bluuebunny/crossref_metadata_2025 huggingface dataset:
The human Vps29 retromer component is a metallo-phosphoesterase for a cation-independent mannose 6-phosphate receptor substrate peptide
Authors: Damen Ester , Krieger Elmar , Nielsen Jens E. , Eygensteyn Jelle , Van Leeuwen Jeroen E. M.
Published: August 2006

The retromer complex is involved in the retrograde transport of the CI-M6PR (cation-independent mannose 6-phosphate receptor) from endosomes to the Golgi. It is a hetero-trimeric complex composed of Vps26 (vacuolar sorting protein 26), Vps29 and Vps35 proteins, which are conserved in eukaryote evolution. Recently, elucidation of the crystal structure of Vps29 revealed that Vps29 contains a metallo-phosphoesterase fold [Wang, Guo, Liang, Fan, Zhu, Zang, Zhu, Li, Teng, Niu et al. (2005) J. Biol. Chem. 280, 22962–22967; Collins, Skinner, Watson, Seaman and Owen (2005) Nat. Struct. Mol. Biol. 12, 594–602]. We demonstrate that recombinant hVps29 (human Vps29) displays in vitro phosphatase activity towards a serine-phosphorylated peptide, containing the acidic-cluster dileucine motif of the cytoplasmatic tail of the CI-M6PR. Efficient dephosphorylation required the additional presence of recombinant hVps26 and hVps35 proteins, which interact with hVps29. Phosphatase activity of hVps29 was greatly decreased by alanine substitutions of active-site residues that are predicted to co-ordinate metal ions. Using inductively coupled plasma MS, we demonstrate that recombinant hVps29 binds zinc. Moreover, hVps29-dependent phosphatase activity is greatly reduced by non-specific and zinc-specific metal ion chelators, which can be completely restored by addition of excess ZnCl2. The binuclear Zn2+ centre and phosphate group were modelled into the hVps29 catalytic site and pKa calculations provided further insight into the molecular mechanisms of Vps29 phosphatase activity. We conclude that the retromer complex displays Vps29-dependent in vitro phosphatase activity towards a serinephosphorylated acidic-cluster dileucine motif that is involved in endosomal trafficking of the CI-M6PR. The potential significance of these findings with respect to regulation of transport of cycling trans-Golgi network proteins is discussed.
Inhibition of a metal-dependent viral RNA triphosphatase by decavanadate
Authors: Bougie Isabelle , Bisaillon Martin
Published: August 2006

Paramecium bursaria chlorella virus, a large DNA virus that replicates in unicellular Chlorella-like algae, encodes an RNA triphosphatase which is involved in the synthesis of the RNA cap structure found at the 5′ end of the viral mRNAs. The Chlorella virus RNA triphosphatase is the smallest member of the metal-dependent RNA triphosphatases that include enzymes from fungi, DNA viruses, protozoans and microsporidian parasites. In the present study, we investigated the ability of various vanadate oxoanions to inhibit the phosphohydrolase activity of the enzyme. Fluorescence spectroscopy and CD studies were used to directly monitor the binding of decavanadate to the enzyme. Moreover, competition assays show that decavanadate is a potent non-competitive inhibitor of the phosphohydrolase activity, and mutagenesis studies indicate that the binding of decavanadate does not involve amino acids located in the active site of the enzyme. In order to provide additional insight into the relationship between the enzyme structure and decavanadate binding, we correlated the effect of decavanadate binding on protein structure using both CD and guanidinium chloride-induced denaturation as structural indicators. Our data indicated that no significant modification of the overall protein architecture was occurring upon decavanadate binding. However, both fluorescence spectroscopy and CD experiments clearly revealed that the binding of decavanadate to the enzyme significantly decreased the structural stability of the enzyme. Taken together, these studies provide crucial insights into the inhibition of metal-dependent RNA triphosphatases by decavanadate.
Sphingosine 1-phosphate receptor expression profile and regulation of migration in human thyroid cancer cells
Authors: Balthasar Sonja , Samulin Johanna , Ahlgren Hanna , Bergelin Nina , Lundqvist Mathias , Toescu Emil C. , Eggo Margaret C. , Törnquist Kid
Published: August 2006

S1P (sphingosine 1-phosphate) receptor expression and the effects of S1P on migration were studied in one papillary (NPA), two follicular (ML-1, WRO) and two anaplastic (FRO, ARO) thyroid cancer cell lines, as well as in human thyroid cells in primary culture. Additionally, the effects of S1P on proliferation, adhesion and calcium signalling were addressed in ML-1 and FRO cells. All cell types expressed multiple S1P receptors. S1P evoked intracellular calcium signalling in primary cultures, ML-1 cells and FRO cells. Neither proliferation nor migration was affected in primary cultures, whereas S1P partly inhibited proliferation in ML-1 and FRO cells. Low nanomolar concentrations of S1P inhibited migration in FRO, WRO and ARO cells, but stimulated ML-1 cell migration. Consistently, S1P1 and S1P3, which mediate migratory responses, were strongly expressed in ML-1 cells, and S1P2, which inhibits migration, was the dominating receptor in the other cell lines. The migratory effect in ML-1 cells was mediated by Gi and phosphatidylinositol 3-kinase. Both S1P and the S1P1-specific agonist SEW-2871 induced Akt phosphorylation at Ser473. However, SEW-2871 failed to stimulate migration, whereas the S1P1/S1P3 antagonist VPC 23019 inhibited S1P-induced migration. The results suggest that aberrant S1P receptor expression may enhance thyroid cancer cell migration and thus contribute to the metastatic behaviour of some thyroid tumours.
Conformational stability of human frataxin and effect of Friedreich's ataxia-related mutations on protein folding
Authors: Correia Ana R. , Adinolfi Salvatore , Pastore Annalisa , Gomes Cláudio M.
Published: August 2006

The neurodegenerative disorder FRDA (Friedreich's ataxia) results from a deficiency in frataxin, a putative iron chaperone, and is due to the presence of a high number of GAA repeats in the coding regions of both alleles of the frataxin gene, which impair protein expression. However, some FRDA patients are heterozygous for this triplet expansion and contain a deleterious point mutation on the other allele. In the present study, we investigated whether two particular FRDA-associated frataxin mutants, I154F and W155R, result in unfolded protein as a consequence of a severe structural modification. A detailed comparison of the conformational properties of the wild-type and mutant proteins combining biophysical and biochemical methodologies was undertaken. We show that the FRDA mutants retain the native fold under physiological conditions, but are differentially destabilized as reflected both by their reduced thermodynamic stability and a higher tendency towards proteolytic digestion. The I154F mutant has the strongest effect on fold stability as expected from the fact that the mutated residue contributes to the hydrophobic core formation. Functionally, the iron-binding properties of the mutant frataxins are found to be partly impaired. The apparently paradoxical situation of having clinically aggressive frataxin variants which are folded and are only significantly less stable than the wild-type form in a given adverse physiological stress condition is discussed and contextualized in terms of a mechanism determining the pathology of FRDA heterozygous.
LASS3 (longevity assurance homologue 3) is a mainly testis-specific (dihydro)ceramide synthase with relatively broad substrate specificity
Authors: Mizutani Yukiko , Kihara Akio , Igarashi Yasuyuki
Published: August 2006

The LASS (longevity assurance homologue) family members are highly conserved from yeasts to mammals. Five mouse and human LASS family members, namely LASS1, LASS2, LASS4, LASS5 and LASS6, have been identified and characterized. In the present study we cloned two transcriptional variants of hitherto-uncharacterized mouse LASS3 cDNA, which encode a 384-amino-acid protein (LASS3) and a 419-amino-acid protein (LASS3-long). In vivo, [3H]dihydrosphingosine labelling and electrospray-ionization MS revealed that overproduction of either LASS3 isoform results in increases in several ceramide species, with some preference toward those having middle- to long-chain-fatty acyl-CoAs. A similar substrate preference was observed in an in vitro (dihydro)ceramide synthase assay. These results indicate that LASS3 possesses (dihydro)ceramide synthesis activity with relatively broad substrate specificity. We also found that, except for a weak display in skin, LASS3 mRNA expression is limited almost solely to testis, implying that LASS3 plays an important role in this gland.
Identification and characteristics of the structural gene for the Drosophila eye colour mutant sepia, encoding PDA synthase, a member of the Omega class glutathione S-transferases
Authors: Kim Jaekwang , Suh Hyunsuk , Kim Songhee , Kim Kiyoung , Ahn Chiyoung , Yim Jeongbin
Published: August 2006

The eye colour mutant sepia (se1) is defective in PDA {6-acetyl-2-amino-3,7,8,9-tetrahydro-4H-pyrimido[4,5-b]-[1,4]diazepin-4-one or pyrimidodiazepine} synthase involved in the conversion of 6-PTP (2-amino-4-oxo-6-pyruvoyl-5,6,7,8-tetrahydropteridine; also known as 6-pyruvoyltetrahydropterin) into PDA, a key intermediate in drosopterin biosynthesis. However, the identity of the gene encoding this enzyme, as well as its molecular properties, have not yet been established. Here, we identify and characterize the gene encoding PDA synthase and show that it is the structural gene for sepia. Based on previously reported information [Wiederrecht, Paton and Brown (1984) J. Biol. Chem. 259, 2195–2200; Wiederrecht and Brown (1984) J. Biol. Chem. 259, 14121–14127; Andres (1945) Drosoph. Inf. Serv. 19, 45; Ingham, Pinchin, Howard and Ish-Horowicz (1985) Genetics 111, 463–486; Howard, Ingham and Rushlow (1988) Genes Dev. 2, 1037–1046], we isolated five candidate genes predicted to encode GSTs (glutathione S-transferases) from the presumed sepia locus (region 66D5 on chromosome 3L). All cloned and expressed candidates exhibited relatively high thiol transferase and dehydroascorbate reductase activities and low activity towards 1-chloro-2,4-dinitrobenzene, characteristic of Omega class GSTs, whereas only CG6781 catalysed the synthesis of PDA in vitro. The molecular mass of recombinant CG6781 was estimated to be 28 kDa by SDS/PAGE and 56 kDa by gel filtration, indicating that it is a homodimer under native conditions. Sequencing of the genomic region spanning CG6781 revealed that the se1 allele has a frameshift mutation from ‘AAGAA’ to ‘GTG’ at nt 190–194, and that this generates a premature stop codon. Expression of the CG6781 open reading frame in an se1 background rescued the eye colour defect as well as PDA synthase activity and drosopterins content. The extent of rescue was dependent on the dosage of transgenic CG6781. In conclusion, we have discovered a new catalytic activity for an Omega class GST and that CG6781 is the structural gene for sepia which encodes PDA synthase.
Evolution of a signalling system that incorporates both redundancy and diversity:ArabidopsisSUMOylation
Authors: Chosed Renee , Mukherjee Sohini , Lois Luisa Maria , Orth Kim
Published: August 2006

The reversible post-translational modifier, SUMO (small ubiquitin-related modifier), modulates the activity of a diverse set of target proteins, resulting in important consequences to the cellular machinery. Conjugation machinery charges the processed SUMO so that it can be linked via an isopeptide bond to a target protein. The removal of SUMO moieties from conjugated proteins by isopeptidases regenerates pools of processed SUMOs and unmodified target proteins. The evolutionarily conserved SUMO-conjugating proteins, E1 and E2, recognize a diverse set of Arabidopsis SUMO proteins using them to modify protein substrates. In contrast, the deSUMOylating enzymes differentially recognize the Arabidopsis SUMO proteins, resulting in specificity of the deconjugating machinery. The specificity of the Arabidopsis deSUMOylating enzymes is further diversified by the addition of regulatory domains. Therefore the SUMO proteins, in this signalling system, have evolved to contain information that allows not only redundancy with the conjugation system but also diversity with the deconjugating enzymes.
Biosynthesis of hyaluronan: direction of chain elongation
Authors: Prehm Peter
Published: August 2006

The mechanism of hyaluronan biosynthesis in vertebrates had been proposed to occur at the reducing end of growing chains. This mechanism was questioned because a recombinant synthase appeared to add new monosaccharides to the non-reducing end. I reinvestigated this problem with membranes from the eukaryotic B6 cell line. The membranes were incubated with UDP-[3H]GlcNAc and UDP-[14C]GlcA to yield differentially labelled reducing terminal and non-reducing terminal domains. Digestion of the product with a mixture of the exoglycosidases β-glucuronidase and β-N-acetylglucosaminidase truncated the hyaluronan chain strictly from the non-reducing end. The change in 3H/14C ratio of the remaining hyaluronan fraction, during the course of exoglycosidase digestion, confirmed the original results that the native eukaryotic synthase extended hyaluronan at the reducing end. This mechanism demands that the UDP-hyaluronan terminus is bound to the active site within the synthase and should compete with the substrates for binding. Accordingly, increasing substrate concentrations enhanced hyaluronan release from the synthase. A model is proposed that explains the direction of chain elongation at the reducing end by the native synthase and at the non-reducing end by the recombinant synthase based on a loss of binding affinity of the synthase towards the growing UDP-hyaluronan chain.
Mechanisms of RecQ helicases in pathways of DNA metabolism and maintenance of genomic stability
Authors: Sharma Sudha , Doherty Kevin M. , Brosh Robert M.
Published: August 2006

Helicases are molecular motor proteins that couple the hydrolysis of NTP to nucleic acid unwinding. The growing number of DNA helicases implicated in human disease suggests that their vital specialized roles in cellular pathways are important for the maintenance of genome stability. In particular, mutations in genes of the RecQ family of DNA helicases result in chromosomal instability diseases of premature aging and/or cancer predisposition. We will discuss the mechanisms of RecQ helicases in pathways of DNA metabolism. A review of RecQ helicases from bacteria to human reveals their importance in genomic stability by their participation with other proteins to resolve DNA replication and recombination intermediates. In the light of their known catalytic activities and protein interactions, proposed models for RecQ function will be summarized with an emphasis on how this distinct class of enzymes functions in chromosomal stability maintenance and prevention of human disease and cancer.
HIV-1 integrase is capable of targeting DNA to the nucleus via an Importin α/β-dependent mechanism
Authors: Hearps Anna C. , Jans David A.
Published: August 2006

In addition to its well-documented role in integration of the viral genome, the HIV-1 enzyme IN (integrase) is thought to be involved in the preceding step of importing the viral cDNA into the nucleus. The ability of HIV to transport its cDNA through an intact nuclear envelope allows HIV-1 to infect non-dividing cells, which is thought to be crucial for the persistent nature of HIV/AIDS. Despite this, the mechanism utilized by HIV-1 to import its cDNA into the nucleus, and the viral proteins involved, remains ill-defined. In the present study we utilize in vitro techniques to assess the nuclear import properties of the IN protein, and show that IN interacts with members of the Imp (Importin) family of nuclear transport proteins with high affinity and exhibits rapid nuclear accumulation within an in vitro assay, indicating that IN possesses potent nucleophilic potential. IN nuclear import appears to be dependent on the Imp α/β heterodimer and Ran GTP (Ran in its GTP-bound state), but does not require ATP. Importantly, we show that IN is capable of binding DNA and facilitating its import into the nucleus of semi-intact cells via a process that involves basic residues within amino acids 186–188 of IN. These results confirm IN as an efficient mediator of DNA nuclear import in vitro and imply the potential for IN to fulfil such a role in vivo. These results may not only aid in highlighting potential therapeutic targets for impeding the progression of HIV/AIDS, but may also be relevant for non-viral gene delivery.
Retinal is formed from apo-carotenoids in Nostoc sp. PCC7120: in vitro characterization of an apo-carotenoid oxygenase
Authors: Scherzinger Daniel , Ruch Sandra , Kloer Daniel P. , Wilde Annegret , Al-Babili Salim
Published: August 2006

The sensory rhodopsin from Anabaena (Nostoc) sp. PCC7120 is the first cyanobacterial retinylidene protein identified. Here, we report on NosACO (Nostoc apo-carotenoid oxygenase), encoded by the ORF (open reading frame) all4284, as the candidate responsible for the formation of the required chromophore, retinal. In contrast with the enzymes from animals, NosACO converts β-apo-carotenals instead of β-carotene into retinal in vitro. The identity of the enzymatic products was proven by HPLC and gas chromatography–MS. NosACO exhibits a wide substrate specificity with respect to chain lengths and functional end-groups, converting β-apo-carotenals, (3R)-3-hydroxy-β-apo-carotenals and the corresponding alcohols into retinal and (3R)-3-hydroxyretinal respectively. However, kinetic analyses revealed very divergent Km and Vmax values. On the basis of the crystal structure of SynACO (Synechocystis sp. PCC6803 apo-carotenoid oxygenase), a related enzyme showing similar enzymatic activity, we designed a homology model of the native NosACO. The deduced structure explains the absence of β-carotene-cleavage activity and indicates that NosACO is a monotopic membrane protein. Accordingly, NosACO could be readily reconstituted into liposomes. To localize SynACO in vivo, a Synechocystis knock-out strain was generated expressing SynACO as the sole carotenoid oxygenase. Western-blot analyses showed that the main portion of SynACO occurred in a membrane-bound form.
Health as a consumption object: research notes and preliminary investigation
Authors: Gould Nicholas , Gould Elizabeth
Published: August 2006

Through the processes of commodification and marketization, materials and human activities are brought within the domain of market exchange. The results of these accelerating processes are observed in the consumer culture centred on objects of consumption. We contend that, in addition to healthcare, health itself has become yet another object incorporated within consumption space. This contention is consistent with the perspective of consumption as the dominant social paradigm in the structuring of health and healthcare practices. In this paper we present the conceptual backdrop for our contentions, together with details of a heuristic study. Our findings support the view that people regard health as a consumption object. Furthermore, the evidence suggests a patterning of responses by social grade and gender. Given our wider interest in class‐based health inequalities, we use our results to comment on the broader policy debate concerning this phenomenon in relation to consumerism.
Tailoring electronic and charge transport properties of molecular π-stacked heterojunctions
Authors: Rochefort Alain , Boyer Paul
Published: August 2006

The electronic structure and charge transport properties of π-stacked heterojunctions formed by two different 3,6-R2-1-ethylnaphthalene (R: H, CH3, Cl) fragments have been investigated with a tight binding method. The extent of the evanescent wave function that escapes across the interface near EF is shorter when chloride groups are used to modify the π-electron distribution of the naphthalene core than when methyl groups are used. Consequently, the tunneling of carriers in CH3-heterojunction is significantly larger than for systems containing chloride groups. This shows that specific electronic properties can be tailored on naphthalene-based assemblies in which a judicious combination of functional groups is considered.
Thermoelastic martensitic transformation in ferromagnetic Ni–Fe–Al alloys: Effect of site disorder
Authors: Kaul S. N. , Annie D’ Santhoshini B. , Abhyankar A. C. , Barquín L. Fernández , Henry Paul
Published: August 2006

Thermoelastic martensitic transformation from a face-centered-cubic austenite phase to tetragonal martensite phase has been established in a new ternary ferromagnetic alloy system Ni–Fe–Al (“prepared” in different states of site disorder) based on the results of a detailed neutron diffraction, electrical resistivity, and magnetization studies. Ordered (annealed) Ni55Fe20Al25 has a high Curie temperature TC⪢300K and an extremely wide temperature range over which martensite and austenite phases coexist. By comparison, site-disordered (quenched) Ni55Fe20Al25 has a lower TC (=225K), higher ductility (shape memory effect), higher saturation magnetization, and a very well-defined martensitic transformation around TC.
Theoretical demonstration of enhancement of light extraction of flip-chip GaN light-emitting diodes with photonic crystals
Authors: Chao Chia-Hsin , Chuang S. L. , Wu Tzong-Lin
Published: August 2006

The authors demonstrate, using finite-difference time-domain modeling, an enhancement in the extraction efficiency of flip-chip GaN light-emitting diodes (LEDs) using photonic crystals. The authors compare the extraction efficiencies of four configurations of a flip-chip GaN LED: with and without photonic crystal (PhC) layers, with a perfect reflecting mirror, and a bottom PhC reflector on GaN in combination with a top PhC extractor on sapphire. The authors show that, by using a photonic crystal layer as a bottom reflector, they can enhance the extraction efficiency similar to that of a mirror, yet the PhC reflector has the advantage that the metallic mirror loss can be avoided.
Two-subband-populated AlGaN∕GaN heterostructures probed by electrically detected and microwave-modulated magnetotransport measurements
Authors: Hang D. R. , Huang C. F. , Chen Y. F.
Published: August 2006

The authors apply the microwave-modulated technique to study the transport properties of two-subband-populated AlGaN∕GaN heterostructures. The microwave modulation enhances the small Shubnikov–de Haas oscillations at low magnetic fields, providing a direct way to compare the mobilities of different subbands from the experimental data. In addition, this technique can help us to determine the subband-energy separation, especially when the population of the second subband is much lower than that of the first one. Variation of subband-energy separation due to different spacer thicknesses is obtained. Therefore, the authors showed a powerful way to probe parameters of two-subband-populated AlGaN∕GaN heterostructures.
Superconducting single-phase Sr1−xLaxCuO2 thin films with improved crystallinity grown by pulsed laser deposition
Authors: Leca Victor , Blank Dave H. A. , Rijnders Guus , Bals Sara , van Tendeloo Gustaaf
Published: August 2006

Sr 1 − x La x Cu O 2 − δ  (x=0.10–0.20) thin films exhibiting an oxygen-deficient 22ap×22ap×c structure (ap and c represent the cell parameters of the perovskite subcell) were epitaxially grown by means of pulsed laser deposition in low-pressure oxygen ambient. (001) KTaO3 and (001) SrTiO3 single crystals were used as substrates, with BaTiO3 as buffer layer. The Sr1−xLaxCuO2−δ films were oxidized during cooling down in order to yield the infinite-layer-type structure. By applying this method, high quality single-phase Sr1−xLaxCuO2 thin films could be obtained for 0.10⩽x⩽0.175 doping range. The films grown on BaTiO3∕KTaO3 show superconductivity for 0.15⩽x⩽0.175 with optimum doping at x=0.15, in contrast with previously reported data.
Electronic transport properties of Cs-encapsulated single-walled carbon nanotubes created by plasma ion irradiation
Authors: Izumida T. , Hatakeyama R. , Neo Y. , Mimura H. , Omote K. , Kasama Y.
Published: August 2006

The electronic transport properties of Cs-encapsulated single-walled carbon nanotubes (Cs@SWNTs), which are created by a plasma ion irradiation method, are experimentally investigated at both room and low temperatures by fabricating field-effect transistor devices with these modified SWNTs. It is found that Cs@SWNTs exhibit air stable n-type transport characteristics at room temperature, where Cs atoms function as an electron donor. Moreover, Coulomb oscillations are observed under a low temperature, which is derived from the electronic structure modulated mainly by the encapsulated Cs atoms.
Fiber-optic temperature sensor based on interference of selective higher-order modes
Authors: Li Enbang , Wang Xiaolin , Zhang Chao
Published: August 2006

A fiber-optic temperature sensor based on the interference of selective higher-order modes in circular optical fibers is described. The authors demonstrate that by coupling the LP01 mode in a standard single-mode fiber to the LP0m modes in a multimode fiber, and utilizing the interference of the higher-order modes, a fiber-optic temperature sensor which has an extremely simple structure and is suitable for high-temperature measurements can be constructed. The sensing principle, temperature measurement experiments, and results are presented.
Electroluminescence from coupled InGaAs∕GaAs quantum dots embedded in lateral p-i-n junctions
Authors: Xu Xiulai , Andreev Aleksey , Williams David A. , Cleaver John R. A.
Published: August 2006

The authors report an observation of coupling in single quantum dot molecules embedded in lateral p-i-n junctions using electroluminescence spectra. With a graded dot density wafer, electroluminescence spectra from uncoupled and coupled stacked quantum dots have been observed. For coupled pairs of quantum dots, an anticrossing of direct and indirect recombinations is observed with a forward biased electric field where the two dots are in resonance.
Measuring interface strains at the atomic resolution in depth using x-ray Bragg-surface diffraction
Authors: Sun W. C. , Chang H. C. , Wu B. K. , Chen Y. R. , Chu C. H. , Chang S. L. , Hong M. , Tang M. T. , Stetsko Yu. P.
Published: August 2006

A generic x-ray diffraction method, using three-wave Bragg-surface diffraction, is developed to measure strains at the interface of molecular beam epitaxial Au∕GaAs(001), where grazing-incidence diffraction cannot be applied due to the difference in refractive index between Au and GaAs. Changes in diffraction images of the surface reflection (1−13) of GaAs(006)∕(1−13) three-wave Bragg-surface diffraction and the (−1−13) of GaAs(006)∕(−1−13) at different azimuth and Bragg angles give the depth penetration of 2Å resolution and variations of lattice constant, −49%, −27%, and 2%, along the surface normal [001] and in-plane directions [−1−10] and [1−10] within the depths of 18, 72, and 72Å, respectively.
Icositetrahedral and icosahedral atomic configurations observed in the Nb–Ag metallic glasses synthesized by ion beam mixing
Authors: Tai K. P. , Gao N. , Dai X. D. , Li J. H. , Lai W. S. , Liu B. X.
Published: August 2006

Metallic glasses are obtained in an immiscible Nb–Ag system by ion beam mixing and an atomic configuration in the amorphous structure is discovered, i.e., an icositetrahedral ordering, which, together with an icosahedral ordering also observed in the Nb–Ag metallic glasses and in some previously reported systems, helps in formulating a structural spectrum of the amorphous solids. The experimental characterization and atomistic modeling with an ab initio derived Nb–Ag potential demonstrate the significance of structural heredity, i.e., the crystalline structures of the constituent metals play a decisive role in determining the atomic structure of the metallic glasses in the system.
Ab initio study of the potential energy surface for the OH+CO→H+CO2 reaction
Authors: Song Xinli , Li Jicun , Hou Hua , Wang Baoshan
Published: August 2006

Potential energy surface for the reaction OH+CO→H+CO2 has been calculated using the complete active space self-consistent-field and multireference configuration interaction methods with the correlation consistent triple-, quadruple-, and quintuple-zeta basis sets. A specific- reaction-parameters density functional theory has been suggested, in which the B3LYP functional is reoptimized to give the highly accurate potential energy surface with less computational efforts.
Novel interaction of selenium-binding protein with glyceraldehyde-3-phosphate dehydrogenase and fructose-bisphosphate aldolase of Arabidopsis thaliana
Authors: Agalou Adamantia , Spaink Herman P. , Roussis Andreas
Published: August 2006

The metabolic role and regulation of selenium, particularly in plants, is poorly understood. One of the proteins probably involved in the metabolic regulation of this element is the selenium-binding protein (SBP) with homologues present across prokaryotic and eukaryotic species. The high degree of conservation of SBP in different organisms suggests that this protein may play a role in fundamental biological processes. In order to gain insight into the biochemical function of SBP in plants we used the yeast two-hybrid system to identify proteins that potentially interact with an Arabidopsis thaliana (L.) Heynh. homologue. Among the putative binding partners of SBP, a NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a fructose-bisphosphate aldolase (FBA) were found as reliable positive candidates. The interaction of these proteins with SBP was confirmed by in vitro binding assays. Previous findings in Escherichia coli, demonstrated the direct binding of selenium to both GAPDH and aldolase. Therefore our results reveal the interaction, at least in pairs, of three proteins that are possibly linked to selenium and suggest the existence of a protein network consisting of at least SBP, GAPDH and FBA, triggered by or regulating selenium metabolism in plant cells.
The antioxidative function of lutein: electron spin resonance studies and chemical detection
Authors: Peng Chang-Lian , Lin Zhi-Fang , Su Yue-Zeng , Lin Gui-Zhu , Dou Hong-Yan , Zhao Cheng-Xue
Published: August 2006

In the present study, both electron spin resonance (ESR) and chemical detection confirmed that lutein [extracted from alfalfa (Medicago sativa L.)], the most abundant xanthophyll in thylakoids of chloroplasts, could serve as an antioxidant to scavenge reactive oxygen species (ROS) in vitro. Lutein exhibited a greater capacity for scavenging hydroxyl (OH·) and superoxide (O2·–) radicals than β-carotene at the same concentration, whereas the opposite trend was observed in the capacity for scavenging singlet oxygen (1O2). The capacity of lutein for scavenging ROS from high to low is OH· > O2·– > 1O2. We hypothesise that lutein plays an important photoprotective role in scavenging O2·– and OH· under severe stress. This hypothesis is consistent with our previous report that the lut2 (lutein-deficient) Arabidopsis mutant is more susceptible to damage than the npq1 (lutein-replete but violaxanthin de-epoxidase-deficient) Arabidopsis mutant under severe stress during exposure to high light intensity at low temperature (Peng and Gilmore 2003).
Isolation and characterisation of six putative wheat cell wall-associated kinases
Authors: Liu Yong , Liu Dongcheng , Zhang Haiying , Gao Hongbo , Guo Xiaoli , Fu Xiangdong , Zhang Aimin
Published: August 2006

The plant cell wall-associated kinase (WAK) and WAK-like kinase (WAKL) make up a unique group in the receptor-like protein kinase (RLK) superfamily. Previous studies on Arabidopsis have revealed that the WAK gene family members play an important role in both cell elongation and stress response signalling. Here we show that four putative WAKs (TaWAK1, TaWAKL2, TaWAKL3, and TaWAK4) and two WAKLs (TaWAKL1 and TaWAKL2) were isolated from wheat based on the DNA sequence similarity and the protein structure conservation of Arabidopsis WAKs genes. TaWAK1, TaWAK2, TaWAK3 and TaWAKL1 each encode a putative intact protein with the characteristic of the WAK / WAKL gene family members, except for the abbreviated TaWAK4 and TaWAKL2 which were caused by nucleotide mutation and alternative splicing, respectively. Southern analysis revealed that TaWAKL1, TaWAK1, TaWAK2 and TaWAK3 are all multiple-copy members. Real-time PCR analysis revealed that the TaWAK1 and TaWAK3 displayed similar expression patterns, while expressions of TaWAKL1, TaWAKL2, and TaWAK2 were organ specific. Further, we analysed the conservation of introns and intron–exon structure and the putative protein structures between wheat and Arabidopsis, which showed the putative wheat WAKs are different from those of Arabidopsis and make up a new subgroup in the polygenetic tree.
Genotypic variation in water-soluble carbohydrate accumulation in wheat
Authors: Ruuska Sari A. , Rebetzke Greg J. , van Herwaarden Anthony F. , Richards Richard A. , Fettell Neil A. , Tabe Linda , Jenkins Colin L. D.
Published: August 2006

The water-soluble carbohydrate (WSC) that accumulates in the stems of wheat during growth can be an important contributor to grain filling, particularly under conditions when assimilation is limited, such as during end-of-season drought. WSC concentration was measured at anthesis across a diverse set of wheat genotypes over multiple environments. Environmental differences in WSC concentration were large (means for the set ranging between 108 and 203 mg g–1 dry weight), and there were significant and repeatable differences in WSC accumulation among genotypes (means ranging from 112 to 213 mg g–1 dry weight averaged across environments), associated with large broad-sense heritability (H = 0.90 ± 0.12). These results suggest that breeding for high WSC should be possible in wheat. The composition of the WSC, examined in selected genotypes, indicated that the variation in total WSC was attributed mainly to variation in the fructan component, with the other major soluble carbohydrates, sucrose and hexose, varying less. The degree of polymerisation (DP) of fructo-oligosaccharides was up to ~13 in samples where higher levels of WSC were accumulated, owing either to genotype or environment, but the higher DP components (DP > 6) were decreased in samples of lower total WSC. The results are consistent with fructan biosynthesis occurring via a sequential mechanism that is dependent on the availability of sucrose, and differences in WSC contents of genotypes are unlikely to be due to major mechanistic differences.
Rats produced by interspecies spermatogonial transplantation in mice andin vitromicroinsemination
Authors: Shinohara Takashi , Kato Megumi , Takehashi Masanori , Lee Jiyoung , Chuma Shinichiro , Nakatsuji Norio , Kanatsu-Shinohara Mito , Hirabayashi Masumi
Published: August 2006

Spermatogonial transplantation has demonstrated a unique opportunity for studying spermatogenesis and provided an assay for spermatogonial stem cells. However, it has remained unknown whether germ cells that matured in a xenogeneic environment are functionally normal. In this investigation, we demonstrate the successful production of xenogeneic offspring by using spermatogonial transplantation. Rat spermatogonial stem cells were collected from immature testis and transplanted into the seminiferous tubules of busulfan-treated nude mouse testis. Using rat spermatids or spermatozoa that developed in xenogeneic surrogate mice, rat offspring were born from fresh and cryopreserved donor cells after microinsemination with rat oocytes. These offspring were fertile and had a normal imprinting pattern. The xenogeneic offspring production by interspecies germ cell transplantation andin vitromicroinsemination will become a powerful tool in animal transgenesis and species conservation.
Understanding Spatial Diagram Structure: An Analysis of Hierarchies, Matrices, and Networks
Authors: Novick Laura R.
Published: August 2006

Abstract diagrams are powerful tools for comprehension and problem solving in diverse contexts. Two studies examined the structural properties of (i.e., applicability conditions for) three interrelated spatial diagrams—hierarchies, matrices, and networks. College students from two groups with distinct educational backgrounds and learning histories—advanced computer science students and representative undergraduates—rated the diagnosticity of the hypothesized applicability conditions for each of the 3 diagrams. The results validated 24–26 of the 30 hypothesized applicability conditions and provided evidence regarding the relative importance, or diagnosticity, of the validated properties for each type of diagram. A different set of properties was identified as most highly diagnostic for each type of diagram, indicating that the three spatial diagrams are optimized to serve different representational functions: The matrix stores static information about the kind of relation that exists between pairs of items in different sets, the network conveys dynamic information by showing the local connections and global routes connecting the items being represented, and the hierarchy depicts a rigid structure of power or precedence relations among items. The quantitative and qualitative differences in representational knowledge due to educational background are discussed.
Does word frequency affect lexical selection in speech production?
Authors: Navarrete Eduardo , Basagni Benedetta , Alario F.-Xavier , Costa Albert
Published: August 2006

We evaluated whether lexical selection in speech production is affected by word frequency by means of two experiments. In Experiment 1 participants named pictures using utterances with the structure “pronoun + verb + adjective”. In Experiment 2 participants had to perform a gender decision task on the same pictures. Access to the noun's grammatical gender is needed in both tasks, and therefore lexical selection (lemma retrieval) is required. However, retrieval of the phonological properties (lexeme retrieval) of the referent noun is not needed to perform the tasks. In both experiments we observed faster latencies for high-frequency pictures than for low-frequency pictures. This frequency effect was stable over four repetitions of the stimuli. Our results suggest that lexical selection (lemma retrieval) is sensitive to word frequency. This interpretation runs against the hypothesis that a word's frequency exerts its effects only at the level at which the phonological properties of words are retrieved.
The role of encoding in reality monitoring: A running memory test with Alzheimer's type dementia
Authors: Mammarella Nicola , Fairfield Beth
Published: August 2006

Reality monitoring refers to the discrimination between memories of internal and external events (e.g., Johnson & Raye, 1981). A total of 28 healthy older adults and 28 older adults with Alzheimer's type dementia (DAT) were asked to perform or to imagine performing simple action statements in a running memory test. This task required participants to tell whether the action statement had been carried out or imagined, or whether it was new at unpredictable intervals. The results indicated that older adults with DAT had greater difficulty in reality monitoring than did the healthy control group. The finding is discussed in terms of the role of working memory functions in reality monitoring.
How does running memory span work?
Authors: Bunting Michael , Cowan Nelson , Scott Saults J.
Published: August 2006

In running memory span, a list ends unpredictably, and the last few items are to be recalled. This task is of increasing importance in recent research. We argue that there are two very different strategies for performing running span tasks: a low-effort strategy in which items are passively held until the list ends, when retrieval into a capacity-limited store takes place; and a higher-effort strategy in which working memory is continually updated using rehearsal processes during the list presentation. In two experiments, we examine the roles of these two strategies and the consequences of two types of interference.
Dual Role of the Cysteine-String Domain in Membrane Binding and Palmitoylation-dependent Sorting of the Molecular Chaperone Cysteine-String Protein
Authors: Greaves Jennifer , Chamberlain Luke H.
Published: August 2006

S-palmitoylation occurs on intracellular membranes and, therefore, membrane anchoring of proteins must precede palmitate transfer. However, a number of palmitoylated proteins lack any obvious membrane targeting motifs and it is unclear how this class of proteins become membrane associated before palmitoylation. Cysteine-string protein (CSP), which is extensively palmitoylated on a “string” of 14 cysteine residues, is an example of such a protein. In this study, we have investigated the mechanisms that govern initial membrane targeting, palmitoylation, and membrane trafficking of CSP. We identified a hydrophobic 31 amino acid domain, which includes the cysteine-string, as a membrane-targeting motif that associates predominantly with endoplasmic reticulum (ER) membranes. Cysteine residues in this domain are not merely sites for the addition of palmitate groups, but play an essential role in membrane recognition before palmitoylation. Membrane association of the cysteine-string domain is not sufficient to trigger palmitoylation, which requires additional downstream residues that may regulate the membrane orientation of the cysteine-string domain. CSP palmitoylation-deficient mutants remain “trapped” in the ER, suggesting that palmitoylation may regulate ER exit and correct intracellular sorting of CSP. These results reveal a dual function of the cysteine-string domain: initial membrane binding and palmitoylation-dependent sorting.
A Novel Function of 14-3-3 Protein: 14-3-3ζ Is a Heat-Shock–related Molecular Chaperone That Dissolves Thermal-aggregated Proteins
Authors: Yano Mihiro , Nakamuta Shinichi , Wu Xueji , Okumura Yuushi , Kido Hiroshi
Published: August 2006

The 14-3-3 proteins are highly conserved molecules that function as intracellular adaptors in a variety of biological processes, such as signal transduction, cell cycle control, and apoptosis. Here, we show that a 14-3-3 protein is a heat-shock protein (Hsp) that protects cells against physiological stress as its new cellular function. We have observed that, in Drosophila cells, the 14-3-3ζ is up-regulated under heat stress conditions, a process mediated by a heat shock transcription factor. As the biological action linked to heat stress, 14-3-3ζ interacted with apocytochrome c, a mitochondrial precursor protein of cytochrome c, in heat-treated cells, and the suppression of 14-3-3ζ expression by RNA interference resulted in the formation of significant amounts of aggregated apocytochrome c in the cytosol. The aggregated apocytochrome c was converted to a soluble form by the addition of 14-3-3ζ protein and ATP in vitro. 14-3-3ζ also resolubilized heat-aggregated citrate synthase and facilitated its reactivation in cooperation with Hsp70/Hsp40 in vitro. Our observations provide the first direct evidence that a 14-3-3 protein functions as a stress-induced molecular chaperone that dissolves and renaturalizes thermal-aggregated proteins.
Irr regulates brucebactin and 2,3-dihydroxybenzoic acid biosynthesis, and is implicated in the oxidative stress resistance and intracellular survival of Brucella abortus
Authors: Martínez Marcela , Ugalde Rodolfo A. , Almirón Marta
Published: August 2006

Brucella abortusfaces iron deprivation in both nature and the host. To overcome this limitation,Brucellasecretes the siderophores 2,3-dihydroxybenzoic acid and brucebactin. A Fur-like protein named Irr has previously been characterized inB. abortus; this protein is present in theα-2 group ofProteobacteriaonly, where it negatively regulates haem biosynthesis when iron is scarce. Additional evidence that Irr also regulates the synthesis of both siderophores is presented here. TranscriptionallacZfusion and chemical determinations revealed that Irr induced the transcription of the operon involved in the synthesis of the catecholic siderophores, which were consequently secreted under conditions of iron limitation. Irr was able to bind the upstream region of the operon, as shown by electrophoretic mobility shift assay. AB. abortus irrmutant showed higher intracellular haem content, catalase activity and resistance to hydrogen peroxide than the wild-type strain. The mutation also improved the replication and survival of iron-depleted bacteria within cultured mammalian cells. Although the pathogenesis ofBrucellacorrelates with its ability to replicate intracellularly, pathogenicity was not attenuated when assayed in a murine model.
EST analysis of cDNA libraries from the entomopathogenic fungus Beauveria (Cordyceps) bassiana. I. Evidence for stage-specific gene expression in aerial conidia, in vitro blastospores and submerged conidia
Authors: Cho Eun-Min , Liu Li , Farmerie William , Keyhani Nemat O.
Published: August 2006

The entomopathogenic fungus Beauveria (Cordyceps) bassiana holds much promise as a pest biological control agent. B. bassiana produces at least three in vitro single cell infectious propagules, including aerial conidia, vegetative cells termed blastospores and submerged conidia, that display different morphological, biochemical and virulence properties. Populations of aerial conidia, blastospores and submerged conidia were produced on agar plates, rich liquid broth cultures and under conditions of nutrient limitation in submerged cultures, respectively. cDNA libraries were generated from mRNA isolated from each B. bassiana cell type and ∼2500 5′ end sequences were determined from each library. Sequences derived from aerial conidia clustered into 284 contigs and 963 singlets, with those derived from blastospores and submerged conidia forming 327 contigs with 788 singlets, and 303 contigs and 1079 contigs, respectively. Almost half (40–45 %) of the sequences in each library displayed either no significant similarity (e value >10−4) or similarity to hypothetical proteins found in the NCBI database. The expressed sequence tag dataset also included sequences representing a significant portion of proteins in cellular metabolism, information storage and processing, transport and cell processes, including cell division and posttranslational modifications. Transcripts encoding a diverse array of pathogenicity-related genes, including proteases, lipases, esterases, phosphatases and enzymes producing toxic secondary metabolites, were also identified. Comparative analysis between the libraries identified 2416 unique sequences, of which 20–30 % were unique to each library, and only ∼6 % of the sequences were shared between all three libraries. The unique and divergent representation of the B. bassiana transcriptome in the cDNA libraries from each cell type suggests robust differential gene expression profiles in response to environmental conditions.
AopP, a type III effector protein of Aeromonas salmonicida, inhibits the NF-κB signalling pathway
Authors: Fehr Désirée , Casanova Carlo , Liverman Amy , Blazkova Hana , Orth Kim , Dobbelaere Dirk , Frey Joachim , Burr Sarah E.
Published: August 2006

Aeromonas salmonicida subsp. salmonicida contains a functional type III secretion system that is responsible for the secretion of the ADP-ribosylating toxin AexT. In this study, the authors identified AopP as a second effector protein secreted by this system. The aopP gene was detected in both typical and atypical A. salmonicida isolates and was found to be encoded on a small plasmid of approximately 6.4 kb. Sequence analysis indicates that AopP is a member of the YopJ family of effector proteins, a group of proteins that interfere with mitogen-activated protein kinase (MAPK) and/or nuclear factor kappa B (NF-κB) signalling pathways. AopP inhibits the NF-κB pathway downstream of IκB kinase (IKK) activation, while a catalytically inactivated mutant, AopPC177A, does not possess this inhibitory effect. Unlike other effectors of the YopJ family, such as YopJ and VopA, AopP does not inhibit the MAPK signalling pathway.