colloid-Facilitated Transport of 137Cs in Fracture-Fill Material. Experiments and Modeling

    SciTech Connect

    Dittrich, Timothy M.; Reimus, Paul William

    2015-10-29

    In this study, we demonstrate how a combination of batch sorption/desorption experiments and column transport experiments were used to effectively parameterize a model describing the colloid-facilitated transport of Cs in the Grimsel granodiorite/FFM system. Cs partition coefficient estimates onto both the colloids and the stationary media obtained from the batch experiments were used as initial estimates of partition coefficients in the column experiments, and then the column experiment results were used to obtain refined estimates of the number of different sorption sites and the adsorption and desorption rate constants of the sites. The desorption portion of the column breakthrough curves highlighted the importance of accounting for adsorption-desorption hysteresis (or a very nonlinear adsorption isotherm) of the Cs on the FFM in the model, and this portion of the breakthrough curves also dictated that there be at least two different types of sorption sites on the FFM. In the end, the two-site model parameters estimated from the column experiments provided excellent matches to the batch adsorption/desorption data, which provided a measure of assurance in the validity of the model.

  20. Expression and regulation of facilitative glucose transporters in equine insulin-sensitive tissue: from physiology to pathology.

    PubMed

    Lacombe, Véronique A

    2014-01-01

    Glucose uptake is the rate-limiting step in glucose utilization in mammalians and is tightly regulated by a family of specialized proteins, called the facilitated glucose transporters (GLUTs/SLC2). GLUT4, the major isoform in insulin-responsive tissue, translocates from an intracellular pool to the cell surface and as such determines insulin-stimulated glucose uptake. However, despite intensive research over 50 years, the insulin-dependent and -independent pathways that mediate GLUT4 translocation are not fully elucidated in any species. Insulin resistance (IR) is one of the hallmarks of equine metabolic syndrome and is the most common metabolic predisposition for laminitis in horses. IR is characterized by the impaired ability of insulin to stimulate glucose disposal into insulin-sensitive tissues. Similar to other species, the functional capability of the insulin-responsive GLUTs is impaired in muscle and adipose tissue during IR in horses. However, the molecular mechanisms of altered glucose transport remain elusive in all species, and there is still much to learn about the physiological and pathophysiological functions of the GLUT family members, especially in regard to class III. Since GLUTs are key regulators of whole-body glucose homeostasis, they have received considerable attention as potential therapeutic targets to treat metabolic disorders in human and equine patients. PMID:24977043

  1. Structure and Function of the Reduced Folate Carrier: A Paradigm of A Major Facilitator Superfamily Mammalian Nutrient Transporter

    PubMed Central

    Matherly, Larry H.; Hou, Zhanjun

    2013-01-01

    Folates are essential for life and folate deficiency contributes to a host of health problems including cardiovascular disease, fetal abnormalities, neurologic disorders, and cancer. Antifolates, represented by methotrexate, continue to occupy a unique niche among the modern day pharmacopoeia for cancer along with other pathologic conditions. This review focuses on the biology of the membrane transport system termed the “reduced folate carrier” or RFC with a particular emphasis on RFC structure and function. The ubiquitously expressed RFC is the major transporter for folates in mammalian cells and tissues. Loss of RFC expression or function portends potentially profound physiologic or developmental consequences. For chemotherapeutic antifolates used for cancer, loss of RFC expression or synthesis of mutant RFC protein with impaired function results in antifolate resistance due to incomplete inhibition of cellular enzyme targets and low levels of substrate for polyglutamate synthesis. The functional properties for RFC were first documented nearly 40 years ago in murine leukemia cells. Since 1994, when RFC was first cloned, tremendous advances in the molecular biology of RFC and biochemical approaches for studying the structure of polytopic membrane proteins have led to an increasingly detailed picture of the molecular structure of the carrier, including its membrane topology, its N-glycosylation, identification of functionally and structurally important domains and amino acids, and helix packing associations. Although no crystal structure for RFC is yet available, biochemical and molecular studies, combined with homology modeling, based on homologous bacterial Major Facilitator Superfamily transporters such as LacY, now permit the development of experimentally testable hypotheses designed to establish RFC structure and mechanism. PMID:18804694

  2. Isoform-selective inhibition of facilitative glucose transporters: elucidation of the molecular mechanism of HIV protease inhibitor binding.

    PubMed

    Hresko, Richard C; Kraft, Thomas E; Tzekov, Anatoly; Wildman, Scott A; Hruz, Paul W

    2014-06-01

    Pharmacologic HIV protease inhibitors (PIs) and structurally related oligopeptides are known to reversibly bind and inactivate the insulin-responsive facilitative glucose transporter 4 (GLUT4). Several PIs exhibit isoform selectivity with little effect on GLUT1. The ability to target individual GLUT isoforms in an acute and reversible manner provides novel means both to investigate the contribution of individual GLUTs to health and disease and to develop targeted treatment of glucose-dependent diseases. To determine the molecular basis of transport inhibition, a series of chimeric proteins containing transmembrane and cytosolic domains from GLUT1 and GLUT4 and/or point mutations were generated and expressed in HEK293 cells. Structural integrity was confirmed via measurement of N-[2-[2-[2-[(N-biotinylcaproylamino)ethoxy)ethoxyl]-4-[2-(trifluoromethyl)-3H-diazirin-3-yl]benzoyl]-1,3-bis(mannopyranosyl-4-yloxy)-2-propylamine (ATB-BMPA) labeling of the chimeric proteins in low density microsome fractions isolated from stably transfected 293 cells. Functional integrity was assessed via measurement of zero-trans 2-deoxyglucose (2-DOG) uptake. ATB-BMPA labeling studies and 2-DOG uptake revealed that transmembrane helices 1 and 5 contain amino acid residues that influence inhibitor access to the transporter binding domain. Substitution of Thr-30 and His-160 in GLUT1 to the corresponding positions in GLUT4 is sufficient to completely transform GLUT1 into GLUT4 with respect to indinavir inhibition of 2-DOG uptake and ATB-BMPA binding. These data provide a structural basis for the selectivity of PIs toward GLUT4 over GLUT1 that can be used in ongoing novel drug design. PMID:24706759

  3. A Re-Examination of Nucleobases in Carbonaceous Chondrites

    NASA Astrophysics Data System (ADS)

    Martins, Z.; Botta, O.; de Vries, M.; Becker, L.; Ehrenfreund, E.

    The biomolecular building blocks of life, as we know it, are amino acids, purines and pyrimidines. The latter two form the bases of DNA and RNA, molecules that are used in the storage, transcription and translation of genetic information in all terrestrial organisms. A dedicated search for these compounds in meteorites can shed light on the origins of life in two ways: (i) Results can help assess the plausibility of extraterrestrial formation of prebiotic molecules followed by their meteoritic delivery to the early Earth. (ii) Such studies can also provide insights into possible prebiotic synthetic routes. We will search for these compounds in selected carbonaceous chondrites using formic acid extraction and reverse phase high performance liquid chromatography (HPLC) to isolate specific nucleobases from the bulk meteorite material as previously reported [1,2,3]. We will also use a new technique, resonant two-photon ionization mass spectrometry (R2PI) that can, not only identify organic compounds by their mass, but at the same time by their vibronic spectroscopy [4]. R2PI dramatically enhances the specificity for certain compounds (e.g. amino acids, nucleobases) and allows for distinction of structural isomers, tautomers and enantiomers as well as providing additional information due to isotope shifts. The optical spectroscopy can thus help us to further discriminate between terrestrial and extraterrestrial nucleobases. References: [1] Van Der Velden, W. and Schwarts, A. W. (1977) Geochim. Cosmochim. Acta, 41, 961-968. [2] Stoks, P. G. and Schwartz, A. W. (1979a) Nature, 282, 709-10. [3] Glavin, D. P. and Bada, J. L. (2004) In Lunar and Planetary Science XXXV, Abstract # 1022, Houston. [4] Nir, E., Grace, L. I., Brauer, B. and de Vries, M. S. (1999) Journal of the American Chemical Society, 121, 4896-4897.

  4. Fluorescent 2-Aminopyridine Nucleobases for Triplex-Forming Peptide Nucleic Acids.

    PubMed

    Cheruiyot, Samwel K; Rozners, Eriks

    2016-08-17

    Development of new fluorescent peptide nucleic acids (PNAs) is important for fundamental research and practical applications. The goal of this study was the design of fluorogenic nucleobases for incorporation in triplex-forming PNAs. The underlying design principle was the use of a protonation event that accompanied binding of a 2-aminopyridine (M) nucleobase to a G-C base pair as an on switch for a fluorescence signal. Two fluorogenic nucleobases, 3-(1-phenylethynyl)-M and phenylpyrrolo-M, were designed, synthesized and studied. The new M derivatives provided modest enhancement of fluorescence upon protonation but showed reduced RNA binding affinity and quenching of fluorescence signal upon triple-helix formation with cognate double-stranded RNA. Our study illustrates the principal challenges of design and provides guidelines for future improvement of fluorogenic PNA nucleobases. The 3-(1-phenylethynyl)-M may be used as a fluorescent nucleobase to study PNA-RNA triple-helix formation. PMID:27223320

  5. Probing nucleobase photo protection with soft x-rays

    NASA Astrophysics Data System (ADS)

    Gühr, Markus

    2013-05-01

    We [1] present a new method for ultrafast spectroscopy of molecular photoexcited dynamics. The technique uses a pair of femtosecond pulses: a photoexcitation pulse initiating excited state dynamics followed by a soft x-ray (SXR) probe pulse that core ionizes certain atoms inside the molecule. We observe the Auger decay of the core hole as a function of delay between the photoexcitation and SXR pulses. The core hole decay is particularly sensitive to the local valence electrons near the core and shows new types of propensity rules, compared to dipole selection rules in SXR absorption or emission spectroscopy. We apply the delayed ultrafast x-ray Auger probing (DUXAP) method to the specific problem of nucleobase photoprotection to demonstrate its potential. The ultraviolet photoexcited ππ * states of nucleobases are prone to chemical reactions with neighboring bases. To avoid this, the single molecules funnel the ππ * population to lower lying electronic states on an ultrafast timescale under violation of the Born-Oppenheimer approximation. The new type of propensity rule, which is confirmed by Auger decay simulations, allows us to have increased sensitivity on the direct relaxation from the ππ * state to the vibrationally hot electronic ground state. For the nucleobase thymine, we measure a decay of the ππ * state and a subsequent filling of the vibrationally hot ground state in 300 fs. This work was supported by the AMOS program within the Chemical Sciences, Geosciences, and Biosciences Division of the Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy.Portions of this research were carried out at the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory. LCLS is an Office of Science User Facility operated for the U.S. Department of Energy Office of Science by Stanford University. Other portions of this research were carried out at the Advanced Light Source, which is supported by the Director, Office of

  6. Adeninealkylresorcinol, the first alkylresorcinol tethered with nucleobase from Lasiodiplodia sp.

    PubMed

    Gao, Yu-Meng; Sun, Tian-Yu; Ma, Min; Chen, Guo-Dong; Zhou, Zheng-Qun; Wang, Chuan-Xi; Hu, Dan; Chen, Li-Guo; Yao, Xin-Sheng; Gao, Hao

    2016-07-01

    Adeninealkylresorcinol (1), an unusual alkylresorcinol with adenine-alkylresorcinol conjoined skeleton, was isolated from an endophytic fungus Lasiodiplodia sp. obtained from a traditional Chinese medicine Houttuynia cordata Thunb., together with three new biogenetically related compounds (2-4). Their structures were elucidated by comprehensive spectroscopic analysis, and the absolute configuration of 4 was determined by the modified Mosher's method and quantum chemical calculation. Among them, adeninealkylresorcinol (1) is the first alkylresorcinol tethered with nucleobase. In addition, the antioxidant, cytotoxic, and antimicrobial activities of 1-3 were evaluated. PMID:27343368

  7. A Versatile Approach Towards Nucleobase-Modified Aptamers.

    PubMed

    Tolle, Fabian; Brändle, Gerhard M; Matzner, Daniel; Mayer, Günter

    2015-09-01

    A novel and versatile method has been developed for modular expansion of the chemical space of nucleic acid libraries, thus enabling the generation of nucleobase-modified aptamers with unprecedented recognition properties. Reintroduction of the modification after enzymatic replication gives broad access to many chemical modifications. This wide applicability, which is not limited to a single modification, will rapidly advance the application of in vitro selection approaches beyond what is currently feasible and enable the generation of aptamers to many targets that have so far not been addressable. PMID:26224087

  8. Progress report on colloid-facilitated transport at Yucca Mountain: Yucca Mountain site characterization program milestone 3383

    SciTech Connect

    Triay, I.R.; Degueldre, C.; Wistrom, A.O.; Cotter, C.R.; Lemons, W.W.

    1996-06-01

    To assess colloid-facilitated radionuclide transport in groundwaters at the potential nuclear waste repository at Yucca Mountain, it is very important to understand the generation and stability of colloids, including naturally occurring colloids. To this end, we measured the colloid concentration in waters from Well J-13, which is on the order of 106 particles per milliliter (for particle sizes larger than 100 manometers). At this low particle loading, the sorption of radionuclides to colloids would have to be extremely high before the colloids could carry a significant amount of radionuclides from the repository to the accessible environment. We also performed aggregation experiments to evaluate the stability of silica (particle diameter: 85 nm) and clay colloids (particle diameter: 140 nm) as a function of ionic strength in a carbonate-rich synthetic groundwater. When the concentration of electrolyte is increased to induce aggregation, the aggregation is irreversible and the rate of aggregation increases with increasing electrolyte strength. We used autocorrelation photon spectroscopy to estimate the rate of particle aggregation for both types of colloids. By relating the measured aggregation rate to the Smoluchowski rate expression, we determined the stability ratio, W. Aggregation of silica particles and kaolinite clay particles decreased dramatically for an electrolyte concentration, C{sub NaCl}, below 300 mM and 200 mM, respectively.

  9. Preparation of a Facilitated Transport Membrane Composed of Carboxymethyl Chitosan and Polyethylenimine for CO2/N2 Separation

    PubMed Central

    Shen, Jiang-Nan; Yu, Chang-Chao; Zeng, Gan-Ning; van der Bruggen, Bart

    2013-01-01

    The miscibility of carboxymethyl chitosan/polyethylenimine (CMCS/PEI) blends was analyzed by FT-IR, TGA and SEM. Defect-free CMCS/PEI blend membranes were prepared with polysulfone (PSf) ultrafiltration membranes as support layer for the separation of CO2/N2 mixtures. The results demonstrate that the CMCS/PEI blend is miscible, due to the hydrogen bonding interaction between the two targeted polymers. For the blended membrane without water, the permeability of CO2 gas is 3.6 × 10−7 cm3 cm−2 s−1 cmHg−1 and the corresponding separation factor for CO2 and N2 gas is about 33 at the pressure of 15.2 cmHg. Meanwhile, the blended membrane with water has the better permselectivity. The blended membrane containing water with PEI content of 30 wt% has the permeance of 6.3 × 10−4 cm3 cm−2 s−1 cmHg−1 for CO2 gas and a separation factor of 325 for CO2/N2 mixtures at the same feed pressure. This indicates that the CO2 separation performance of the CMCS/PEI blend membrane is higher than that of other facilitated transport membranes reported for CO2/N2 mixture separation. PMID:23434661

  10. Distinction of nucleobases – a tip-enhanced Raman approach

    PubMed Central

    Treffer, Regina; Lin, Xiumei; Bailo, Elena; Deckert-Gaudig, Tanja

    2011-01-01

    Summary The development of novel DNA sequencing methods is one of the ongoing challenges in various fields of research seeking to address the demand for sequence information. However, many of these techniques rely on some kind of labeling or amplification steps. Here we investigate the intrinsic properties of tip-enhanced Raman scattering (TERS) towards the development of a novel, label-free, direct sequencing method. It is known that TERS allows the acquisition of spectral information with high lateral resolution and single-molecule sensitivity. In the presented experiments, single stranded adenine and uracil homopolymers were immobilized on different kinds of substrates (mica and gold nanoplates) and TERS experiments were conducted, which demonstrated the reproducibility of the technique. To elucidate the signal contributions from the specific nucleobases, TERS spectra were collected on single stranded calf thymus DNA with arbitrary sequence. The results show that, while the Raman signals with respect to the four nucleobases differ remarkably, specific markers can be determined for each respective base. The combination of sensitivity and reproducibility shows that the crucial demands for a sequencing procedure are met. PMID:22003468

  11. Two-Photon-Induced Fluorescence of Isomorphic Nucleobase Analogs

    PubMed Central

    Lane, Richard S. K.; Jones, Rosemary; Sinkeldam, Renatus W.

    2014-01-01

    Five isomorphic fluorescent uridine mimics have been subjected to two-photon (2P) excitation analysis to investigate their potential applicability as non-perturbing probes for the single-molecule detection of nucleic acids. We find that small structural differences can cause major changes in the two-photon excitation probability, with the 2P cross sections varying by over one order of magnitude. Two of the probes, both furan-modified uridine analogs, have the highest 2P cross sections (3.8 GM and 7.6 GM) reported for nucleobase analogs, using a conventional Ti:sapphire laser for excitation at 690 nm; they also have the lowest emission quantum yields. In contrast, the analogs with the highest reported quantum yields have the lowest 2P cross sections. The structure-photophysical property relationship presented here is a first step towards the rational design of emissive nucleobase analogs with controlled 2P characteristics. The results demonstrate the potential for major improvements through judicious structural modifications. PMID:24604669

  12. The Roles of Dopamine Transport Inhibition and Dopamine Release Facilitation in Wake Enhancement and Rebound Hypersomnolence Induced by Dopaminergic Agents

    PubMed Central

    Gruner, John A.; Marcy, Val R.; Lin, Yin-Guo; Bozyczko-Coyne, Donna; Marino, Michael J.; Gasior, Maciej

    2009-01-01

    of other DAT inhibitors. Enhancing wake while mitigating RHS can be achieved by combining DAT-inhibiting and DA-releasing agents. Citation: Gruner JA; Marcy VR; LinYG; Bozyczko-Coyne D; Marino MJ; Gasior M. The roles of dopamine transport inhibition and dopamine release facilitation in wake enhancement and rebound hypersomnolence induced by dopaminergic agents. SLEEP 2009;32(11):1425-1438. PMID:19928382

  13. Click Reaction on Solid Phase Enables High Fidelity Synthesis of Nucleobase-Modified DNA.

    PubMed

    Tolle, Fabian; Rosenthal, Malte; Pfeiffer, Franziska; Mayer, Günter

    2016-03-16

    The post-synthetic functionalization of nucleic acids via click chemistry (CuAAC) has seen tremendous implementation, extending the applicability of nucleobase-modified nucleic acids in fields like fluorescent labeling, nanotechnology, and in vitro selection. However, the production of large quantities of high-density functionalized material via solid phase synthesis has been hampered by oxidative by-product formation associated with the alkaline workup conditions. Herein, we describe a rapid and cost-effective protocol for the high fidelity large-scale production of nucleobase-modified nucleic acids, exemplified with a recently described nucleobase-modified aptamer. PMID:26850226

  14. Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA

    PubMed Central

    Malik, Shuja S.; Coey, Christopher T.; Varney, Kristen M.; Pozharski, Edwin; Drohat, Alexander C.

    2015-01-01

    Thymine DNA Glycosylase (TDG) performs essential functions in maintaining genetic integrity and epigenetic regulation. Initiating base excision repair, TDG removes thymine from mutagenic G·T mispairs caused by 5-methylcytosine (mC) deamination and other lesions including uracil (U) and 5-hydroxymethyluracil (hmU). In DNA demethylation, TDG excises 5-formylcytosine (fC) and 5-carboxylcytosine (caC), which are generated from mC by Tet (ten–eleven translocation) enzymes. Using improved crystallization conditions, we solved high-resolution (up to 1.45 Å) structures of TDG enzyme–product complexes generated from substrates including G·U, G·T, G·hmU, G·fC and G·caC. The structures reveal many new features, including key water-mediated enzyme–substrate interactions. Together with nuclear magnetic resonance experiments, the structures demonstrate that TDG releases the excised base from its tight product complex with abasic DNA, contrary to previous reports. Moreover, DNA-free TDG exhibits no significant binding to free nucleobases (U, T, hmU), indicating a Kd >> 10 mM. The structures reveal a solvent-filled channel to the active site, which might facilitate dissociation of the excised base and enable caC excision, which involves solvent-mediated acid catalysis. Dissociation of the excised base allows TDG to bind the beta rather than the alpha anomer of the abasic sugar, which might stabilize the enzyme–product complex. PMID:26358812

  15. Metal ion mediated nucleobase recognition by the ZTP riboswitch

    PubMed Central

    Trausch, Jeremiah J.; Marcano-Velázquez, Joan G.; Matyjasik, Michal M.; Batey, Robert T.

    2015-01-01

    SUMMARY The ZTP riboswitch is a widespread family of regulatory RNAs that upregulate de novo purine synthesis in response to increased intracellular levels of ZTP or ZMP (AICAR). As an important intermediate in purine biosynthesis, ZMP also serves as a proxy for the concentration of 10-formyltetrahydrofolate, a key component of one carbon metabolism. Here we report the structure of the ZTP riboswitch bound to ZMP at a resolution of 1.80 Å. The RNA contains two subdomains brought together through a long-range pseudoknot further stabilized through helix-helix packing. ZMP is bound at the subdomain interface of the RNA through a set of interactions with the ligand's base, ribose sugar and phosphate moieties. Unique to nucleobase recognition by RNAs, the Z base is inner sphere coordinated to a magnesium cation bound by two backbone phosphates. This interaction, along with steric hindrance by the backbone, imparts specificity over related analogs such as ATP/AMP. PMID:26144884

  16. Photo-Irradiation of Pyrimidine in Interstellar Ice Analogs: Searching for Nucleobases

    NASA Astrophysics Data System (ADS)

    Milam, S. N.; Nuevo, M.; Sandford, S. A.; Elsila, J. E.; Dworkin, J. P.

    2009-03-01

    Nucleobases have been detected in meteorites and possibly form in space. The functionalization of PAHs from UV photons in mixed ices has proven effective in the lab. Here we investigate how irradiation affects pyrimidine in interstellar ice analogs.

  17. Nucleobases and Other Prebiotic Species from the Ultraviolet Irradiation of Pyrimidine in Astrophysical Ices

    NASA Astrophysics Data System (ADS)

    Sandford, S. A.; Nuevo, M.; Materese, C. K.; Milam, S. N.

    2012-03-01

    We discuss the results of UV irradiation of ices containing pyrimidine and show that such processing efficiently forms the nucleobases uracil and cytosine, but not thymine, a pattern similar to what is seen in carbonaceous meteorites.

  18. Formation of Nucleobases from the UV Photo-Irradiation of Pyrimidine in Astrophysical Ice Analogs

    NASA Astrophysics Data System (ADS)

    Milam, S. N.; Nuevo, M.; Sandford, S. A.; Elsila, J. E.; Dworkin, J. P.

    2010-04-01

    This work shows how pyrimidic nucleobases (uracil, cytosine, etc.) can be formed under abiotic conditions from the UV irradiation of pyrimidine in astrophysical ices. The formation mechanisms and the photo-stability of such compounds are discussed.

  19. Binding Strength of Nucleobases and Nucleosides on Silver Nanoparticles Probed by a Colorimetric Method.

    PubMed

    Yu, Lu; Li, Na

    2016-06-01

    Because of their unique and tunable properties, oligonucleotide-functionalized noble metal nanoparticles have provided a versatile platform for various engineering and biomedical applications. The vast majority of such applications were demonstrated with gold nanoparticles (AuNPs) while only a few were demonstrated with sliver nanoparticles (AgNPs). This is largely due to the lack of robust protocols to functionalize AgNPs with thiol-modified oligonucleotides. Previous studies have revealed strong interactions between nucleobases and AgNPs. This could enable an alternative way to functionalize AgNPs with non-thiolated oligonucleotides. However, there is no quantitative study on the interaction strengths between AgNPs and oligonucleotides. Several methods have been used for quantitative evaluation of the interaction strengths between AuNPs and oligonucleotides. These methods often require specialized equipment that might not be widely accessible or rely on labor-intensive procedures to obtain the adsorption isotherms. Herein, we developed a colorimetric method, as a simple and high-throughput alternative of existing methods, to quantify the binding strength between AgNPs and nucleobases/nucleosides. In this colorimetric method, concentration-dependent destabilizing effects of nucleobase/nucleoside adsorption on AgNPs are utilized to indirectly quantify the amount of nucleobases/nucleosides adsorbed on AgNPs, thus deriving the binding strength between AgNPs and nucleobases/nucleosides. First, the concentration-dependent AgNP aggregation kinetics in the presence of nucleobases/nucleosides were systematically investigated. Then, this colorimetric method was used to determine the binding strengths between AgNPs and various DNA/RNA nucleobases/nucleosides. It was found that the ranking of interaction strengths between AgNPs and DNA/RNA nucleosides (dC < dT < dA, rC < rU < rA) is generally agreed with that between AgNPs and corresponding nucleobases (C < T < U < A). This

  20. The Major Facilitative Folate Transporters Solute Carrier 19A1 and Solute Carrier 46A1: Biology and Role in Antifolate Chemotherapy of Cancer

    PubMed Central

    Wilson, Mike R.; Hou, Zhanjun

    2014-01-01

    This review summarizes the biology of the major facilitative membrane transporters, the reduced folate carrier (RFC) (Solute Carrier 19A1) and the proton-coupled folate transporter (PCFT) (Solute Carrier 46A1). Folates are essential vitamins, and folate deficiency contributes to a variety of health disorders. RFC is ubiquitously expressed and is the major folate transporter in mammalian cells and tissues. PCFT mediates the intestinal absorption of dietary folates and appears to be important for transport of folates into the central nervous system. Clinically relevant antifolates for cancer, such as methotrexate and pralatrexate, are transported by RFC, and loss of RFC transport is an important mechanism of methotrexate resistance in cancer cell lines and in patients. PCFT is expressed in human tumors, and is active at pH conditions associated with the tumor microenvironment. Pemetrexed is an excellent substrate for both RFC and PCFT. Novel tumor-targeted antifolates related to pemetrexed with selective membrane transport by PCFT over RFC are being developed. In recent years, there have been major advances in understanding the structural and functional properties and the regulation of RFC and PCFT. The molecular bases for methotrexate resistance associated with loss of RFC transport and for hereditary folate malabsorption, attributable to mutant PCFT, were determined. Future studies should continue to translate molecular insights from basic studies of RFC and PCFT biology into new therapeutic strategies for cancer and other diseases. PMID:24396145

  1. Synthesis of alanyl nucleobase amino acids and their incorporation into proteins.

    PubMed

    Talukder, Poulami; Dedkova, Larisa M; Ellington, Andrew D; Yakovchuk, Petro; Lim, Jaebum; Anslyn, Eric V; Hecht, Sidney M

    2016-09-15

    Proteins which bind to nucleic acids and regulate their structure and functions are numerous and exceptionally important. Such proteins employ a variety of strategies for recognition of the relevant structural elements in their nucleic acid substrates, some of which have been shown to involve rather subtle interactions which might have been difficult to design from first principles. In the present study, we have explored the preparation of proteins containing unnatural amino acids having nucleobase side chains. In principle, the introduction of multiple nucleobase amino acids into the nucleic acid binding domain of a protein should enable these modified proteins to interact with their nucleic acid substrates using Watson-Crick and other base pairing interactions. We describe the synthesis of five alanyl nucleobase amino acids protected in a fashion which enabled their attachment to a suppressor tRNA, and their incorporation into each of two proteins with acceptable efficiencies. The nucleobases studied included cytosine, uracil, thymine, adenine and guanine, i.e. the major nucleobase constituents of DNA and RNA. Dihydrofolate reductase was chosen as one model protein to enable direct comparison of the facility of incorporation of the nucleobase amino acids with numerous other unnatural amino acids studied previously. The Klenow fragment of DNA polymerase I was chosen as a representative DNA binding protein whose mode of action has been studied in detail. PMID:27452282

  2. Adsorption of nucleobase pairs on hexagonal boron nitride sheet: hydrogen bonding versus stacking.

    PubMed

    Ding, Ning; Chen, Xiangfeng; Wu, Chi-Man Lawrence; Li, Hui

    2013-07-14

    The adsorption of hydrogen-bonded and stacked nucleobase pairs on the hexagonal boron nitride (h-BN) surface was studied by density functional theory and molecular dynamics methods. Eight types of nucleobase pairs (i.e., GG, AA, TT, CC, UU, AT, GC, and AU) were chosen as the adsorbates. The adsorption configurations, interaction energies, and electronic properties of the nucleobase pair on the h-BN surface were obtained and compared. The density of states analysis result shows that both the hydrogen-bonded and stacked nucleobase pairs were physisorbed on h-BN with minimal charge transfer. The hydrogen-bonded base pairs lying on the h-BN surface are significantly more stable than the stacked forms in both the gas and water phase. The molecular dynamics simulation result indicates that h-BN possessed high sensitivity for the nucleobases and the h-BN surface adsorption could revert the base pair interaction from stacking back to hydrogen bonding in aqueous environment. The h-BN surface could immobilize the nucleobases on its surface, which suggests the use of h-BN has good potential in DNA/RNA detection biosensors and self-assembly nanodevices. PMID:23689542

  3. Adsorption of DNA/RNA nucleobases on hexagonal boron nitride sheet: an ab initio study.

    PubMed

    Lin, Qing; Zou, Xiaolong; Zhou, Gang; Liu, Rui; Wu, Jian; Li, Jia; Duan, Wenhui

    2011-07-14

    Our ab initio calculations indicate that the interaction of deoxyribonucleic/ribonucleic acid (DNA/RNA) nucleobases [guanine (G), adenine (A), thymine (T), cytosine (C), and uracil (U)] with the hexagonal boron nitride (h-BN) sheet, a polar but chemically inert surface, is governed by mutual polarization. Unlike the case of graphene, all nucleobases exhibit the same stacking arrangement on the h-BN sheet due to polarization effects: the anions (N and O atoms) of nucleobases prefer to stay on top of cations (B) of the substrate as far as possible, regardless of the biological properties of nucleobases. The adsorption energies, ranging from 0.5 eV to 0.69 eV, increase in the order of U, C, T, A and G, which can be attributed to different side groups or atoms of nucleobases. The fundamental nature of DNA/RNA nucleobases and h-BN sheet remains unchanged upon adsorption, suggesting that the h-BN sheet is a promising template for DNA/RNA-related research, such as self-assembly. PMID:21637870

  4. Which Electronic and Structural Factors Control the Photostability of DNA and RNA Purine Nucleobases?

    NASA Astrophysics Data System (ADS)

    Pollum, Marvin; Reichardt, Christian; Crespo-Hernández, Carlos E.; Martínez-Fernández, Lara; Corral, Inés; Rauer, Clemens; Mai, Sebastian; Marquetand, Philipp; González, Leticia

    2015-06-01

    Following ultraviolet excitation, the canonical purine nucleobases, guanine and adenine, are able to efficiently dissipate the absorbed energy within hundreds of femtoseconds. This property affords these nucleobases with great photostability. Conversely, non-canonical purine nucleobases exhibit high fluorescence quantum yields or efficiently populate long-lived triplet excited states from which chemistry can occur. Using femtosecond broadband transient absorption spectroscopy in combination with ab initio static and surface hopping dynamics simulations we have determined the electronic and structural factors that regulate the excited state dynamics of the purine nucleobase derivatives. Importantly, we have uncovered that the photostability of the guanine and adenine nucleobases is not due to the structure of the purine core itself and that the substituent at the C6 position of the purine nucleobase plays a more important role than that at the C2 position in the ultrafast relaxation of deleterious electronic energy. [The authors acknowledge the CAREER program of the National Science Foundation (Grant No. CHE-1255084) for financial support.

  5. Inhibition of Mycoplasma pneumoniae growth by FDA-approved anticancer and antiviral nucleoside and nucleobase analogs

    PubMed Central

    2013-01-01

    Background Mycoplasma pneumoniae (Mpn) is a human pathogen that causes acute and chronic respiratory diseases and has been linked to many extrapulmonary diseases. Due to the lack of cell wall, Mpn is resistant to antibiotics targeting cell wall synthesis such as penicillin. During the last 10 years macrolide-resistant Mpn strains have been frequently reported in Asian countries and have been spreading to Europe and the United States. Therefore, new antibiotics are needed. In this study, 30 FDA-approved anticancer or antiviral drugs were screened for inhibitory effects on Mpn growth and selected analogs were further characterized by inhibition of target enzymes and metabolism of radiolabeled substrates. Results Sixteen drugs showed varying inhibitory effects and seven showed strong inhibition of Mpn growth. The anticancer drug 6-thioguanine had a MIC (minimum inhibitory concentration required to cause 90% of growth inhibition) value of 0.20 μg ml-1, whereas trifluorothymidine, gemcitabine and dipyridamole had MIC values of approximately 2 μg ml-1. In wild type Mpn culture the presence of 6-thioguanine and dipyridamole strongly inhibited the uptake and metabolism of hypoxanthine and guanine while gemcitabine inhibited the uptake and metabolism of all nucleobases and thymidine. Trifluorothymidine and 5-fluorodeoxyuridine, however, stimulated the uptake and incorporation of radiolabeled thymidine and this stimulation was due to induction of thymidine kinase activity. Furthermore, Mpn hypoxanthine guanine phosphoribosyl transferase (HPRT) was cloned, expressed, and characterized. The 6-thioguanine, but not other purine analogs, strongly inhibited HPRT, which may in part explain the observed growth inhibition. Trifluorothymidine and 5-fluorodeoxyuridine were shown to be good substrates and inhibitors for thymidine kinase from human and Mycoplasma sources. Conclusion We have shown that several anticancer and antiviral nucleoside and nucleobase analogs are potent

  6. Bcmfs1, a Novel Major Facilitator Superfamily Transporter from Botrytis cinerea, Provides Tolerance towards the Natural Toxic Compounds Camptothecin and Cercosporin and towards Fungicides

    PubMed Central

    Hayashi, Keisuke; Schoonbeek, Henk-jan; De Waard, Maarten A.

    2002-01-01

    Bcmfs1, a novel major facilitator superfamily gene from Botrytis cinerea, was cloned, and replacement and overexpression mutants were constructed to study its function. Replacement mutants showed increased sensitivity to the natural toxic compounds camptothecin and cercosporin, produced by the plant Camptotheca acuminata and the plant pathogenic fungus Cercospora kikuchii, respectively. Overexpression mutants displayed decreased sensitivity to these compounds and to structurally unrelated fungicides, such as sterol demethylation inhibitors (DMIs). A double-replacement mutant of Bcmfs1 and the ATP-binding cassette (ABC) transporter gene BcatrD was more sensitive to DMI fungicides than a single-replacement mutant of BcatrD, known to encode an important ABC transporter of DMIs. The sensitivity of the wild-type strain and mutants to DMI fungicides correlated with Bcmfs1 expression levels and with the initial accumulation of oxpoconazole by germlings of these isolates. The results indicate that Bcmfs1 is a major facilitator superfamily multidrug transporter involved in protection against natural toxins and fungicides and has a substrate specificity that overlaps with the ABC transporter BcatrD. Bcmfs1 may be involved in protection of B. cinerea against plant defense compounds during the pathogenic phase of growth on host plants and against fungitoxic antimicrobial metabolites during its saprophytic phase of growth. PMID:12324349

  7. A primary fish gill cell culture model to assess pharmaceutical uptake and efflux: evidence for passive and facilitated transport.

    PubMed

    Stott, Lucy C; Schnell, Sabine; Hogstrand, Christer; Owen, Stewart F; Bury, Nic R

    2015-02-01

    The gill is the principle site of xenobiotic transfer to and from the aqueous environment. To replace, refine or reduce (3Rs) the large numbers of fish used in in vivo uptake studies an effective in vitro screen is required that mimics the function of the teleost gill. This study uses a rainbow trout (Oncorhynchus mykiss) primary gill cell culture system grown on permeable inserts, which tolerates apical freshwater thus mimicking the intact organ, to assess the uptake and efflux of pharmaceuticals across the gill. Bidirectional transport studies in media of seven pharmaceuticals (propranolol, metoprolol, atenolol, formoterol, terbutaline, ranitidine and imipramine) showed they were transported transcellularly across the epithelium. However, studies conducted in water showed enhanced uptake of propranolol, ranitidine and imipramine. Concentration-equilibrated conditions without a concentration gradient suggested that a proportion of the uptake of propranolol and imipramine is via a carrier-mediated process. Further study using propranolol showed that its transport is pH-dependent and at very low environmentally relevant concentrations (ng L(-1)), transport deviated from linearity. At higher concentrations, passive uptake dominated. Known inhibitors of drug transport proteins; cimetidine, MK571, cyclosporine A and quinidine inhibited propranolol uptake, whilst amantadine and verapamil were without effect. Together this suggests the involvement of specific members of SLC and ABC drug transporter families in pharmaceutical transport. PMID:25544062

  8. A primary fish gill cell culture model to assess pharmaceutical uptake and efflux: Evidence for passive and facilitated transport

    PubMed Central

    Stott, Lucy C.; Schnell, Sabine; Hogstrand, Christer; Owen, Stewart F.; Bury, Nic R.

    2015-01-01

    The gill is the principle site of xenobiotic transfer to and from the aqueous environment. To replace, refine or reduce (3Rs) the large numbers of fish used in in vivo uptake studies an effective in vitro screen is required that mimics the function of the teleost gill. This study uses a rainbow trout (Oncorhynchus mykiss) primary gill cell culture system grown on permeable inserts, which tolerates apical freshwater thus mimicking the intact organ, to assess the uptake and efflux of pharmaceuticals across the gill. Bidirectional transport studies in media of seven pharmaceuticals (propranolol, metoprolol, atenolol, formoterol, terbutaline, ranitidine and imipramine) showed they were transported transcellularly across the epithelium. However, studies conducted in water showed enhanced uptake of propranolol, ranitidine and imipramine. Concentration-equilibrated conditions without a concentration gradient suggested that a proportion of the uptake of propranolol and imipramine is via a carrier-mediated process. Further study using propranolol showed that its transport is pH-dependent and at very low environmentally relevant concentrations (ng L−1), transport deviated from linearity. At higher concentrations, passive uptake dominated. Known inhibitors of drug transport proteins; cimetidine, MK571, cyclosporine A and quinidine inhibited propranolol uptake, whilst amantadine and verapamil were without effect. Together this suggests the involvement of specific members of SLC and ABC drug transporter families in pharmaceutical transport. PMID:25544062

  9. Unified reaction pathways for the prebiotic formation of RNA and DNA nucleobases.

    PubMed

    Jeilani, Yassin Aweis; Williams, Phoenix N; Walton, Sofia; Nguyen, Minh Tho

    2016-07-27

    The reaction pathways for the prebiotic formation of nucleobases are complex and lead to the formation of a mixture of products. In the past 50 years, there has been a concerted effort for identifying a unified mechanism for the abiotic origin of the biomolecules but with little success. In the present theoretical study, we identified two prominent precursors for the building up of RNA and DNA nucleobases under prebiotic conditions: (a) 1,2-diaminomaleonitrile (DAMN), which is a tetramer of hydrogen cyanide (HCN), and (b) formamide, a hydrolysis product of HCN; it is important to emphasize that HCN is the source of both precursors. We find that free radical pathways are potentially appropriate to account for the origin of nucleobases from HCN. The current study unites the formamide pathways with the DAMN pathways. The mechanisms for the formation of the RNA and DNA nucleobases (uracil, adenine, purine, cytosine) were studied by quantum chemical computations using density functional theory at the B3LYP/6-311G(d,p) level. All the routes involved proceed with relatively low energy barriers (within the error margin of DFT methods). We showed that the radical mechanisms for the formation of nucleobases could be unified through common precursors. The results demonstrated that 4-aminoimidazole-5-carbonitrile (AICN), which is a known precursor for nucleobases, is a product of DAMN. The overall mechanisms are internally consistent with the abiotic formation of the nucleobases, namely (a) under a meteoritic impact scenario on the early Earth's surface that generated high internal energy, and/or (b) in the (gas phase) interstellar regions without the presence of catalysts. PMID:27220279

  10. Seeding the Pregenetic Earth: Meteoritic Abundances of Nucleobases and Potential Reaction Pathways

    NASA Astrophysics Data System (ADS)

    Pearce, Ben K. D.; Pudritz, Ralph E.

    2015-07-01

    Carbonaceous chondrites are a class of meteorite known for having high contents of water and organics. In this study, the abundances of the nucleobases, i.e., the building blocks of RNA and DNA, found in carbonaceous chondrites are collated from a variety of published data and compared across various meteorite classes. An extensive review of abiotic chemical reactions producing nucleobases is then performed. These reactions are then reduced to a list of 15 individual reaction pathways that could potentially occur within meteorite parent bodies. The nucleobases guanine, adenine, and uracil are found in carbonaceous chondrites in amounts of 1–500 ppb. It is currently unknown which reaction is responsible for their synthesis within the meteorite parent bodies. One class of carbonaceous meteorite dominates the abundances of both amino acids and nucleobases—the so-called CM2 (e.g., Murchison meteorite). CR2 meteorites (e.g., Graves Nunataks) also dominate the abundances of amino acids, but are the least abundant in nucleobases. The abundances of total nucleobases in these two classes are 330 ± 250 and 16 ± 13 ppb, respectively. Guanine most often has the greatest abundances in carbonaceous chondrites with respect to the other nucleobases, but is 1–2 orders of magnitude less abundant in CM2 meteorites than glycine (the most abundant amino acid). Our survey of the reaction mechanisms for nucleobase formation suggests that Fischer–Tropsch synthesis (i.e., CO, H2, and NH3 gases reacting in the presence of a catalyst such as alumina or silica) is the most likely candidate for conditions that characterize the early states of planetesimals.

  11. Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases.

    PubMed

    Niether, Doreen; Afanasenkau, Dzmitry; Dhont, Jan K G; Wiegand, Simone

    2016-04-19

    Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007)Proc Natl Acad Sci USA104(22):9346-9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ∼85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45-90 d, starting with an initial formamide weight fraction of[Formula: see text]wt % that is typical for concentrations in shallow lakes on early Earth. PMID:27044100

  12. Nucleobases in Space: Laboratory Studies of Polycyclic Aromatic Nitrogen Heterocycles

    NASA Technical Reports Server (NTRS)

    Elsila, Jamie; Mattioda, Andy; Bernstein, Max; Sandford, Scott; Hudgins, Doug

    2005-01-01

    Polycyclic Aromatic Nitrogen Heterocycles (PANHs) are heterocyclic aromatics Le., PAHs with carbon atoms replaced by a nitrogen atom. These molecules have been detected in meteorite extracts, and in general these nitrogen heterocycles are of astrobiological interest since this class of molecules include nucleobases, basic components of our nucleic acids. These compounds are predicted to be present in the interstellar medium and in Titan tholin, but have received relatively little attention. We will present spectra and reactions of PANHs, frozen in solid H2O at 12 K, conditions germane to astronomical observations. In contrast to simple PAHs, that do not interact strongly with solid H2O, the nitrogen atoms in PANHs are potentially capable of hydrogen bonding with H20 changing their spectra, complicating their remote detection on the surfaces of icy bodies. Moreover, we have studied the photo-chemistry of these interesting compounds under astrophysical conditions and will use our lab studies to assess a potential interstellar heritage of these compounds in carbonaceous chondrites.

  13. Synthesis and characterization of nucleobase-carbon nanotube hybrids.

    PubMed

    Singh, Prabhpreet; Kumar, Jitendra; Toma, Francesca Maria; Raya, Jesus; Prato, Maurizio; Fabre, Bruno; Verma, Sandeep; Bianco, Alberto

    2009-09-23

    We report the synthesis and characterization of adenine-single-walled carbon nanotube (SWCNT) hybrid materials, where for the first time nucleobases are covalently attached to the exosurface of SWCNTs. The structural properties of all hybrids have been characterized using usual spectroscopic and microscopic techniques. The degree of functional groups for functionalized SWCNTs (f-SWCNTs) 2a and 2b is one adenine group for each 26 and 37 carbon atoms, respectively. Solid-state magic angle spinning (13)C NMR spectroscopy (MAS NMR) and electrochemistry have been also applied for the characterization of these f-SWCNTs. AFM images of f-SWCNT 2b showed an interesting feature of horizontally aligned nanotubes along the surface when deposited on highly oriented pyrolytic graphite surface. Furthermore, we evaluated the coordinating ability of these hybrid materials toward silver ions, and interestingly, we found a pattern of silver nanoparticles localized over the surface of the carbon nanotube network. The presence of aligned and randomly oriented CNTs and their ability to coordinate with metal ions make this class of materials very interesting for applications in the development of novel electronic devices and as new supports for different catalytic transformations. PMID:19673527

  14. Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch.

    PubMed

    Trausch, Jeremiah J; Marcano-Velázquez, Joan G; Matyjasik, Michal M; Batey, Robert T

    2015-07-23

    The ZTP riboswitch is a widespread family of regulatory RNAs that upregulate de novo purine synthesis in response to increased intracellular levels of ZTP or ZMP. As an important intermediate in purine biosynthesis, ZMP also serves as a proxy for the concentration of N10-formyl-tetrahydrofolate, a key component of one-carbon metabolism. Here, we report the structure of the ZTP riboswitch bound to ZMP at a resolution of 1.80 Å. The RNA contains two subdomains brought together through a long-range pseudoknot further stabilized through helix-helix packing. ZMP is bound at the subdomain interface of the RNA through a set of interactions with the base, ribose sugar, and phosphate moieties of the ligand. Unique to nucleobase recognition by RNAs, the Z base is inner-sphere coordinated to a magnesium cation bound by two backbone phosphates. This interaction, along with steric hindrance by the backbone, imparts specificity over chemically similar compounds such as ATP/AMP. PMID:26144884

  15. Anharmonic IR Spectra of Biomolecules: Nucleobases and Their Oligomers

    NASA Astrophysics Data System (ADS)

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Carnimeo, Ivan; Fornaro, Teresa

    2014-06-01

    Computational spectroscopy techniques have become in the last years effective means to predict and characterize spectra, such as infrared, for molecular systems of increasing dimensions with account for different environments. We are actively developing a comprehensive and robust computational protocol, set within a perturbative vibrational framework [1], aimed at a quantitative reproduction of the spectra of biomolecules. In order to model the vibrational spectra of weakly bound molecular complexes, dispersion interactions should be taken into proper account. In this work, we present critical assessment of dispersion-corrected DFT approaches for anharmonic vibrational frequency calculations. It is shown that fully anharmonic IR spectra, simulated through full and reduced-dimensionality generalized second-order vibrational perturbation theory (GVPT2)[1] with the potential energy surfaces computed with the B3LYP-D3 approach, may be used to interpret experimental data of nucleobases and their complexes[2] by the direct comparison of experimental IR spectra with their theoretical anharmonic counterpart, taking into account also overtones and combination bands. [1] V. Barone, M. Biczysko, J. Bloino, Phys. Chem. Chem. Phys., 2014,16, 1759-1787 [2] T. Fornaro, M. Biczysko, S. Monti, V. Barone, Phys. Chem. Chem. Phys., 2014, DOI: 10.1039/C3CP54724H

  16. AtSWEET4, a hexose facilitator, mediates sugar transport to axial sinks and affects plant development

    PubMed Central

    Liu, Xiaozhu; Zhang, Yan; Yang, Chao; Tian, Zhihong; Li, Jianxiong

    2016-01-01

    Plants transport photoassimilates from source organs to sink tissues through the phloem translocation pathway. In the transport phloem, sugars that escape from the sieve tubes are released into the apoplasmic space between the sieve element/companion cell complex (SE/CC) and phloem parenchyma cells (PPCs) during the process of long-distance transport. The competition for sugar acquisition between SE/CC and adjoining PPCs is mediated by plasma membrane translocators. YFP-tagged AtSWEET4 protein is localized in the plasma membrane, and PromoterAtSWEET4-GUS analysis showed that AtSWEET4 is expressed in the stele of roots and veins of leaves and flowers. Overexpression of AtSWEET4 in Arabidopsis increases plant size and accumulates more glucose and fructose. By contrast, knock-down of AtSWEET4 by RNA-interference leads to small plant size, reduction in glucose and fructose contents, chlorosis in the leaf vein network, and reduction in chlorophyll content in leaves. Yeast assays demonstrated that AtSWEET4 is able to complement both fructose and glucose transport deficiency. Transgenic plants of AtSWEET4 overexpression exhibit higher freezing tolerance and support more growth of bacterium Pseudomonas syringae pv. phaseolicola NPS3121. We conclude that AtSWEET4 plays an important role in mediating sugar transport in axial tissues during plant growth and development. PMID:27102826

  17. AtSWEET4, a hexose facilitator, mediates sugar transport to axial sinks and affects plant development.

    PubMed

    Liu, Xiaozhu; Zhang, Yan; Yang, Chao; Tian, Zhihong; Li, Jianxiong

    2016-01-01

    Plants transport photoassimilates from source organs to sink tissues through the phloem translocation pathway. In the transport phloem, sugars that escape from the sieve tubes are released into the apoplasmic space between the sieve element/companion cell complex (SE/CC) and phloem parenchyma cells (PPCs) during the process of long-distance transport. The competition for sugar acquisition between SE/CC and adjoining PPCs is mediated by plasma membrane translocators. YFP-tagged AtSWEET4 protein is localized in the plasma membrane, and PromoterAtSWEET4-GUS analysis showed that AtSWEET4 is expressed in the stele of roots and veins of leaves and flowers. Overexpression of AtSWEET4 in Arabidopsis increases plant size and accumulates more glucose and fructose. By contrast, knock-down of AtSWEET4 by RNA-interference leads to small plant size, reduction in glucose and fructose contents, chlorosis in the leaf vein network, and reduction in chlorophyll content in leaves. Yeast assays demonstrated that AtSWEET4 is able to complement both fructose and glucose transport deficiency. Transgenic plants of AtSWEET4 overexpression exhibit higher freezing tolerance and support more growth of bacterium Pseudomonas syringae pv. phaseolicola NPS3121. We conclude that AtSWEET4 plays an important role in mediating sugar transport in axial tissues during plant growth and development. PMID:27102826

  18. Formation of Nucleobases and Other Prebiotic Species from the UV Irradiation of Pyrimidine in Astrophysical Ices

    NASA Astrophysics Data System (ADS)

    Nuevo, M.; Sandford, S. A.; Milam, S. N.; Materese, C. K.; Elsila, J. E.; Dworkin, J. P.

    2011-05-01

    Nucleobases are N-heterocycles which are the informational subunits of DNA and RNA. Biological nucleobases are divided in two types: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites and their extraterrestrial origin has been confirmed by isotope measurements, but no N-heterocycle has ever been observed in the ISM. Experiments showed that the UV irradiation of pyrimidine mixed in astrophysical ices such as H_2O, NH_3, CH_3OH, or any combination of these at low temperature (20-30 K) leads to the formation of multiple photo-products derived from pyrimidine including the nucleobases uracil and cytosine. Theoretical studies on the formation of uracil confirmed its experimental formation pathway and demonstrated that the H_2O matrix plays a key role in the chemistry [9]. Thymine, however, was not found in any of the samples, though other pyrimidine derivatives, as well as other species of prebiotic interest such as urea and the amino acid glycine, could be identified [8]. We will extend this study to the formation of nucleobases and other prebiotic species from the UV irradiation of pyrimidine in astrophysically relevant ice mixtures containing H_2O, NH_3, CH_3OH, CO, and CO_2.

  19. Identification of nucleobases using variable currents through graphene nanopores: A first principles study

    NASA Astrophysics Data System (ADS)

    Haraldsen, J. T.; McFarland, H.; Ahmed, T.; Zhu, J.-X.; Balatsky, A. V.

    2015-03-01

    Nanopore-based technology has the potential to be an efficient method for DNA/RNA base sequencing, as well as an identifier of other biomolecules. However, the thickness of the nanopore substrate is critical for the identification of individual nucleobases due to resulting noise and resolution problems. Recently, graphene has been suggested as a possible nanopore substrate due to its single atomic thickness and robust strength. In this study, we examine a possible device mechanism for the voltage dependence of nucleobases passing through a graphene nanopore. We utilize density functional theory with a generalized gradient approach on a graphene ribbon with a nucleobase in order to calculate the transmission spectra for each base. Transmission spectra for each base allows for the calculation of the ballistic current and differential current as a function of voltage. We show that applying various bias voltages across a graphene ribbon for the general, energy-minimized position of the translocated nucleobase, it is possible to distinguish individual bases using the resulting current. Overall, our goal is to improve nanopore device design by helping to further DNA/RNA nucleobase identification and sequencing.

  20. The Formation of Nucleobases from the Irradiation of Purine in Astophysical Ices and Comparisons with Meteorites.

    NASA Technical Reports Server (NTRS)

    Sandford, S. A.; Materese, C. K.; Nuevo, M.

    2016-01-01

    N-heterocycles have been identified in meteorites and their extraterrestrial origins are suggested by isotopic ratio measurements. Although small N- heterocycles have not been detected in the interstellar medium (ISM), recent experiments in our lab have shown that the irradiation of the aromatic molecules like benzene (C6H6) and naphthalene (C10H8) in mixed molecular ices leads to the formation of O- and N-heterocyclic molecules. Among the class of N-heterocycles are the nucleobases, which are of astrobiological interest because they are the information bearing units of DNA and RNA. Nucleobases have been detected in meteorites [3-5], with isotopic signatures that are also consistent with an extraterrestrial origin. Three of the biologically relevant nucleobases (uracil, cytosine, and guanine) have a pyrimidine core structure while the remaining two (adenine and guanine) possess a purine core. Previous experiments in our lab have demonstrated that all of the bio-logical nucleobases (and numerous other molecules) with a pyrimidine core structure can be produced by irradiating pyrimidine in mixed molecular ices of several compositions [6-8]. In this work, we study the formation of purine-based molecules, including the nucleobases adenine, and guanine, from the ultraviolet (UV) irradiation of purine in ices consisting mixtures of H2O and NH3 at low temperature. The experiments are designed to simulate the astrophysical conditions under which these species may be formed in dense molecular clouds, protoplanetary disks, or on the surfaces of icy bodies in planetary systems.

  1. A single-component multidrug transporter of the major facilitator superfamily is part of a network that protects E scherichia coli from bile salt stress

    PubMed Central

    Paul, Stephanie; Alegre, Kamela O; Holdsworth, Scarlett R; Rice, Matthew; Brown, James A; McVeigh, Paul; Kelly, Sharon M; Law, Christopher J

    2014-01-01

    Resistance to high concentrations of bile salts in the human intestinal tract is vital for the survival of enteric bacteria such as E scherichia coli. Although the tripartite AcrAB–TolC efflux system plays a significant role in this resistance, it is purported that other efflux pumps must also be involved. We provide evidence from a comprehensive suite of experiments performed at two different pH values (7.2 and 6.0) that reflect pH conditions that E . coli may encounter in human gut that MdtM, a single-component multidrug resistance transporter of the major facilitator superfamily, functions in bile salt resistance in E . coli by catalysing secondary active transport of bile salts out of the cell cytoplasm. Furthermore, assays performed on a chromosomal ΔacrB mutant transformed with multicopy plasmid encoding MdtM suggested a functional synergism between the single-component MdtM transporter and the tripartite AcrAB–TolC system that results in a multiplicative effect on resistance. Substrate binding experiments performed on purified MdtM demonstrated that the transporter binds to cholate and deoxycholate with micromolar affinity, and transport assays performed on inverted vesicles confirmed the capacity of MdtM to catalyse electrogenic bile salt/H+ antiport. PMID:24684269

  2. MdMYB1 Regulates Anthocyanin and Malate Accumulation by Directly Facilitating Their Transport into Vacuoles in Apples1[OPEN

    PubMed Central

    Hu, Da-Gang; Sun, Cui-Hui; Ma, Qi-Jun; You, Chun-Xiang; Hao, Yu-Jin

    2016-01-01

    Tonoplast transporters, including proton pumps and secondary transporters, are essential for plant cell function and for quality formation of fleshy fruits and ornamentals. Vacuolar transport of anthocyanins, malate, and other metabolites is directly or indirectly dependent on the H+-pumping activities of vacuolar H+-ATPase (VHA) and/or vacuolar H+-pyrophosphatase, but how these proton pumps are regulated in modulating vacuolar transport is largely unknown. Here, we report a transcription factor, MdMYB1, in apples that binds to the promoters of two genes encoding the B subunits of VHA, MdVHA-B1 and MdVHA-B2, to transcriptionally activate its expression, thereby enhancing VHA activity. A series of transgenic analyses in apples demonstrates that MdMYB1/10 controls cell pH and anthocyanin accumulation partially by regulating MdVHA-B1 and MdVHA-B2. Furthermore, several other direct target genes of MdMYB10 are identified, including MdVHA-E2, MdVHP1, MdMATE-LIKE1, and MdtDT, which are involved in H+-pumping or in the transport of anthocyanins and malates into vacuoles. Finally, we show that the mechanism by which MYB controls malate and anthocyanin accumulation in apples also operates in Arabidopsis (Arabidopsis thaliana). These findings provide novel insights into how MYB transcription factors directly modulate the vacuolar transport system in addition to anthocyanin biosynthesis, consequently controlling organ coloration and cell pH in plants. PMID:26637549

  3. MdMYB1 Regulates Anthocyanin and Malate Accumulation by Directly Facilitating Their Transport into Vacuoles in Apples.

    PubMed

    Hu, Da-Gang; Sun, Cui-Hui; Ma, Qi-Jun; You, Chun-Xiang; Cheng, Lailiang; Hao, Yu-Jin

    2016-03-01

    Tonoplast transporters, including proton pumps and secondary transporters, are essential for plant cell function and for quality formation of fleshy fruits and ornamentals. Vacuolar transport of anthocyanins, malate, and other metabolites is directly or indirectly dependent on the H(+)-pumping activities of vacuolar H(+)-ATPase (VHA) and/or vacuolar H(+)-pyrophosphatase, but how these proton pumps are regulated in modulating vacuolar transport is largely unknown. Here, we report a transcription factor, MdMYB1, in apples that binds to the promoters of two genes encoding the B subunits of VHA, MdVHA-B1 and MdVHA-B2, to transcriptionally activate its expression, thereby enhancing VHA activity. A series of transgenic analyses in apples demonstrates that MdMYB1/10 controls cell pH and anthocyanin accumulation partially by regulating MdVHA-B1 and MdVHA-B2. Furthermore, several other direct target genes of MdMYB10 are identified, including MdVHA-E2, MdVHP1, MdMATE-LIKE1, and MdtDT, which are involved in H(+)-pumping or in the transport of anthocyanins and malates into vacuoles. Finally, we show that the mechanism by which MYB controls malate and anthocyanin accumulation in apples also operates in Arabidopsis (Arabidopsis thaliana). These findings provide novel insights into how MYB transcription factors directly modulate the vacuolar transport system in addition to anthocyanin biosynthesis, consequently controlling organ coloration and cell pH in plants. PMID:26637549

  4. Glucocorticoid-dependent induction of interleukin-6 receptor expression in human hepatocytes facilitates interleukin-6 stimulation of amino acid transport.

    PubMed Central

    Fischer, C P; Bode, B P; Takahashi, K; Tanabe, K K; Souba, W W

    1996-01-01

    OBJECTIVE: The authors studied the effects of interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-alpha) on glutamine and alanine transport in isolated human hepatocytes. They also evaluated the role of dexamethasone in modulating this response and its effects on the expression of the plasma membrane high-affinity IL-6 receptor. SUMMARY BACKGROUND DATA: Animal studies indicate that cytokines are important mediators of the increased hepatic amino acid uptake that occurs during cancer and sepsis, but studies in human tissues are lacking. The control of transport by cytokines and cytokine receptor expression in the liver may provide a mechanism by which hepatocytes can modulate amino acid availability during catabolic disease states. METHODS: Human hepatocytes were isolated from wedge biopsy specimens and plated in 24-well trays. Interleukin-6 and TNF-alpha, in combination with the synthetic glucocorticoid dexamethasone, were added to hepatocytes in culture, and the transport of radiolabeled glutamine and alanine was measured. Fluorescent-activated cell sorter (FACS) analysis was used to study the effects of dexamethasone on IL-6 receptor number in the well-differentiated human hepatoma HepG2. RESULTS: Both IL-6 and TNF-alpha exerted a small stimulatory effect on alanine and glutamine transport. Dexamethasone alone did not alter transport rates, but pretreatment of cells augmented the effects of both cytokines on carrier-mediated amino acid uptake. Dexamethasone pretreatment and a combination of IL-6 and TNF-alpha resulted in a greater than twofold increase in transport activity. Fluorescent-activated cell sorter analysis demonstrated that dexamethasone induced a threefold increase in the expression of high-affinity IL-6 receptors. CONCLUSIONS: Interleukin-6 and TNF-alpha work coordinately with glucocorticoids to stimulate amino acid uptake in human hepatocytes. Dexamethasone exerts a permissive effect on cytokine-mediated increases in transport by increasing IL

  5. Humic acid facilitates the transport of ARS-labeled hydroxyapatite nanoparticles in iron oxyhydroxide-coated sand

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hydroxyapatite nanoparticles (nHAP) have been widely used to remediate soil and wastewater contaminated with metals and radionuclides. However, our understanding of nHAP transport and fate is limited in natural environments that exhibit significant variability in solid and solution chemistry. The tr...

  6. Overexpression of specific proton motive force-dependent transporters facilitate the export of surfactin in Bacillus subtilis.

    PubMed

    Li, Xu; Yang, Huan; Zhang, Donglai; Li, Xue; Yu, Huimin; Shen, Zhongyao

    2015-01-01

    A novel surfactin producer, Bacillus subtilis THY-7, was isolated from soil. Using liposomes and transmembrane transport inhibitors, the surfactin efflux in THY-7 was determined to be mainly dependent on proton motive force (PMF), not ATP hydrolysis. YcxA, KrsE and YerP, three putative lipopeptide transporters with PMF as energy source, were then highlighted in this work. A mutant YcxA named as YcxAmt, with 2 transmembrane helices deletion due to a code-shift mutation of the encoding gene, was identified in THY-7. This truncated YcxAmt was confirmed unable to transfer surfactin; on the contrary, overexpression of the natural full-lengthYcxA enhanced the secretion of surfactin by 89 %. KrsE, a putative kurstakin transporter, was found also capable of transporting surfactin. Overexpression of KrsE increased the production of surfactin by 52 %. In the culture of YerP-overexpressing strain at 24 h, surfactin titer reached 1.58 g L(-1), which was 145 % higher than that of the control. This indicated that YerP acted as the major surfactin exporter in B. subtilis THY-7. PMID:25366377

  7. Reptation-induced coalescence of tunnels and cavities in Escherichia Coli XylE transporter conformers accounts for facilitated diffusion.

    PubMed

    Cunningham, Philip; Naftalin, Richard J

    2014-11-01

    Structural changes and xylose docking to eight conformers of Escherichia Coli XylE, a xylose transporter similar to mammalian passive glucose transporters GLUTs, have been examined. Xylose docks to inward and outward facing conformers at a high affinity central site (K(i) 4-20 µM), previously identified by crystallography and additionally consistently docks to lower affinity sites in the external and internal vestibules (K(i) 12-50 µM). All these sites lie within intramolecular tunnels and cavities. Several local regions in the central transmembrane zone have large positional divergences of both skeleton carbon Cα positions and side chains. One such in TM 10 is the destabilizing sequence G388-P389-V390-C391 with an average RMSD (4.5 ± 0.4 Å). Interchange between conformer poses results in coalescence of tunnels with adjacent cavities, thereby producing a transitory channel spanning the entire transporter. A fully open channel exists in one inward-facing apo-conformer, (PDB 4ja4c) as demonstrated by several different tunnel-finding algorithms. The conformer interchanges produce a gated network within a branched central channel that permits staged ligand diffusion across the transporter during the open gate periods. Simulation of this model demonstrates that small-scale conformational changes required for sequentially opening gate with frequencies in the ns-μs time domain accommodate diffusive ligand flow between adjacent sites with association-dissociation rates in the μs-ms domain without imposing delays. This current model helps to unify the apparently opposing concepts of alternate access and multisite models of ligand transport. PMID:25163893

  8. Nucleobases and Other Prebiotic Species from the UV Irradiation of Pyrimidine in Astrophysical Ices

    NASA Technical Reports Server (NTRS)

    Sandford, Scott; Materese, Christopher; Nuevo, Michel

    2012-01-01

    Nucleobases are aromatic N-heterocycles that constitute the informational subunits of DNA and RNA and are divided into two families: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites and their extraterrestrial origin confirmed by isotope measurement. Although no N-heterocycles have been individually identified in the ISM, the 6.2-micron interstellar emission feature seen towards many astronomical objects suggests a population of such molecules is likely present. We report on a study of the formation of pyrimidine-based molecules, including nucleobases and other species of prebiotic interest, from the ultraviolet (UV) irradiation of pyrimidine in low temperature ices containing H2O, NH3, C3OH, and CH4, to simulate the astrophysical conditions under which prebiotic species may be formed in the Solar System.

  9. An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases.

    PubMed

    Cooper, Valentino R; Thonhauser, T; Langreth, David C

    2008-05-28

    We apply the van der Waals density functional (vdW-DF) to study hydrogen bonding and stacking interactions between nucleobases. The excellent agreement of our results with high level quantum chemical calculations highlights the value of the vdW-DF for first-principles investigations of biologically important molecules. Our results suggest that, in the case of hydrogen-bonded nucleobase pairs, dispersion interactions reduce the cost of propeller twists while having a negligible effect on buckling. Furthermore, the efficient scaling of DFT methods allowed for the easy optimization of separation distance between nucleobase stacks, indicating enhancements in the interaction energy of up to 3 kcalmol over previous fixed distance calculations. We anticipate that these results are significant for extending the vdW-DF method to model larger vdW complexes and biological molecules. PMID:18513005

  10. A graphene field-effect transistor as a molecule-specific probe of DNA nucleobases.

    PubMed

    Dontschuk, Nikolai; Stacey, Alastair; Tadich, Anton; Rietwyk, Kevin J; Schenk, Alex; Edmonds, Mark T; Shimoni, Olga; Pakes, Chris I; Prawer, Steven; Cervenka, Jiri

    2015-01-01

    Fast and reliable DNA sequencing is a long-standing target in biomedical research. Recent advances in graphene-based electrical sensors have demonstrated their unprecedented sensitivity to adsorbed molecules, which holds great promise for label-free DNA sequencing technology. To date, the proposed sequencing approaches rely on the ability of graphene electric devices to probe molecular-specific interactions with a graphene surface. Here we experimentally demonstrate the use of graphene field-effect transistors (GFETs) as probes of the presence of a layer of individual DNA nucleobases adsorbed on the graphene surface. We show that GFETs are able to measure distinct coverage-dependent conductance signatures upon adsorption of the four different DNA nucleobases; a result that can be attributed to the formation of an interface dipole field. Comparison between experimental GFET results and synchrotron-based material analysis allowed prediction of the ultimate device sensitivity, and assessment of the feasibility of single nucleobase sensing with graphene. PMID:25800494

  11. Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA

    NASA Astrophysics Data System (ADS)

    Deck, Christopher; Jauker, Mario; Richert, Clemens

    2011-08-01

    The transition from inanimate materials to the earliest forms of life must have involved multiplication of a catalytically active polymer that is able to replicate. The semiconservative replication that is characteristic of genetic information transfer requires strands that contain more than one type of nucleobase. Short strands of RNA can act as catalysts, but attempts to induce efficient self-copying of mixed sequences (containing four different nucleobases) have been unsuccessful with ribonucleotides. Here we show that inhibition by spent monomers, formed by the hydrolysis of the activated nucleotides, is the cause for incomplete extension of growing daughter strands on RNA templates. Immobilization of strands and periodic displacement of the solution containing the activated monomers overcome this inhibition. Any of the four nucleobases (A/C/G/U) is successfully copied in the absence of enzymes. We conclude therefore that in a prebiotic world, oligoribonucleotides may have formed and undergone self-copying on surfaces.

  12. Understanding Stacking Interactions between an Aromatic Ring and Nucleobases in Aqueous Solution: Experimental and Theoretical Study.

    PubMed

    Kataev, Evgeny A; Shumilova, Tatiana A; Fiedler, Benjamin; Anacker, Tony; Friedrich, Joachim

    2016-08-01

    Stacking interactions between aromatic compounds and nucleobases are crucial in recognition of nucleotides and nucleic acids, but a comprehensive understanding of the strength and selectivity of these interactions in aqueous solution has been elusive. To this end, model complexes have been designed and analyzed by experiment and theory. For the first time, stacking free energies between five nucleobases and anthracene were determined experimentally from thermodynamic double mutant cycles. Three different experimental methods were proposed and evaluated. The dye prefers to bind nucleobases in the order (kcal/mol): G (1.3) > T (0.9) > U (0.8) > C (0.5) > A (0.3). The respective trend of interaction free energies extracted from DFT calculations correlates to that obtained experimentally. Analysis of the data suggests that stacking interactions dominate over hydrophobic effects in an aqueous solution and can be predicted with DFT calculations. PMID:27314892

  13. A graphene field-effect transistor as a molecule-specific probe of DNA nucleobases

    NASA Astrophysics Data System (ADS)

    Dontschuk, Nikolai; Stacey, Alastair; Tadich, Anton; Rietwyk, Kevin J.; Schenk, Alex; Edmonds, Mark T.; Shimoni, Olga; Pakes, Chris I.; Prawer, Steven; Cervenka, Jiri

    2015-03-01

    Fast and reliable DNA sequencing is a long-standing target in biomedical research. Recent advances in graphene-based electrical sensors have demonstrated their unprecedented sensitivity to adsorbed molecules, which holds great promise for label-free DNA sequencing technology. To date, the proposed sequencing approaches rely on the ability of graphene electric devices to probe molecular-specific interactions with a graphene surface. Here we experimentally demonstrate the use of graphene field-effect transistors (GFETs) as probes of the presence of a layer of individual DNA nucleobases adsorbed on the graphene surface. We show that GFETs are able to measure distinct coverage-dependent conductance signatures upon adsorption of the four different DNA nucleobases; a result that can be attributed to the formation of an interface dipole field. Comparison between experimental GFET results and synchrotron-based material analysis allowed prediction of the ultimate device sensitivity, and assessment of the feasibility of single nucleobase sensing with graphene.

  14. Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases

    NASA Astrophysics Data System (ADS)

    Niether, Doreen; Afanasenkau, Dzmitry; Dhont, Jan K. G.

    2016-04-01

    Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007) Proc Natl Acad Sci USA 104(22):9346-9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ˜85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45-90 d, starting with an initial formamide weight fraction of 10-310-3 wt % that is typical for concentrations in shallow lakes on early Earth.

  15. Dissociative electron attachment to the gas-phase nucleobase hypoxanthine

    SciTech Connect

    Dawley, M. Michele; Tanzer, Katrin; Denifl, Stephan E-mail: Sylwia.Ptasinska.1@nd.edu; Carmichael, Ian; Ptasińska, Sylwia E-mail: Sylwia.Ptasinska.1@nd.edu

    2015-06-07

    We present high-resolution measurements of the dissociative electron attachment (DEA) to isolated gas-phase hypoxanthine (C{sub 5}H{sub 4}N{sub 4}O, Hyp), a tRNA purine base. The anion mass spectra and individual ion efficiency curves from Hyp were measured as a function of electron energy below 9 eV. The mass spectra at 1 and 6 eV exhibit the highest anion yields, indicating possible common precursor ions that decay into the detectable anionic fragments. The (Hyp − H) anion (C{sub 5}H{sub 3}N{sub 4}O{sup −}) exhibits a sharp resonant peak at 1 eV, which we tentatively assign to a dipole-bound state of the keto-N1H,N9H tautomer in which dehydrogenation occurs at either the N1 or N9 position based upon our quantum chemical computations (B3LYP/6-311+G(d,p) and U(MP2-aug-cc-pVDZ+)) and prior studies with adenine. This closed-shell dehydrogenated anion is the dominant fragment formed upon electron attachment, as with other nucleobases. Seven other anions were also observed including (Hyp − NH){sup −}, C{sub 4}H{sub 3}N{sub 4}{sup −}/C{sub 4}HN{sub 3}O{sup −}, C{sub 4}H{sub 2}N{sub 3}{sup −}, C{sub 3}NO{sup −}/HC(HCN)CN{sup −}, OCN{sup −}, CN{sup −}, and O{sup −}. Most of these anions exhibit broad but weak resonances between 4 and 8 eV similar to many analogous anions from adenine. The DEA to Hyp involves significant fragmentation, which is relevant to understanding radiation damage of biomolecules.

  16. Synthesis of novel conjugates of a saccharide, amino acids, nucleobase and the evaluation of their cell compatibility.

    PubMed

    Yuan, Dan; Du, Xuewen; Shi, Junfeng; Zhou, Ning; Baoum, Abdulgader Ahmed; Xu, Bing

    2014-01-01

    This article reports the synthesis of a novel type of conjugate of three fundamental biological build blocks (i.e., saccharide, amino acids, and nucleobase) and their cell compatibility. The facile synthesis starts with the synthesis of nucleobase and saccharide derivatives, then uses solid-phase peptide synthesis (SPPS) to build the peptide segment (Phe-Arg-Gly-Asp or naphthAla-Phe-Arg-Gly-Asp with fully protected groups), and later, an amidation reaction in liquid phase connects these three parts together. The overall yield of these multiple step synthesis is about 34%. Besides exhibiting excellent solubility, these conjugates of saccharide-amino acids-nucleobase (SAN), like the previously reported conjugates of nucleobase-amino acids-saccharide (NAS) and nucleobase-saccharide-amino acids (NSA), are mammalian cell compatible. PMID:25383110

  17. BC4707 Is a Major Facilitator Superfamily Multidrug Resistance Transport Protein from Bacillus cereus Implicated in Fluoroquinolone Tolerance

    PubMed Central

    Simm, Roger; Vörös, Aniko; Ekman, Jaakko V.; Sødring, Marianne; Nes, Ingerid; Kroeger, Jasmin K.; Saidijam, Massoud; Bettaney, Kim E.; Henderson, Peter J. F.; Salkinoja-Salonen, Mirja; Kolstø, Anne-Brit

    2012-01-01

    Transcriptional profiling highlighted a subset of genes encoding putative multidrug transporters in the pathogen Bacillus cereus that were up-regulated during stress produced by bile salts. One of these multidrug transporters (BC4707) was selected for investigation. Functional characterization of the BC4707 protein in Escherichia coli revealed a role in the energized efflux of xenobiotics. Phenotypic analyses after inactivation of the gene bc4707 in Bacillus cereus ATCC14579 suggested a more specific, but modest role in the efflux of norfloxacin. In addition to this, transcriptional analyses showed that BC4707 is also expressed during growth of B. cereus under non-stressful conditions where it may have a role in the normal physiology of the bacteria. Altogether, the results indicate that bc4707, which is part of the core genome of the B. cereus group of bacteria, encodes a multidrug resistance efflux protein that is likely involved in maintaining intracellular homeostasis during growth of the bacteria. PMID:22615800

  18. Humic acid facilitates the transport of ARS-labeled hydroxyapatite nanoparticles in iron oxyhydroxide-coated sand.

    PubMed

    Wang, Dengjun; Bradford, Scott A; Harvey, Ronald W; Gao, Bin; Cang, Long; Zhou, Dongmei

    2012-03-01

    Hydroxyapatite nanoparticles (nHAP) have been widely used to remediate soil and wastewater contaminated with metals and radionuclides. However, our understanding of nHAP transport and fate is limited in natural environments that exhibit significant variability in solid and solution chemistry. The transport and retention kinetics of Alizarin red S (ARS)-labeled nHAP were investigated in water-saturated packed columns that encompassed a range of humic acid concentrations (HA, 0-10 mg L(-1)), fractional surface coverage of iron oxyhydroxide coatings on sand grains (λ, 0-0.75), and pH (6.0-10.5). HA was found to have a marked effect on the electrokinetic properties of ARS-nHAP, and on the transport and retention of ARS-nHAP in granular media. The transport of ARS-nHAP was found to increase with increasing HA concentration because of enhanced colloidal stability and the reduced aggregate size. When HA = 10 mg L(-1), greater ARS-nHAP attachment occurred with increasing λ because of increased electrostatic attraction between negatively charged nanoparticles and positively charged iron oxyhydroxides, although alkaline conditions (pH 8.0 and 10.5) reversed the surface charge of the iron oxyhydroxides and therefore decreased deposition. The retention profiles of ARS-nHAP exhibited a hyperexponential shape for all test conditions, suggesting some unfavorable attachment conditions. Retarded breakthrough curves occurred in sands with iron oxyhydroxide coatings because of time-dependent occupation of favorable deposition sites. Consideration of the above effects is necessary to improve remediation efficiency of nHAP for metals and actinides in soils and subsurface environments. PMID:22316080

  19. Identification of a Stelar-Localized Transport Protein That Facilitates Root-to-Shoot Transfer of Chloride in Arabidopsis.

    PubMed

    Li, Bo; Byrt, Caitlin; Qiu, Jiaen; Baumann, Ute; Hrmova, Maria; Evrard, Aurelie; Johnson, Alexander A T; Birnbaum, Kenneth D; Mayo, Gwenda M; Jha, Deepa; Henderson, Sam W; Tester, Mark; Gilliham, Mathew; Roy, Stuart J

    2016-02-01

    Under saline conditions, higher plants restrict the accumulation of chloride ions (Cl(-)) in the shoot by regulating their transfer from the root symplast into the xylem-associated apoplast. To identify molecular mechanisms underpinning this phenomenon, we undertook a transcriptional screen of salt stressed Arabidopsis (Arabidopsis thaliana) roots. Microarrays, quantitative RT-PCR, and promoter-GUS fusions identified a candidate gene involved in Cl(-) xylem loading from the Nitrate transporter 1/Peptide Transporter family (NPF2.4). This gene was highly expressed in the root stele compared to the cortex, and its expression decreased after exposure to NaCl or abscisic acid. NPF2.4 fused to fluorescent proteins, expressed either transiently or stably, was targeted to the plasma membrane. Electrophysiological analysis of NPF2.4 in Xenopus laevis oocytes suggested that NPF2.4 catalyzed passive Cl(-) efflux out of cells and was much less permeable to NO3(-). Shoot Cl(-) accumulation was decreased following NPF2.4 artificial microRNA knockdown, whereas it was increased by overexpression of NPF2.4. Taken together, these results suggest that NPF2.4 is involved in long-distance transport of Cl(-) in plants, playing a role in the loading and the regulation of Cl(-) loading into the xylem of Arabidopsis roots during salinity stress. PMID:26662602

  20. Basic residues R260 and K357 affect the conformational dynamics of the major facilitator superfamily multidrug transporter LmrP.

    PubMed

    Wang, Wei; van Veen, Hendrik W

    2012-01-01

    Secondary-active multidrug transporters can confer resistance on cells to pharmaceuticals by mediating their extrusion away from intracellular targets via substrate/H(+)(Na(+)) antiport. While the interactions of catalytic carboxylates in these transporters with coupling ions and substrates (drugs) have been studied in some detail, the functional importance of basic residues has received much less attention. The only two basic residues R260 and K357 in transmembrane helices in the Major Facilitator Superfamily transporter LmrP from Lactococcus lactis are present on the outer surface of the protein, where they are exposed to the phospholipid head group region of the outer leaflet (R260) and inner leaflet (K357) of the cytoplasmic membrane. Although our observations on the proton-motive force dependence and kinetics of substrate transport, and substrate-dependent proton transport demonstrate that K357A and R260A mutants are affected in ethidium-proton and benzalkonium-proton antiport compared to wildtype LmrP, our findings suggest that R260 and K357 are not directly involved in the binding of substrates or the translocation of protons. Secondary-active multidrug transporters are thought to operate by a mechanism in which binding sites for substrates are alternately exposed to each face of the membrane. Disulfide crosslinking experiments were performed with a double cysteine mutant of LmrP that reports the substrate-stimulated transition from the outward-facing state to the inward-facing state with high substrate-binding affinity. In the experiments, the R260A and K357A mutations were found to influence the dynamics of these major protein conformations in the transport cycle, potentially by removing the interactions of R260 and K357 with phospholipids and/or other residues in LmrP. The R260A and K357A mutations therefore modify the maximum rate at which the transport cycle can operate and, as the transitions between conformational states are differently affected by

  1. Geographically distributed classification of surface water chemical parameters influencing fate and behavior of nanoparticles and colloid facilitated contaminant transport.

    PubMed

    Hammes, Julia; Gallego-Urrea, Julián A; Hassellöv, Martin

    2013-09-15

    The current production and use of nanomaterials in consumer products have increased the concern about the possibility that these enter the rivers during their entire life cycle. Further, many aquatic contaminants undergo partitioning to the ubiquitous aquatic colloids. Here is presented the development of a set of European water types for environmental risk assessment of chemicals transported as nanovectors as is the case of environmental fate of manufactured nanoparticles and colloid-bound contaminants. A compilation of river quality geochemical data with information about multi-element composition for near 800 rivers in Europe was used to perform a principal component analysis (PCA) and define 6 contrasting water classes. With the aid of geographical information system algorithms, it was possible to analyse how the different sampling locations were predominantly represented within each European water framework directive drainage basin. These water classes and their associated Debye-Hückel parameter are determining factors to evaluate the large scale fate and behaviour of nanomaterials and other colloid-transported pollutants in the European aquatic environment. PMID:23863373

  2. Organophosphate Hydrolase Is a Lipoprotein and Interacts with Pi-specific Transport System to Facilitate Growth of Brevundimonas diminuta Using OP Insecticide as Source of Phosphate.

    PubMed

    Parthasarathy, Sunil; Parapatla, Hari; Nandavaram, Aparna; Palmer, Tracy; Siddavattam, Dayananda

    2016-04-01

    Organophosphate hydrolase (OPH), encoded by the organophosphate degradation (opd) island, hydrolyzes the triester bond found in a variety of organophosphate insecticides and nerve agents. OPH is targeted to the inner membrane ofBrevundimonas diminutain a pre-folded conformation by thetwinargininetransport (Tat) pathway. The OPH signal peptide contains an invariant cysteine residue at the junction of the signal peptidase (Spase) cleavage site along with a well conserved lipobox motif. Treatment of cells producing native OPH with the signal peptidase II inhibitor globomycin resulted in accumulation of most of the pre-OPH in the cytoplasm with negligible processed OPH detected in the membrane. Substitution of the conserved lipobox cysteine to serine resulted in release of OPH into the periplasm, confirming that OPH is a lipoprotein. Analysis of purified OPH revealed that it was modified with the fatty acids palmitate and stearate. Membrane-bound OPH was shown to interact with the outer membrane efflux protein TolC and with PstS, the periplasmic component of the ABC transporter complex (PstSACB) involved in phosphate transport. Interaction of OPH with PstS appears to facilitate transport of Pigenerated from organophosphates due to the combined action of OPH and periplasmically located phosphatases. Consistent with this model,opdnull mutants ofB. diminutafailed to grow using the organophosphate insecticide methyl parathion as sole source of phosphate. PMID:26861877

  3. A novel major facilitator transporter TrSTR1 is essential for pentose utilization and involved in xylanase induction in Trichoderma reesei.

    PubMed

    Huang, Zhen-Bang; Chen, Xiu-Zhen; Qin, Li-Na; Wu, Hong-Qing; Su, Xiao-Yun; Dong, Zhi-Yang

    2015-05-01

    Trichoderma reesei (teleomorph Hypocrea jecorina) is an industrially important filamentous fungus for glycoside hydrolases production, with its xylanolytic enzymes widely applied in many areas. However, the molecular mechanisms underlying xylanase expression are still insufficiently understood. In particular, the effect of sugar transporter on the induction of xylanase expression is unclear. In this work, we identified a novel major facilitator transporter TrSTR1 that is capable of transporting xylose by using a xylose utilization system in Saccharomyces cerevisiae. In T. reesei, TrSTR1 is essential for the utilization of d-xylose, l-arabinose, and even their downstream metabolites D-xylitol and L-arabitol. TrSTR1 is also involved in the induction of xylanase expression since both the xylanase activity and extracellular protein concentration in the Tu6△str1 strain were decreased, which further confirmed by a qRT-PCR analysis of the transcript levels of the key transcriptional regulators. Our observations provide new insights into connections between pentose utilization and xylanase production in T. reesei. PMID:25817789

  4. Macroscopic and microscopic observations of particle-facilitated mercury transport from New Idria and Sulphur Bank mercury mine tailings

    USGS Publications Warehouse

    Lowry, G.V.; Shaw, S.; Kim, C.S.; Rytuba, J.J.; Brown, Gordon E., Jr.

    2004-01-01

    Mercury (Hg) release from inoperative Hg mines in the California Coast Range has been documented, but little is known about the release and transport mechanisms. In this study, tailings from Hg mines located in different geologic settings-New Idria (NI), a Si-carbonate Hg deposit, and Sulphur Bank (SB), a hot-spring Hg deposit-were characterized, and particle release from these wastes was studied in column experiments to (1) investigate the mechanisms of Hg release from NI and SB mine wastes, (2) determine the speciation of particle-bound Hg released from the mine wastes, and (3) determine the effect of calcinations on Hg release processes. The physical and chemical properties of tailings and the colloids released from them were determined using chemical analyses, selective chemical extractions, XRD, SEM, TEM, and X-ray absorption spectroscopy techniques. The total Hg concentration in tailings increased with decreasing particle size in NI and SB calcines (roasted ore), but reached a maximum at an intermediate particle size in the SB waste rock (unroasted ore). Hg in the tailings exists predominantly as low-solubility HgS (cinnabar and metacinnabar), with NI calcines having >50% HgS, SB calcines having >89% HgS, and SB waste rock having ???100% HgS. Leaching experiments with a high-ionic-strength solution (0.1 M NaCl) resulted in a rapid but brief release of soluble and particulate Hg. Lowering the ionic strength of the leach solution (0.005 M NaCl) resulted in the release of colloidal Hg from two of the three mine wastes studied (NI calcines and SB waste rock). Colloid-associated Hg accounts for as much as 95% of the Hg released during episodic particle release. Colloids generated from the NI calcines are produced by a breakup and release mechanism and consist of hematite, jarosite/alunite, and Al-Si gel with particle sizes of 10-200 nm. ATEM and XAFS analyses indicate that the majority (???78%) of the mercury is present in the form of HgS. SB calcines also

  5. Monitoring of event based mobilization of hydrophobic pollutants in rivers: Calibration of turbidity as a proxy for particle facilitated transport

    NASA Astrophysics Data System (ADS)

    Rügner, Hermann; Schwientek, Marc; Grathwohl, Peter

    2014-05-01

    Transport of many pollutants in rivers is coupled to transport of suspended particles which is typically enhanced during events such as floods, snow melts etc. As the amount of total suspended solids (TSS) in rivers can be monitored by turbidity measurements this may be used as a proxy for the total concentration of particle associated pollutants in rivers such as polycyclic aromatic hydrocarbons (PAHs), PCBs, etc. and several heavy metals. On-line turbidity measurements (e.g. by optical backscattering sensors) then allow for an assessment of particle and pollutant flux dynamics. In this study, pronounced flood and thus turbidity events were sampled at high temporal resolution in three contrasting catchments in Southwest Germany (Rivers Ammer, Goldersbach, Steinlach) as well as in the River Neckar. Samples were analyzed for turbidity, the total amount of PAH and total suspended solids (TSS) in water. Additionally, the grain size distributions of suspended solids were determined. Discharge and turbidity were measured on-line at gauging stations in three of the catchments. Results showed that turbidity and TSS were linearly correlated over an extended turbidity range up to 2000 NTU for the flood samples (i.e. independent on grain size). This also holds for total PAH concentrations which can be reasonably well predicted based on the turbidity measurements and TSS versus PAH relationships - even for very high turbidity or TSS values (> 2000 NTU or mg l-1, respectively). From these linear regressions concentrations of PAHs on suspended particles were obtained which varied by catchment. The values comprise a robust measure of the average sediment quality in a river network and may be correlated to the degree of urbanization represented by the number of inhabitants per total flux of suspended particles. Based on long-term on-line turbidity measurements mass flow rates of particle bound pollutants over time could be calculated. Results showed that by far the largest amount

  6. Synthesis of carbocyclic nucleoside analogs with five-membered heterocyclic nucleobases

    PubMed Central

    Cho, Jong hyun; Coats, Steven J.; Schinazi, Raymond F.

    2015-01-01

    New carbocyclic nucleoside analogs with five-membered heterocyclic nucleobases were synthesized and evaluated as potential anti-HIV and anti-HCV agents. Among the synthesized carbocyclic nucleoside analogs, the pyrazole amide 15f exhibited modest selective anti-HIV-1 activity (EC50 = 24 µM). PMID:26028788

  7. The Photochemistry of Pyrimidine in Realistic Astrophysical Ices and the Production of Nucleobases

    NASA Astrophysics Data System (ADS)

    Nuevo, Michel; Materese, Christopher K.; Sandford, Scott A.

    2014-10-01

    Nucleobases, together with deoxyribose/ribose and phosphoric acid, are the building blocks of DNA and RNA for all known life. The presence of nucleobase-like compounds in carbonaceous chondrites delivered to the Earth raises the question of an extraterrestrial origin for the molecules that triggered life on our planet. Whether these molecules are formed in interstellar/protostellar environments, in small parent bodies in the solar system, or both, is currently unclear. Recent experiments show that the UV irradiation of pyrimidine (C4H4N2) in H2O-rich ice mixtures that contain NH3, CH3OH, or CH4 leads to the formation of the pyrimidine-based nucleobases uracil, cytosine, and thymine. In this work, we discuss the low-temperature UV irradiation of pyrimidine in realistic astrophysical ice mixtures containing H2O, CH3OH, and NH3, with or without CH4, to search for the production of nucleobases and other prebiotic compounds. These experiments show the presence of uracil, urea, glycerol, hexamethylenetetramine, small amino acids, and small carboxylic acids in all samples. Cytosine was only found in one sample produced from ices irradiated with a higher UV dose, while thymine was not found in any sample, even after irradiation with a higher UV dose. Results are discussed to evaluate the role of the photochemistry of pyrimidine in the inventory of organic molecules detected in meteorites and their astrophysical/astrobiological implications.

  8. 6-Pyrazolylpurine as an Artificial Nucleobase for Metal-Mediated Base Pairing in DNA Duplexes

    PubMed Central

    Léon, J. Christian; Sinha, Indranil; Müller, Jens

    2016-01-01

    The artificial nucleobase 6-pyrazol-1-yl-purine (6PP) has been investigated with respect to its usability in metal-mediated base pairing. As was shown by temperature-dependent UV spectroscopy, 6PP may form weakly stabilizing 6PP–Ag(I)–6PP homo base pairs. Interestingly, 6PP can be used to selectively recognize a complementary pyrimidine nucleobase. The addition of Ag(I) to a DNA duplex comprising a central 6PP:C mispair (C = cytosine) leads to a slight destabilization of the duplex. In contrast, a stabilizing 6PP–Ag(I)–T base pair is formed with a complementary thymine (T) residue. It is interesting to note that 6PP is capable of differentiating between the pyrimidine moieties despite the fact that it is not as sterically crowded as 6-(3,5-dimethylpyrazol-1-yl)purine, an artificial nucleobase that had previously been suggested for the recognition of nucleic acid sequences via the formation of a metal-mediated base pair. Hence, the additional methyl groups of 6-(3,5-dimethylpyrazol-1-yl)purine may not be required for the specific recognition of the complementary nucleobase. PMID:27089326

  9. Enhanced vascular permeability facilitates entry of plasma HDL and promotes macrophage-reverse cholesterol transport from skin in mice.

    PubMed

    Kareinen, Ilona; Cedó, Lídia; Silvennoinen, Reija; Laurila, Pirkka-Pekka; Jauhiainen, Matti; Julve, Josep; Blanco-Vaca, Francisco; Escola-Gil, Joan Carles; Kovanen, Petri T; Lee-Rueckert, Miriam

    2015-02-01

    Reverse cholesterol transport (RCT) pathway from macrophage foam cells initiates when HDL particles cross the endothelium, enter the interstitial fluid, and induce cholesterol efflux from these cells. We injected [(3)H]cholesterol-loaded J774 macrophages into the dorsal skin of mice and measured the transfer of macrophage-derived [(3)H]cholesterol to feces [macrophage-RCT (m-RCT)]. Injection of histamine to the macrophage injection site increased locally vascular permeability, enhanced influx of intravenously administered HDL, and stimulated m-RCT from the histamine-treated site. The stimulatory effect of histamine on m-RCT was abolished by prior administration of histamine H1 receptor (H1R) antagonist pyrilamine, indicating that the histamine effect was H1R-dependent. Subcutaneous administration of two other vasoactive mediators, serotonin or bradykinin, and activation of skin mast cells to secrete histamine and other vasoactive compounds also stimulated m-RCT. None of the studied vasoactive mediators affected serum HDL levels or the cholesterol-releasing ability of J774 macrophages in culture, indicating that acceleration of m-RCT was solely due to increased availability of cholesterol acceptors in skin. We conclude that disruption of the endothelial barrier by vasoactive compounds enhances the passage of HDL into interstitial fluid and increases the rate of RCT from peripheral macrophage foam cells, which reveals a novel tissue cholesterol-regulating function of these compounds. PMID:25473102

  10. Zinc transporter SLC39A10/ZIP10 facilitates antiapoptotic signaling during early B-cell development

    PubMed Central

    Miyai, Tomohiro; Hojyo, Shintaro; Ikawa, Tomokatsu; Kawamura, Masami; Irié, Tarou; Ogura, Hideki; Hijikata, Atsushi; Bin, Bum-Ho; Yasuda, Takuwa; Kitamura, Hiroshi; Nakayama, Manabu; Ohara, Osamu; Yoshida, Hisahiro; Koseki, Haruhiko; Mishima, Kenji; Fukada, Toshiyuki

    2014-01-01

    The immune system is influenced by the vital zinc (Zn) status, and Zn deficiency triggers lymphopenia; however, the mechanisms underlying Zn-mediated lymphocyte maintenance remain elusive. Here we investigated ZIP10, a Zn transporter expressed in the early B-cell developmental process. Genetic ablation of Zip10 in early B-cell stages resulted in significant reductions in B-cell populations, and the inducible deletion of Zip10 in pro-B cells increased the caspase activity in parallel with a decrease in intracellular Zn levels. Similarly, the depletion of intracellular Zn by a chemical chelator resulted in spontaneous caspase activation leading to cell death. Collectively, these findings indicated that ZIP10-mediated Zn homeostasis is essential for early B-cell survival. Moreover, we found that ZIP10 expression was regulated by JAK-STAT pathways, and its expression was correlated with STAT activation in human B-cell lymphoma, indicating that the JAK-STAT-ZIP10-Zn signaling axis influences the B-cell homeostasis. Our results establish a role of ZIP10 in cell survival during early B-cell development, and underscore the importance of Zn homeostasis in immune system maintenance. PMID:25074913

  11. A Salt Bridge Linking the First Intracellular Loop with the C Terminus Facilitates the Folding of the Serotonin Transporter*

    PubMed Central

    Koban, Florian; El-Kasaby, Ali; Häusler, Cornelia; Stockner, Thomas; Simbrunner, Benedikt M.; Sitte, Harald H.; Freissmuth, Michael; Sucic, Sonja

    2015-01-01

    The folding trajectory of solute carrier 6 (SLC6) family members is of interest because point mutations result in misfolding and thus cause clinically relevant phenotypes in people. Here we examined the contribution of the C terminus in supporting folding of the serotonin transporter (SERT; SLC6A4). Our working hypothesis posited that the amphipathic nature of the C-terminal α-helix (Thr603–Thr613) was important for folding of SERT. Accordingly, we disrupted the hydrophobic moment of the α-helix by replacing Phe604, Ile608, or Ile612 by Gln. The bulk of the resulting mutants SERT-F604Q, SERT-I608Q, and SERT-I612Q were retained in the endoplasmic reticulum, but their residual delivery to the cell surface still depended on SEC24C. This indicates that the amphipathic nature of the C-terminal α-helix was dispensable to endoplasmic reticulum export. The folding trajectory of SERT is thought to proceed through the inward facing conformation. Consistent with this conjecture, cell surface expression of the misfolded mutants was restored by (i) introducing second site suppressor mutations, which trap SERT in the inward facing state, or (ii) by the pharmacochaperone noribogaine, which binds to the inward facing conformation. Finally, mutation of Glu615 at the end of the C-terminal α-helix to Lys reduced surface expression of SERT-E615K. A charge reversal mutation in intracellular loop 1 restored surface expression of SERT-R152E/E615K to wild type levels. These observations support a mechanistic model where the C-terminal amphipathic helix is stabilized by an intramolecular salt bridge between residues Glu615 and Arg152. This interaction acts as a pivot in the conformational search associated with folding of SERT. PMID:25869136

  12. Photochemistry of Pyrimidine in Astrophysical Ices: Formation of Nucleobases and Other Prebiotic Species

    NASA Technical Reports Server (NTRS)

    Nuevo, Michel; Sandford, Scott A.; Materese, Christopher K.; Milam, Stefanie N.

    2012-01-01

    Nucleobases are N-heterocycles that are the informational subunits of DNA and RNA. They are divided into two molecular groups: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites, and their extraterrestrial origin confirmed by isotopic measurements. Although no N-heterocycles have ever been observed in the ISM, the positions of the 6.2- m interstellar emission features suggest a population of such molecules is likely to be present. However, laboratory experiments have shown that the ultraviolet (UV) irradiation of pyrimidine in ices of astrophysical relevance such as H2O, NH3, CH3OH, CH4, CO, or combinations of these at low temperature (less than or equal to 20 K) leads to the formation of several pyrimidine derivatives including the nucleobases uracil and cytosine, as well as precursors such as 4(3H)-pyrimidone and 4-aminopyrimidine. Quantum calculations on the formation of 4(3H)-pyrimidone and uracil from the irradiation of pyrimidine in pure H2O ices are in agreement with their experimental formation pathways.10 In those residues, other species of prebiotic interest such as urea as well as the amino acids glycine and alanine could also be identified. However, only very small amounts of pyrimidine derivatives containing CH3 groups could be detected, suggesting that the addition of methyl groups to pyrimidine is not an efficient process. For this reason, the nucleobase thymine was not observed in any of the samples. In this work, we study the formation of nucleobases and other photo-products of prebiotic interest from the UV irradiation of pyrimidine in ices containing H2O, NH3, CH3OH, and CO, mixed in astrophysical proportions.

  13. Colloid facilitated transport of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) to the groundwater at Ma Da area, Vietnam.

    PubMed

    Hofmann, Thilo; Wendelborn, Anke

    2007-06-01

    PCDD/Fs are hydrophobic organic substances and strongly sorbing to soil particles. Once adsorbed to soil particles they are believed to be virtually immobile. However, research in the last decades confirmed that strong sorbing contaminants may reach the groundwater via colloid-facilitated transport. This pathway has not been investigated before in Vietnam. Ma Da area, 100 km north of Ho Chi Minh City, was repeatedly sprayed during the Vietnam War (1962-1971) with herbicides like Agent Orange containing, beside others, the teratogenic contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). 11 surface soil samples and 12 water samples were collected in Ma Da area for analysis of PCDD/Fs in solids. Soil TCDD concentrations ranged from 1-41 ppt with a mean of 8.8 ppt and a mean I-TEQ of 9.7 ppt. Two surface water samples showed colloid bound TCDD (7 and 19 ppt). Groundwater samples showed elevated colloid bound PCDD concentrations (mean 770 ng/kg), mainly octachlorodibenzo-p-dioxin. Groundwater colloids separated by filtration did not show any TCDD. The results support that TCDD/Fs can be relocated from the top soil to the groundwater by colloidal pathway. They did not provide evidence that the dioxins bound to groundwater colloids are leftovers from the Second Indochinese War. However, this study reinforces that the colloidal transport pathway has to be included investigating the relocation of strong sorbing organic contaminants. PMID:17668815

  14. The role of facilitated diffusion in oxygen transport by cell-free hemoglobins: implications for the design of hemoglobin-based oxygen carriers.

    PubMed

    McCarthy, M R; Vandegriff, K D; Winslow, R M

    2001-08-30

    We compared rates of oxygen transport in an in vitro capillary system using red blood cells (RBCs) and cell-free hemoglobins. The axial PO(2) drop down the capillary was calculated using finite-element analysis. RBCs, unmodified hemoglobin (HbA(0)), cross-linked hemoglobin (alpha alpha-Hb) and hemoglobin conjugated to polyethylene-glycol (PEG-Hb) were evaluated. According to their fractional saturation curves, PEG-Hb showed the least desaturation down the capillary, which most closely matched the RBCs; HbA(0) and alpha alpha-Hb showed much greater desaturation. A lumped diffusion parameter, K*, was calculated based on the Fick diffusion equation with a term for facilitated diffusion. The overall rates of oxygen transfer are consistent with hemoglobin diffusion rates according to the Stokes-Einstein Law and with previously measured blood pressure responses in rats. This study provides a conceptual framework for the design of a 'blood substitute' based on mimicking O(2) transport by RBCs to prevent autoregulatory changes in blood flow and pressure. PMID:11527583

  15. ANK, a Host Cytoplasmic Receptor for the Tobacco mosaic virus Cell-to-Cell Movement Protein, Facilitates Intercellular Transport through Plasmodesmata

    PubMed Central

    Ueki, Shoko; Spektor, Roman; Natale, Danielle M.; Citovsky, Vitaly

    2010-01-01

    Plasmodesma (PD) is a channel structure that spans the cell wall and provides symplastic connection between adjacent cells. Various macromolecules are known to be transported through PD in a highly regulated manner, and plant viruses utilize their movement proteins (MPs) to gate the PD to spread cell-to-cell. The mechanism by which MP modifies PD to enable intercelluar traffic remains obscure, due to the lack of knowledge about the host factors that mediate the process. Here, we describe the functional interaction between Tobacco mosaic virus (TMV) MP and a plant factor, an ankyrin repeat containing protein (ANK), during the viral cell-to-cell movement. We utilized a reverse genetics approach to gain insight into the possible involvement of ANK in viral movement. To this end, ANK overexpressor and suppressor lines were generated, and the movement of MP was tested. MP movement was facilitated in the ANK-overexpressing plants, and reduced in the ANK-suppressing plants, demonstrating that ANK is a host factor that facilitates MP cell-to-cell movement. Also, the TMV local infection was largely delayed in the ANK-suppressing lines, while enhanced in the ANK-overexpressing lines, showing that ANK is crucially involved in the infection process. Importantly, MP interacted with ANK at PD. Finally, simultaneous expression of MP and ANK markedly decreased the PD levels of callose, β-1,3-glucan, which is known to act as a molecular sphincter for PD. Thus, the MP-ANK interaction results in the downregulation of callose and increased cell-to-cell movement of the viral protein. These findings suggest that ANK represents a host cellular receptor exploited by MP to aid viral movement by gating PD through relaxation of their callose sphincters. PMID:21124937

  16. Rhizobial homologs of the fatty acid transporter FadL facilitate perception of long-chain acyl-homoserine lactone signals

    PubMed Central

    Krol, Elizaveta; Becker, Anke

    2014-01-01

    Quorum sensing (QS) using N-acyl homoserine lactones (AHLs) as signal molecules is a common strategy used by diverse Gram-negative bacteria. A widespread mechanism of AHL sensing involves binding of these molecules by cytosolic LuxR-type transcriptional regulators, which requires uptake of external AHLs. The outer membrane is supposed to be an efficient barrier for diffusion of long-chain AHLs. Here we report evidence that in Sinorhizobium meliloti, sensing of AHLs with acyl chains composed of 14 or more carbons is facilitated by the outer membrane protein FadLSm, a homolog of the Escherichia coli FadLEc long-chain fatty acid transporter. The effect of fadLSm on AHL sensing was more prominent for longer and more hydrophobic signal molecules. Using reporter gene fusions to QS target genes, we found that fadLSm increased AHL sensitivity and accelerated the course of QS. In contrast to FadLEc, FadLSm did not support uptake of oleic acid, but did contribute to growth on palmitoleic acid. FadLSm homologs from related symbiotic α-rhizobia and the plant pathogen Agrobacterium tumefaciens differed in their ability to facilitate long-chain AHL sensing or to support growth on oleic acid. FadLAt was found to be ineffective toward long-chain AHLs. We obtained evidence that the predicted extracellular loop 5 of FadLSm and further α-rhizobial FadL proteins contains determinants of specificity to long-chain AHLs. Replacement of a part of loop 5 by the corresponding region from α-rhizobial FadL proteins transferred sensitivity for long-chain AHLs to FadLAt. PMID:25002473

  17. Formation of Nucleobases from the UV Irradiation of Pyrimidine in Interstellar Ice Analogs

    NASA Technical Reports Server (NTRS)

    Milam, Stefanie N.; Nuevo, Michel; Sandford, Scott A.; Elsila, Jamie E.; Dworkin, Jason P.

    2010-01-01

    Previous laboratory simulations showed that complex molecules, including prebiotic compounds/can be formed under interstellar conditions from the vacuum UV irradiation of interstellar ice analogs containing H2O, CO, NH3 etc. Although some complex prebiotic species have not been confirmed In the interstellar medium, they are known to be present in meteorites. Nucleobases, the building blocks of DNA and RNA, have also been detected in meteorites. Here, we present a study of the formation of pyrimidine-based compounds from the UV irradiation of pyrimidine in H2O- and/or NH3-ices at 20-30 K, Our results show that various derivatives, induding the nucleobases uracil and cytosine, are formed under these conditions.

  18. First-Principles Photoemission Spectroscopy of DNA and RNA Nucleobases from Koopmans-Compliant Functionals.

    PubMed

    Nguyen, Ngoc Linh; Borghi, Giovanni; Ferretti, Andrea; Marzari, Nicola

    2016-08-01

    The need to interpret ultraviolet photoemission data strongly motivates the refinement of first-principles techniques that are able to accurately predict spectral properties. In this work, we employ Koopmans-compliant functionals, constructed to enforce piecewise linearity in approximate density functionals, to calculate the structural and electronic properties of DNA and RNA nucleobases. Our results show that not only ionization potentials and electron affinities are accurately predicted with mean absolute errors of <0.1 eV, but also that calculated photoemission spectra are in excellent agreement with experimental ultraviolet photoemission spectra. In particular, the role and contribution of different tautomers to the photoemission spectra are highlighted and discussed in detail. The structural properties of nucleobases are also investigated, showing an improved description with respect to local and semilocal density-functional theory. Methodologically, our results further consolidate the role of Koopmans-compliant functionals in providing, through orbital-density-dependent potentials, accurate electronic and spectral properties. PMID:27267665

  19. Binding of nucleobases with graphene and carbon nanotube: a review of computational studies.

    PubMed

    Chehel Amirani, Morteza; Tang, Tian

    2015-01-01

    Functionalized carbon nanotubes (CNTs) constitute a new class of nanostructured materials that have vast applications in CNT purification and separation, biosensing, drug delivery, etc. Hybrids formed from the functionalization of CNT with biological molecules have shown interesting properties and have attracted great attention in recent years. Of particular interest is the hybridization of single- or double-stranded nucleic acid (NA) with CNT. Nucleobases, as the building blocks of NA, interact with CNT and contribute strongly to the stability of the NA-CNT hybrids and their properties. In this work, we present a thorough review of previous studies on the binding of nucleobases with graphene and CNT, with a focus on the simulation works that attempted to evaluate the structure and strength of binding. Discrepancies among these works are identified, and factors that might contribute to such discrepancies are discussed. PMID:25118044

  20. Cytoplasmic Fragment of Alcadein α Generated by Regulated Intramembrane Proteolysis Enhances Amyloid β-Protein Precursor (APP) Transport into the Late Secretory Pathway and Facilitates APP Cleavage*

    PubMed Central

    Takei, Norio; Sobu, Yuriko; Kimura, Ayano; Urano, Satomi; Piao, Yi; Araki, Yoichi; Taru, Hidenori; Yamamoto, Tohru; Hata, Saori; Nakaya, Tadashi; Suzuki, Toshiharu

    2015-01-01

    The neural type I membrane protein Alcadein α (Alcα), is primarily cleaved by amyloid β-protein precursor (APP) α-secretase to generate a membrane-associated carboxyl-terminal fragment (Alcα CTF), which is further cleaved by γ-secretase to secrete p3-Alcα peptides and generate an intracellular cytoplasmic domain fragment (Alcα ICD) in the late secretory pathway. By association with the neural adaptor protein X11L (X11-like), Alcα and APP form a ternary complex that suppresses the cleavage of both Alcα and APP by regulating the transport of these membrane proteins into the late secretory pathway where secretases are active. However, it has not been revealed how Alcα and APP are directed from the ternary complex formed largely in the Golgi into the late secretory pathway to reach a nerve terminus. Using a novel transgenic mouse line expressing excess amounts of human Alcα CTF (hAlcα CTF) in neurons, we found that expression of hAlcα CTF induced excess production of hAlcα ICD, which facilitated APP transport into the nerve terminus and enhanced APP metabolism, including Aβ generation. In vitro cell studies also demonstrated that excess expression of Alcα ICD released both APP and Alcα from the ternary complex. These results indicate that regulated intramembrane proteolysis of Alcα by γ-secretase regulates APP trafficking and the production of Aβ in vivo. PMID:25406318

  1. Cytoplasmic fragment of Alcadein α generated by regulated intramembrane proteolysis enhances amyloid β-protein precursor (APP) transport into the late secretory pathway and facilitates APP cleavage.

    PubMed

    Takei, Norio; Sobu, Yuriko; Kimura, Ayano; Urano, Satomi; Piao, Yi; Araki, Yoichi; Taru, Hidenori; Yamamoto, Tohru; Hata, Saori; Nakaya, Tadashi; Suzuki, Toshiharu

    2015-01-01

    The neural type I membrane protein Alcadein α (Alcα), is primarily cleaved by amyloid β-protein precursor (APP) α-secretase to generate a membrane-associated carboxyl-terminal fragment (Alcα CTF), which is further cleaved by γ-secretase to secrete p3-Alcα peptides and generate an intracellular cytoplasmic domain fragment (Alcα ICD) in the late secretory pathway. By association with the neural adaptor protein X11L (X11-like), Alcα and APP form a ternary complex that suppresses the cleavage of both Alcα and APP by regulating the transport of these membrane proteins into the late secretory pathway where secretases are active. However, it has not been revealed how Alcα and APP are directed from the ternary complex formed largely in the Golgi into the late secretory pathway to reach a nerve terminus. Using a novel transgenic mouse line expressing excess amounts of human Alcα CTF (hAlcα CTF) in neurons, we found that expression of hAlcα CTF induced excess production of hAlcα ICD, which facilitated APP transport into the nerve terminus and enhanced APP metabolism, including Aβ generation. In vitro cell studies also demonstrated that excess expression of Alcα ICD released both APP and Alcα from the ternary complex. These results indicate that regulated intramembrane proteolysis of Alcα by γ-secretase regulates APP trafficking and the production of Aβ in vivo. PMID:25406318

  2. The photochemistry of pyrimidine in realistic astrophysical ices and the production of nucleobases

    SciTech Connect

    Nuevo, Michel; Materese, Christopher K.; Sandford, Scott A.

    2014-10-01

    Nucleobases, together with deoxyribose/ribose and phosphoric acid, are the building blocks of DNA and RNA for all known life. The presence of nucleobase-like compounds in carbonaceous chondrites delivered to the Earth raises the question of an extraterrestrial origin for the molecules that triggered life on our planet. Whether these molecules are formed in interstellar/protostellar environments, in small parent bodies in the solar system, or both, is currently unclear. Recent experiments show that the UV irradiation of pyrimidine (C{sub 4}H{sub 4}N{sub 2}) in H{sub 2}O-rich ice mixtures that contain NH{sub 3}, CH{sub 3}OH, or CH{sub 4} leads to the formation of the pyrimidine-based nucleobases uracil, cytosine, and thymine. In this work, we discuss the low-temperature UV irradiation of pyrimidine in realistic astrophysical ice mixtures containing H{sub 2}O, CH{sub 3}OH, and NH{sub 3}, with or without CH{sub 4}, to search for the production of nucleobases and other prebiotic compounds. These experiments show the presence of uracil, urea, glycerol, hexamethylenetetramine, small amino acids, and small carboxylic acids in all samples. Cytosine was only found in one sample produced from ices irradiated with a higher UV dose, while thymine was not found in any sample, even after irradiation with a higher UV dose. Results are discussed to evaluate the role of the photochemistry of pyrimidine in the inventory of organic molecules detected in meteorites and their astrophysical/astrobiological implications.

  3. Crystal Structures of Non-Natural Nucleobase Pairs in A- and B-DNA†

    PubMed Central

    Georgiadis, Millie M.; Singh, Isha; Kellett, Whitney F.; Hoshika, Shuichi; Benner, Steven A.; Richards, Nigel G. J.

    2015-01-01

    The extent to which synthetic biology can be used to expand genetic information systems compatible with natural enzymes and cells will depend on the extent to which multiple and contiguous non-natural nucleobase pairs fit within the standard double helical conformations of DNA. Toward this goal, two non-standard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) were designed to form a Z:P pair with a standard “edge on” Watson-Crick geometry, but with rearranged hydrogen bond donor and acceptor groups. Here, we present the crystal structures of two self-complementary 16-mer oligonucleotides containing Z:P pairs. The first contained two consecutive Z:P nucleobase pairs and was found to crystallize within a host-guest complex in B-form. The second contained six consecutive Z:P pairs; it was found to crystallize as an A-form DNA duplex, although it can adopt B-form in solution as inferred from circular dichroism spectra. Although Z:P pairs have some structural properties that are similar to those of G:C pairs, unique features include stacking of the nitro group on Z with the adjacent heterocyclic nucleobase ring in A-DNA. In both B-and A-DNA, major groove widths associated with the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs potentially due to the presence of the nitro group in Z. Thus, our structural studies suggest that multiple and consecutive Z:P pairs are readily accommodated in DNA duplex structures recognized by natural polymerases, and therefore the GACTZP synthetic genetic system has the requisite properties to expand sequence space. PMID:25961938

  4. Molecularly resolved label-free sensing of single nucleobase mismatches by interfacial LNA probes

    PubMed Central

    Mishra, Sourav; Lahiri, Hiya; Banerjee, Siddhartha; Mukhopadhyay, Rupa

    2016-01-01

    So far, there has been no report on molecularly resolved discrimination of single nucleobase mismatches using surface-confined single stranded locked nucleic acid (ssLNA) probes. Herein, it is exemplified using a label-independent force-sensing approach that an optimal coverage of 12-mer ssLNA sensor probes formed onto gold(111) surface allows recognition of ssDNA targets with twice stronger force sensitivity than 12-mer ssDNA sensor probes. The force distributions are reproducible and the molecule-by-molecule force measurements are largely in agreement with ensemble on-surface melting temperature data. Importantly, the molecularly resolved detection is responsive to the presence of single nucleobase mismatches in target sequences. Since the labelling steps can be eliminated from protocol, and each force-based detection event occurs within milliseconds' time scale, the force-sensing assay is potentially capable of rapid detection. The LNA probe performance is indicative of versatility in terms of substrate choice - be it gold (for basic research and array-based applications) or silicon (for ‘lab-on-a-chip’ type devices). The nucleic acid microarray technologies could therefore be generally benefited by adopting the LNA films, in place of DNA. Since LNA is nuclease-resistant, unlike DNA, and the LNA-based assay is sensitive to single nucleobase mismatches, the possibilities for label-free in vitro rapid diagnostics based on the LNA probes may be explored. PMID:27025649

  5. Understanding the interaction of DNA-RNA nucleobases with different ZnO nanomaterials.

    PubMed

    Saha, Supriya; Sarkar, Pranab

    2014-08-01

    Due to the potential application of different nanostructure materials in biomedical nanotechnologies, understanding the interaction between the inorganic nanoparticles and biological molecules at the atomic level is of paramount importance. We present here the results of our theoretical investigation of the interaction of different nucleotide bases--adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U) of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)--with different ZnO nanoparticles, such as ZnO nanowires (NWs), nanotubes (NTs), surfaces and quantum dots (QDs). As the size of the systems we studied is relatively large, we have used the self-consistent-charge density-functional tight-binding (SCC-DFTB) method to optimize the complex systems. We have studied in detail the site-specific binding nature and the adsorption strength of these nucleobases with different ZnO nanoparticles. The calculated binding energy order and the interaction strength of nucleobases are very much dependent on the nature of the nanoparticle surfaces and are different for different nanostructures. In most of the cases ZnO prefers to bind either through the top site of the nucleobases or with the ring nitrogen atom having a lone pair relative to other binding sites of the bases. PMID:24942064

  6. Formation of Nucleobases from the UV Irradiation of Pyrimidine in Astrophysical Ice Analogs

    NASA Technical Reports Server (NTRS)

    Sandford, Scott A.; Nuevo, Michel; Materese, Christopher K.

    2014-01-01

    Nucleobases are the informational subunits of DNA and RNA. They consist of Nheterocycles that belong to either the pyrimidine-base group (uracil, cytosine, and thymine) or the purinebase group (adenine and guanine). Several nucleobases, mostly purine bases, have been detected in meteorites [1-3], with isotopic signatures consistent with an extraterrestrial origin [4]. Uracil is the only pyrimidine-base compound formally reported in meteorites [2], though the presence of cytosine cannot be ruled out [5,6]. However, the actual process by which the uracil was made and the reasons for the non-detection of thymine in meteorites have yet to be fully explained. Although no N-heterocycles have ever been observed in the ISM [7,8], the positions of the 6.2-µm interstellar emission features suggest a population of such molecules is likely to be present [9]. In this work we study the formation of pyrimidine-based molecules, including the three nucleobases uracil, cytosine, and thymine from the ultraviolet (UV) irradiation of pyrimidine in ices consisting of several combinations of H(sub2)O, NH(sub3), CH(sub3)OH, and CH(sub4) at low temperature, in order to simulate the astrophysical conditions under which prebiotic species may be formed in the interstellar medium, in the protosolar nebula, and on icy bodies of the Solar System.

  7. Nucleobase and amino acid formation through impacts of meteorites on the early ocean

    NASA Astrophysics Data System (ADS)

    Furukawa, Yoshihiro; Nakazawa, Hiromoto; Sekine, Toshimori; Kobayashi, Takamichi; Kakegawa, Takeshi

    2015-11-01

    The emergence of life's building blocks on the prebiotic Earth was the first crucial step for the origins of life. Extraterrestrial delivery of intact amino acids and nucleobases is the prevailing hypothesis for their availability on prebiotic Earth because of the difficulties associated with the production of these organics from terrestrial carbon and nitrogen sources under plausible prebiotic conditions. However, the variety and amounts of these intact organics delivered by meteorites would have been limited. Previous shock-recovery experiments have demonstrated that meteorite impact reactions could have generated organics on the prebiotic Earth. Here, we report on the simultaneous formation of nucleobases (cytosine and uracil) found in DNA and/or RNA, various proteinogenic amino acids (glycine, alanine, serine, aspartic acid, glutamic acid, valine, leucine, isoleucine, and proline), non-proteinogenic amino acids, and aliphatic amines in experiments simulating reactions induced by extraterrestrial objects impacting on the early oceans. To the best of our knowledge, this is the first report of the formation of nucleobases from inorganic materials by shock conditions. In these experiments, bicarbonate was used as the carbon source. Bicarbonate, which is a common dissolved carbon species in CO2-rich atmospheric conditions, was presumably the most abundant carbon species in the early oceans and in post-impact plumes. Thus, the present results expand the possibility that impact-induced reactions generated various building blocks for life on prebiotic Earth in large quantities through the use of terrestrial carbon reservoirs.

  8. Molecularly resolved label-free sensing of single nucleobase mismatches by interfacial LNA probes.

    PubMed

    Mishra, Sourav; Lahiri, Hiya; Banerjee, Siddhartha; Mukhopadhyay, Rupa

    2016-05-01

    So far, there has been no report on molecularly resolved discrimination of single nucleobase mismatches using surface-confined single stranded locked nucleic acid (ssLNA) probes. Herein, it is exemplified using a label-independent force-sensing approach that an optimal coverage of 12-mer ssLNA sensor probes formed onto gold(111) surface allows recognition of ssDNA targets with twice stronger force sensitivity than 12-mer ssDNA sensor probes. The force distributions are reproducible and the molecule-by-molecule force measurements are largely in agreement with ensemble on-surface melting temperature data. Importantly, the molecularly resolved detection is responsive to the presence of single nucleobase mismatches in target sequences. Since the labelling steps can be eliminated from protocol, and each force-based detection event occurs within milliseconds' time scale, the force-sensing assay is potentially capable of rapid detection. The LNA probe performance is indicative of versatility in terms of substrate choice - be it gold (for basic research and array-based applications) or silicon (for 'lab-on-a-chip' type devices). The nucleic acid microarray technologies could therefore be generally benefited by adopting the LNA films, in place of DNA. Since LNA is nuclease-resistant, unlike DNA, and the LNA-based assay is sensitive to single nucleobase mismatches, the possibilities for label-free in vitro rapid diagnostics based on the LNA probes may be explored. PMID:27025649

  9. Determination of HDV ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics

    PubMed Central

    Kellerman, Daniel L; Simmons, Kandice S; Pedraza, Mayra; Piccirilli, Joseph A; York, Darrin M; Harris, Michael E

    2015-01-01

    Biological catalysis involves interactions distant from the site of chemistry that can position the substrate for reaction. Catalysis of RNA 2′-O-transphosphorylation by the HDV ribozyme is sensitive to the identity of the N(-1) nucleotide flanking the reactive phosphoryl group. However, the interactions that affect the conformation of this position, and in turn the 2′O nucleophile, are unclear. Here, we describe the application of multiple substrate internal competition kinetic analyses to understand how the N(-1) nucleobase contributes to HDV catalysis, and to test the utility of this approach for RNA structure-function studies. Internal competition reactions containing all four substrate sequence variants at the N(-1) position in reactions using ribozyme active site mutations at A77 and A78 were used to test a proposed basepairing interaction. Mutants A78U, A78G and A79G retain significant catalytic activity, but do not alter the specificity for the N(-1) nucleobase. Effects of nucleobase analog substitutions at N(-1) indicate that U is preferred due to the ability to donate an H-bond in the Watson-Crick face and avoid minor groove steric clash. The results provide information essential for evaluating models of the HDV active site, and illustrate multiple-substrate kinetic analyses as a practical approach for characterizing structure-function relationships in RNA reactions. PMID:25937290

  10. DNA STRETCHING AND OPTIMISATION OF NUCLEOBASE RECOGNITION FOR ENZYMATIC NANOPORE SEQUENCING

    PubMed Central

    Stoddart, David; Franceschini, Lorenzo; Heron, Andrew; Bayley, Hagan; Maglia, Giovanni

    2015-01-01

    In nanopore sequencing, where single DNA strands are electrophoretically translocated through a nanopore and the resulting ionic signal is used to identify the four DNA bases, an enzyme has been used to ratchet the nucleic acid stepwise through the pore at a controlled speed. In this work, we investigated the ability of αHL nanopores to distinguish the four DNA bases under conditions that are compatible with the activity of DNA-handling enzymes. Our findings suggest that in immobilised strands, the applied potential exerts a force on DNA (~ 10 pN at +160 mV) that increases the distance between nucleobases by about 2.2 Å/V. The four nucleobases can be resolved over wide ranges of applied potentials (from +60 mV to +220 mV in 1 m KCl) and ionic strengths (from 200 mM KCl to 1 M KCl at +160 mV) and nucleobase recognition can be improved when the ionic strength on the side of the DNA-handling enzyme is low, while the ionic strength on the opposite side is high. PMID:25648138