bluuebunny/crossref_metadata_2025 huggingface dataset:
Green, yellow, and orange defect emission from ZnO nanostructures: Influence of excitation wavelength
Authors: Djurišić A. B. , Leung Y. H. , Tam K. H. , Ding L. , Ge W. K. , Chen H. Y. , Gwo S.
Published: March 2006

ZnO commonly exhibits luminescence in the visible spectral range due to different intrinsic defects. In order to study defect emissions, photoluminescence from ZnO nanostructures prepared by different methods (needles, rods, shells) was measured as a function of excitation wavelength and temperature. Under excitation at 325nm, needles exhibited orange-red defect emission, rods exhibited yellow defect emission, while shells exhibited green defect emission. Obvious color change from orange to green was observed for needles with increasing excitation wavelengths, while nanorods (yellow) showed smaller wavelength shift and shells (green) showed no significant spectral shift. Reasons for different wavelength dependences are discussed.
Probing messenger RNA conformational heterogeneity using single-molecule fluorescence anisotropy
Authors: Sinha Deepak , Sastry Srikanth , Shivashankar G. V.
Published: March 2006

In this letter we describe a method to probe biomolecular conformations and their dynamics at the single molecule level. We show, using fluorescence anisotropy based methods, that the hydrodynamic volume of biomolecules captures the intrinsic heterogeneity within a population. Population distributions of conformations and their dynamics are studied by making anisotropy measurements on one molecule at a time within a confocal volume. The mean anisotropy of mRNA is lowered on addition of salt while the spread remains the same. The intrinsic heterogeneity is revealed when conformational transitions are frozen, resulting in a drastic increase in the spread of the anisotropy. These studies reveal that mRNA samples a broad range of conformations.
Giant enhancement of luminescence induced by second-harmonic surface plasmon resonance
Authors: Lin H. Y. , Chen Y. F.
Published: March 2006

Strong ultraviolet luminescence having intensity comparable with device-quality GaN epifilms has been observed in Au nanoparticles. It is identified that the luminescence involves radiative recombination of electrons in band 6 (sp conduction band) with holes in band 4 (secondary top d band), near the L symmetry point. We show that the strong emission is a consequence of the second-harmonic surface plasmon resonance (SHSPR), which is an inherent nature of metallic nanoparticles with high density of surface plasmons. The newly discovered SHSPR is very different from the conventional second-harmonic generation (SHG). In the conventional SHG, it requires an intense incident laser to generate two-photon absorption and radiation. However, for the SHSPR discussed here, we only need a weak pumping source to trigger the second-harmonic absorption of very dense surface plasmons in Au nanoclusters. In addition to Au nanoparticles, we demonstrate that SHSPR provides a very efficient way to enhance the luminescence of a material incorporated with metal nanoparticles. As an example, incorporation of Au nanoparticles into SiO2 nanoparticles can enhance the luminescence intensity by two orders of magnitude. We thus point out that SHSPR can serve as one of the underlying mechanisms responsible for surface-enhanced nonlinear optical phenomena.
Highly sensitive gas sensor based on integrated titania nanosponge arrays
Authors: Zuruzi A. S. , Kolmakov A. , MacDonald N. C. , Moskovits M.
Published: March 2006

Highly sensitive gas sensors were fabricated using nanostructured titania pad arrays. Nanostructured titania (NST) formed is sponge-like consisting of interconnected nanoscale wires and walls, which are made up of anatase nanocrystals. Electrical characterization indicates that contacts were ohmic and NST was highly sensitive to O2. Variations of hundreds of oxygen molecules over a 20μm NST square pad sensing element were detected at 250°C. The NST-based sensor operates at lower temperatures, has fast response time, and superior sensitivity relative to oxygen sensors based on porous undoped titania reported in the literature.
Raman study of N+-implanted ZnO
Authors: Wang J. B. , Zhong H. M. , Li Z. F. , Lu Wei
Published: March 2006

Raman scattering has been used to study the influence of nitrogen, a potential acceptor in ZnO, on the lattice dynamics of ZnO. It is found that N+ implantation increased the lattice disorder and induced some vibration modes to be Raman active at 275, 504, and 644cm−1, respectively. Based on theoretical and experimental study, the origin of the additional Raman peak at about 275cm−1 is attributed to the vibration of Zn atoms, where part of its first nearest neighbor O atoms are replaced by N atoms in the crystal lattice.
Temperature-dependent strain relaxation of the AlGaN barrier in AlGaN∕GaN heterostructures with and without Si3N4 surface passivation
Authors: Chen D. J. , Zhang K. X. , Tao Y. Q. , Wu X. S. , Xu J. , Zhang R. , Zheng Y. D. , Shen B.
Published: March 2006

The temperature dependence of strain relaxation in Al0.22Ga0.78N layers, with and without a Si3N4 surface passivation layer, was investigated at temperatures from room temperature to 813K using high-resolution x-ray diffraction. A small strain relaxation occurs in the unpassivated Al0.22Ga0.78N layers at high temperature. After passivating, an additional in-plane tensile strain and an initial increase of the residual tensile strain with increasing temperature were observed in Al0.22Ga0.78N layers, and at higher temperatures the residual tensile strain only decreases slightly in the 100-nm-thick Al0.22Ga0.78N layer, but a pronounced strain relaxation occurs in the 50-nm-thick one. The degree of strain relaxation of the passivated 50-nm-thick Al0.22Ga0.78N layer increases by about 33%, which results in the two-dimensional electron gas concentration reduction of about 16% at the whole temperature range in our measurements.
Being Feared: Masculinity and Race in Public Space
Authors: Day Kristen
Published: March 2006

Research on fear of crime typically examines the perceptions of those who fear, emphasizing women's experiences of vulnerability in public space. In this paper, I invert this practice to examine instead men's experiences of being feared in public spaces. Drawing on interviews with 82 male college students, I use a social constructionist approach to examine how men's experiences of being feared interact with men's formation of racial identities and the racialization of public places. Fear is a key mechanism for justifying and maintaining race privilege and exclusion. The experience and interpretation of being feared (or not feared) in public space intersects with men's construction of gender and race identities, and the ways that men assign racial meanings to public places. This paper examines these processes and proposes strategies for challenging fear and the exclusion it supports.
Planning Policy? Between Long-Term Planning and Zoning Amendments in the Israeli Planning System
Authors: Alfasi Nurit
Published: March 2006

The Israeli planning system, like many other Western systems, is a regulatory system, meaning that statutory land-use plans are attempts at both setting long-term planning policy and defining planning rights. However, planning in Israel faces a growing gap between its official structure and what is actually implemented. Mainly, an inconsistency exists between the formal top-to-bottom approach of the system and the flexible dynamics that occur in practice. In this paper I focus on the prevalent local zoning amendment procedure and examine its background as well as its implications. Based on this, the paper claims that in Israel, the tension between certainty and flexibility in planning creates a spatially disturbed behavior, which actively tests the bans and limits of existing possibilities.
Decontextualised? Dissociated? Detached? Mapping the Networks of Bioinformatics Exchange
Authors: Greenhough Beth
Published: March 2006

The author reviews debates surrounding the Icelandic government's Act on a Health Sector Database (139/1998), which provided for the licensing of a private company to build and operate a centralised database of Icelandic medical records for use in gene-discovery research. Using the concept of the ‘boundary object’ drawn from actor-network theory, the author argues that, through their exploitation as bodily commodities, medical records are actively engaged in redefining existing boundaries between medical and scientific space, between civic and individual concerns, and between human subjects and scientific objects.
Bees, Butterflies, and Bacteria: Biotechnology and the Politics of Nonhuman Friendship
Authors: Bingham Nick
Published: March 2006

The author seeks to decentre some already familiar geographies of biotechnology. By asking, with respect to genetically modified (GM) crops, not ‘what is the new?’, but ‘where is the new?’, the intention is to redirect attention (at least briefly) away from the GM technique or genetically modified object and its supposed properties, to the world to which that technique or object is being added. This in turn allows the question concerning GM to be approached from new directions, for example, via the routes taken into the controversy by three specific organisms. Not fully taken into account in the calculations of the biotechnology industry, the honey bee, the Monarch butterfly, and the bacterium Bacillus thuringiensis have all, in very different ways, made their presence felt as they literally and metaphorically encountered GM. In an attempt to do justice to these marginalised lifeforms, the forms of life of which they are part, and the biopolitical questions which they raise, the works of Jacques Derrida on friendship and animality, Jean-Luc Nancy on being with, and Bruno Latour on making things public, are brought into conversation. It is suggested that together what they offer is a way of thinking ourselves as collectively in the midst of things.
Invited Paper. Aspects of Surface Science in Australian Industry
Authors: Smart RS , Baker BG , Turner PS
Published: March 2006

Three techniques giving information on composition and chemical states of atoms in the first few monolayers of a surface are described: X-ray photoelectron spectroscopy, Auger electron spectroscopy and secondary ion mass spectrometry. Their application to industrial problem solving, optimization of process or materials, and long-term research and development is illustrated in three case studies. Analysis of the effectiveness of surface treatments for steel pipe before fusion-bonded epoxy application revealed thin phosphate layers and partial separation of chromate from silicate in passivation. Aluminosilicate layers on glacial quartz used for glass making were detected giving handling and melting difficulties. These problems were overcome by changes to process conditions resulting from the surface investigation and plant trials. Exploratory research has produced a Fischer-Tropsch catalyst effective in totally converting CO and H2 (H2/CO ≥ 1) into short-chain alkenes at 300°, with H2O and CO2 (H2O/CO2 = 2) as by-products. The catalyst is made from natural bauxite. Characterization of the surface properties by surface analysis and electron microscopy is described. Examples of other projects for Australian industry are summarized.
Borane Chemistry. II. Kinetics and Mechanism of Reaction of Chlorodipentylborane With Some Aldehydes
Authors: Bolton R , Gates PN , Jones SAW
Published: March 2006

Chlorodipentylborane causes extensive polymerization of aliphatic aldehydes , even in low concentrations and at 273 K, but its reaction with aromatic aldehydes is more controlled, and allows the study of the rates and products of its addition to a range of these aldehydes by using 1H, 11B and 13C n.m.r. spectroscopy. The second-order rate constant (282 K) for the formation of pent-1-ene increases as the para substituent in benzaldehyde changes in the sequence NMe2, OMe , H, Cl , NO2; the derived Hammett p value (1.6; CDCl3, 282 K) suggests a transition state involving hydride ion transfer to carbonyl oxygen. The significance of an adduct as an intermediate in the reaction is discussed.
The Acidity of Norfloxacin
Authors: Buckingham DA , Clark CR , Nangia A
Published: March 2006

A 1H and 13C n.m.r. investigation of the fluoroquinolone carboxylic acid Norfloxacin (1) in D2O has allowed three pKa values to be determined, which correspond to carboxylic acid oxygen (pKaD 0.6), pyridone nitrogen (pKaD 6.9) and 'external' piperazine nitrogen (pKaD 9.25) ionization.
The Cerium(IV)-Induced Decomposition of Peroxymonosulfate: Acid Dependence and Peroxydisulfate Formation
Authors: Marsh C , Zhang Z , Edwards JO
Published: March 2006

An improved rate law for the CeIV-induced decomposition of HOOSO3- in aqueous H2SO4 has been established by study of the rate as a function of acidity. In aqueous HClO4 the rate is much faster but a rate law could not be obtained. Peroxydisulfate, by a variant of the AsIII and FeII analysis of the redox system, has been shown to be formed in the amount of half of the CeIV lost. A free-radical chain mechanism is postulated.
A Comparison of the Reactions of Some Ethyl N-Arylcarbamates With Those of the Corresponding Acetanilides. II. Amidomethylation With N-Hydroxy-methylphthalimide
Authors: Rosevear J , Wilshire JFK
Published: March 2006

The reactions of some ethyl N- arylcarbamates and of the corresponding acetanilides towards 1 equiv. of N-hydroxymethylphthalimide in concentrated sulfuric acid at 50° have been compared with one another. In the case of certain para-substituted compounds, amidomethylation occurs more readily ortho to the carbamate group than to the N-acetyl group. The diagnostic use of (D6)benzene as a 1H n.m.r. solvent, particularly for the structural elucidation of the ortho-( phthalimidomethyl )- phenylcarbamates and -acetanilides, is reported. Acidic treatment of the ortho -( phthalimidomethyl ) phenylcarbamates, but not of the corresponding acetanilides, gave 8-substituted isoindolo [1,2-b]quinazolin-12(10H)-ones. Amidomethylation of the parent anilines is also described.
Dihydroindol-7(6H)-ones and 6,7-Dihydropyrrolo[2,3-c]azepine-4,8(1H,5H)-dione
Authors: Kasum B , Prager RH , Tsopelas C
Published: March 2006

3-Methylcyclohexenones may be converted into dihydroindol-7(6H)-ones by conversion of the epoxide into the 2-benzylamino-3-methylcyclohexenone, which reacts with dimethyl- formamide dimethyl acetal to give N-benzyldihydroindol-7(6H)-ones. The limitations of the process are discussed, as is the failure to convert the dihydroindol-7(6H)-ones into dihydropyrroloazepinediones by Beckmann or Schmidt rearrangements. An example of the latter compounds was made by a simple procedure from pyrrolecarboxylic acid.
The Chemistry of Phthalide-3-carboxylic Acid. VII. Reaction With Isoquinoline Derivatives
Authors: Donati C , Hung TV , Prager RH
Published: March 2006

Phthalide-3-carboxylic acid has been decarboxylated in the presence of isoquinoline, 1-chloroisoquinoline and isoquinoline N-oxides to give low yields of compounds resulting from alkylation of the isoquinoline heterocycle at C1 with a phthalidyl group. Attempted Barton decarboxylation-alkylation in the presence of isoquinolinium salts was unsuccessful.
Facile Metal-Directed Synthesis and Crystal Structure of a New Amino Acid Ester, Methyl 3-[(2-Aminoethyl)amino]-2-[(2-aminoethyl)aminomethyl]propionate, as the Copper(II) Complex
Authors: Bernhardt PV , Lawrance GA , Skelton BW , White AH
Published: March 2006

Condensation of bis (ethane-1,2-diamine) copper(II) perchlorate with formaldehyde and diethyl malonate in basic methanol generates the new amino acid ester complex (ethyl hydrogen bis [(2-aminoethyl ) aminomethyl ] malonate )copper(II) perchlorate, [Cu(1)] (ClO4)2. Base- catalysed ester hydrolysis and decarboxylation in methanol of[Cu(1)]2+ yields, with reesterification, (methyl 3-[(2-aminoethy )amino]-2-[(2-aminoethyl) aminomethyl ]propionate)copper(II) perchlorate, [Cu(2)](ClO4)2. This complex crystallizes in the monoclinic space group P21/c, a 12.763(6), b 9.176(2), c 16.32(2)Ǻ, β 112.49 (6)°, Z 4, R 0.054 for 2626 independent 'observed' reflections. The copper ion lies in a near plane of four nitrogens with perchlorates occupying axial sites.
Relaxation Processes in the N-Methyl Group of 1,2,2,6,6-Pentamethylpiperidine
Authors: Rae ID , Woolcock ML
Published: March 2006

Relaxation times (T1) and methyl-methyl nuclear Overhauser effects were measured for 1H, 13C and 2H nuclei in 1,2,2,6,6-pentamethylpiperidine and its N-CHD2 analogue which was synthesized by LiAlD4 reduction of the N-CHO compound. The relaxation pathways for hydrogens of the N-CH3 group were estimated to be as follows: spin-rotation 0.046 s-1, dipole-dipole within N-methyl 0.069 s-1, and dipole-dipole with the hydrogens of the C- methyls 0.027 s-1. The 1H{1H) Overhauser effect at the N-CH3 was 7.6%.
The Next Iteration Factor (NIF) Method for Calculating Equilibrium Conditions in Subsurface Waters, for the Isolation of Microorganisms From Petroleum Reservoirs
Authors: Chaston S , Grassia GS , Sheehy AJ
Published: March 2006

A mathematically simple program, based on the next iteration factor (NIF) method, of calculating species concentrations in the 10-component system Na-K-Mg-Ca-Sr-H-Cl-SO4-OH-HCO3-CO3-CO2-BO2-H2O is presented. This method does not have the programming and convergence problems associated with established methods based on Newton- Raphson and free energy minimization techniques. We developed the new program in order to establish the physicochemical conditions of extreme environments, such as petroleum reservoirs, in which resident microorganisms may exist. The knowledge of the conditions that we obtained from these calculations has led to the isolation of thermophilic bacteria and archaea not previously recovered from deep subsurface environments such as petroleum reservoirs.
Synthesis, Crystal Structure and Intramolecular Interactions of 2-Methyl-3-(2-Methylphenyl)but-1-ene-1,1-dicarbonitrile (MMBD)
Authors: Grabowski SJ , Grabowski SJ , Wilamowski J , Wilamowski J , Osman D , Osman D , Sepiol JJ , Sepiol JJ , Rodier N , Rodier N
Published: March 2006

2-Methyl-3-(2-methylphenyl)but-1-ene-1,1-dicarbonitrile (MMBD) has been synthesized from 3-(o-tolyl)butan-2-one. The crystal and molecular structure of this compound was solved by X-ray diffraction, with estimated standard deviations ≤ � 0.005 Ǻ for bond lengths, and ≤ 0.3° for bond angles. Intramolecular interactions of the C≡N group, i.e. of the C-H...N, C-H...π (electrons) and C-H...C type, were observed, and the possibility of weak intramolecular hydrogen bridges in the molecule of MMBD was considered. The geometry of the MMBD molecule from AM1 calculations was compared with the X-ray structure.
The Structures of New Peptides From the Australian Red Tree Frog 'Litoria rubella'. The Skin Peptide Profile as a Probe for the Study of Evolutionary Trends of Amphibians
Authors: Steinborner ST , Wabnitz PA , Waugh RJ , Bowie JH , Gao CW , Tyler MJ , Wallace JC
Published: March 2006

Seventeen peptides have been isolated and characterized from specimens of the red tree frog 'Litoria rubella', collected from 15 locations throughout Australia. These can be classified into two families of peptides, viz. ( i ) the tryptophyllins L, of which Phe Pro Trp Leu (NH2), Phe Pro Trp Pro (NH2) and pGlu Phe Pro Trp Pro (NH2) are the major constituents, (ii) two types of rubellidins, the first of which is unique to 'Litoria rubella' [e.g. Val Asp Phe Phe Ala (OH)], and the second [e.g. Gly Leu Gly Asp Ile Leu Gly Leu Leu Gly Leu (NH2)], containing peptides of the caeridin type (like those isolated from Litoria caerulea and Litoria splendida). These peptides show no significant antimicrobial activity. The tryptophyllins are thought to be neuromodulators or neurotransmitters, but the roles of the anionic rubellidin peptides in the amphibian integument are not understood. A comparison of the skin peptide profiles of live specimens of 'Litoria rubella' collected from different locations suggests that there are a number of discrete populations (perhaps different species or subspecies) in ( i ) an area from Kakadu National Park to the Adelaide River in the Northern Territory, (ii) in and around Alice Springs, (iii) in the north of South Australia, and (iv) in several areas of the Kimberley region of Western Australia. In addition, there appear to be evolving populations along the eastern seaboard of Queensland.
Formation of Cyclopent[hi]acephenanthrylene From 1,2-, 1,3-, 1,4- and 2,3-Triphenylenedicarboxylic Acid Derivatives on Flash Vacuum Pyrolysis at >900°C
Authors: Banciu MD , Brown RFC , Coulston KJ , Eastwood FW , Jurss C , Mavropoulos I , Stanescu M , Wiersum UE
Published: March 2006

The processes involved in the conversion of triphenylene , C18H12, into cyclopent [hi] acephenanthrylene, C18H10, under flash vacuum pyrolytic conditions at 900-1100°C have been investigated by pyrolysing triphenylene-1,2- and -2,3-dicarboxylic anhydrides and diallyl triphenylene-1,3- and -1,4-dicarboxylates to give the corresponding didehydrotriphenylenes in the gas phase. These didehydro intermediates are converted into mixtures of cyclopent [hi] acephenanthrylene and triphenylene in different yields and proportions. Pyrolysis of 9,10-diethynylphenanthrene. C18H10, yields cyclopent [hi] acephenanthrylene in good yield. Pyrolysis of 1-nitrotriphenylene and allyl triphenylene-2-carboxylate to give the triphenylen-1-yl and -2-yl radicals leads to formation of the same products. Mechanisms involving radical rearrangements (C18H11 species) and benzyne-cyclopentadienylidenecarbene and ethyne-ethenylidene rearrangements (C18H10 species) are discussed.
Structural Systematics of Rare Earth Complexes. IX. Tris(nitrato-O,O')(bidentate-N,N')lutetium(III), N,N'-Bidentate Equals 2,2'-Bipyridine or 1,10-Phenanthroline
Authors: Kepert DL , Semenova LI , Sobolev AN , White AH
Published: March 2006

Room-temperature single-crystal X-ray structure determinations of the title compounds, namely, [(ONO2)3Lu(N,N'-bidentate)2], N,N'-bidentate = 'bpy' = 2,2'-bipyridine or 'phen' = 1,10-phenan-throline, are recorded. The complexes are isomorphous with their previously studied lanthanum analogues, being orthorhombic, Pbcn, a 16.517(3), b 9.111(3), c 15.080(3) Ǻ, Z = 4 f.u., and monoclinic, C2/c, a 11.186(7), b 17.785(13), c 12.972(10) Ǻ, β 100.27(5)°, Z = 4 f.u., with R (on |F|) being 0.046 and 0.045 for 1339 and 2097 independent 'observed' (I > 3σ(I)) reflections respectively. The stereochemistries about the metal atoms are also similar, Lu(O2)3(N2)2, the metal atom in each case lying on a crystallographic twofold axis, which also passes through the axis of one of the bidentate nitrate groups; the latter, unlike their counterparts in the La/bpy complexes are not disordered.
Cleavage of a Bicyclo[2.2.1]hepta-2,5-dienyl Ligand During Transfer From Nickel to Ruthenium. X-Ray Structure of Ru2{μ-η1,O:η2-C(CO2Me)=CHC(O) Ome }(CO)4Cp
Authors: Bruce MI , Hall BC , Skelton BW , White AH
Published: March 2006

The reaction between Ru3(CO)12 and Ni{η1,η2-C5H5C2(CO2Me)2}Cp afforded orange Ru2{μ-η1,O:η2-C(CO2Me)=CHC(O) Ome }(CO)4Cp(43%) as the only isolable complex. An X-ray structure determination showed that a C(CO2Me)=CHC(O) OMe ligand bridges an Ru-Ru bond [2.7744(9) Ǻ] via a μ-η1:η2-vinyl interaction and by coordination of one of the ester CO groups [ Ru -O 2.148(2) Ǻ]. One ruthenium atom bears three terminal CO ligands and the other ruthenium atom has one CO ligand and an η5-C5H5 group. In the reaction, transfer of Cp and the vinyl group (from the bicyclo [2.2.1]hepta-2,5-dienyl ligand originally present) from nickel to ruthenium has occurred.
Structural basis of hepatocyte growth factor/scatter factor and MET signalling
Authors: Gherardi Ermanno , Sandin Sara , Petoukhov Maxim V. , Finch John , Youles Mark E. , Öfverstedt Lars-Göran , Miguel Ricardo N. , Blundell Tom L. , Vande Woude George F. , Skoglund Ulf , Svergun Dmitri I.
Published: March 2006

The polypeptide growth factor, hepatocyte growth factor/scatter factor (HGF/SF), shares the multidomain structure and proteolytic mechanism of activation of plasminogen and other complex serine proteinases. HGF/SF, however, has no enzymatic activity. Instead, it controls the growth, morphogenesis, or migration of epithelial, endothelial, and muscle progenitor cells through the receptor tyrosine kinase MET. Using small-angle x-ray scattering and cryo-electron microscopy, we show that conversion of pro(single-chain)HGF/SF into the active two-chain form is associated with a major structural transition from a compact, closed conformation to an elongated, open one. We also report the structure of a complex between two-chain HGF/SF and the MET ectodomain (MET928) with 1:1 stoichiometry in which the N-terminal and first kringle domain of HGF/SF contact the face of the seven-blade β-propeller domain of MET harboring the loops connecting the β-strands b–c and d–a, whereas the C-terminal serine proteinase homology domain binds the opposite “b” face. Finally, we describe a complex with 2:2 stoichiometry between two-chain HGF/SF and a truncated form of the MET ectodomain (MET567), which is assembled around the dimerization interface seen in the crystal structure of the NK1 fragment of HGF/SF and displays the features of a functional, signaling unit. The study shows how the proteolytic mechanism of activation of the complex proteinases has been adapted to cell signaling in vertebrate organisms, offers a description of monomeric and dimeric ligand-receptor complexes, and provides a foundation to the structural basis of HGF/SF-MET signaling.
A systematic screen of β
2
-microglobulin and insulin for amyloid-like segments
Authors: Ivanova Magdalena I. , Thompson Michael J. , Eisenberg David
Published: March 2006

Identifying sequence determinants of fibril-forming proteins is crucial for understanding the processes causing >20 proteins to form pathological amyloid depositions. Our approach to identifying which sequences form amyloid-like fibrils is to screen the amyloid-forming proteins human insulin and β
2
-microglobulin for segments that form fibrils. Our screen is of 60 sequentially overlapping peptides, 59 being six residues in length and 1 being five residues, covering every noncysteine-containing segment in these two proteins. Each peptide was characterized as amyloid-like or nonfibril-forming. Amyloid-like peptides formed fibrils visible in electron micrographs or needle-like microcrystals showing a cross-β diffraction pattern. Eight of the 60 peptides (three from insulin and five from β
2
-microglobulin) were identified as amyloid-like. The results of the screen were used to assess the computational method, and good agreement between prediction and experiments was found. This agreement suggests that the pair-of-sheets, zipper spine model on which the computational method is based is at least approximately correct for the structure of the fibrils and suggests the nature of the sequence signal for formation of amyloid-like fibrils.
Distance and ratio effects in the flanker task are due to different mechanisms
Authors: Mattler Uwe
Published: March 2006

When participants must respond to a relevant central target and ignore irrelevant flanking stimuli the flanking stimuli produce a compatibility effect, with increased response speed and accuracy on compatible as compared to incompatible trials. This flanker effect is larger when compatible trials are more frequent than incompatible trials (the ratio effect). A potential explanation of this ratio effect is that the occurrence of frequent incompatible trials causes the focus of spatial attention to be set narrower than when there are frequent compatible trials. The present investigation tests this hypothesis by comparing the flanker effect with near and far flankers. The hypothesis predicts that the flanker distance should modulate the ratio effect more when incompatible trials are frequent than when compatible trials are frequent. The results, however, show the opposite pattern: Distance effects are larger in conditions with frequent compatible trials. Moreover, the effect of distance but not the ratio effect was eliminated when flanker distance remained fixed across blocks of trials, and also when participants had to attend to flanker stimuli in a go–no-go task. These results suggest that the ratio effect does not result from an adjustment of the focus of spatial attention.
Long-Term Inhibition of Return for Spatial Locations: Evidence for a Memory Retrieval Account
Authors: Wilson Daryl E. , Castel Alan D. , Pratt Jay
Published: March 2006

It has generally been accepted that attention is inhibited from returning to previously attended locations, and that this inhibition of return (IOR) lasts just two or three seconds. Recently, Tipper, Grison, and Kessler (2003) showed that IOR can occur over much longer periods of time provided the inhibition is encoded with a context-rich event. Here we examine standard (i.e., typical time range) and long-term IOR within the same experimental paradigm as a means to compare their properties. Experiment 1 used the simple displays typical of cueing paradigms and revealed that both standard and long-term IOR can be obtained under such conditions. Experiment 2 showed that both standard and long-term IOR occurred when there was incongruence between the required response on the current trial and that stored in memory. Furthermore, IOR was not produced when there was incongruence between a target feature (colour) of the current trial and that stored in memory. These results are consistent with a memory retrieval account of IOR and suggest that the same inhibitory mechanism may underlie both standard and long-term IOR.
Strong laws for weighted sums of i.i.d. random variables
Authors: Cai Guang-hui
Published: March 2006

Strong laws are established for linear statistics that are weighted sums of a random sample. We show extensions of the Marcinkiewicz-Zygmund strong laws under certain moment conditions on both the weights and the distribution. The result obtained extends and sharpens the result of Sung.
Compartmentalization of the Exocyst Complex in Lipid Rafts Controls Glut4 Vesicle Tethering
Authors: Inoue Mayumi , Chiang Shian-Huey , Chang Louise , Chen Xiao-Wei , Saltiel Alan R.
Published: March 2006

Lipid raft microdomains act as organizing centers for signal transduction. We report here that the exocyst complex, consisting of Exo70, Sec6, and Sec8, regulates the compartmentalization of Glut4-containing vesicles at lipid raft domains in adipocytes. Exo70 is recruited by the G protein TC10 after activation by insulin and brings with it Sec6 and Sec8. Knockdowns of these proteins block insulin-stimulated glucose uptake. Moreover, their targeting to lipid rafts is required for glucose uptake and Glut4 docking at the plasma membrane. The assembly of this complex also requires the PDZ domain protein SAP97, a member of the MAGUKs family, which binds to Sec8 upon its translocation to the lipid raft. Exocyst assembly at lipid rafts sets up targeting sites for Glut4 vesicles, which transiently associate with these microdomains upon stimulation of cells with insulin. These results suggest that the TC10/exocyst complex/SAP97 axis plays an important role in the tethering of Glut4 vesicles to the plasma membrane in adipocytes.
Constructing quantitative models from qualitative mutant phenotypes: preferences in selecting sensory organ precursors
Authors: Hsu Chao-Ping , Lee Pei-Hsuan , Chang Ching-Wei , Lee Cheng-Tsung
Published: March 2006

Motivation: To study biology from the systems level, mathematical models that describe the time-evolution of the system offer useful insights. Quantitative information is required for constructing such models, but such information is rarely provided.

Results: We propose a scheme—based on random searches over a parameter space, according to criteria set by qualitative experimental observations—for inferring quantitative parameters from qualitative experimental results. We used five mutant constraints to construct genetic network models for sensory organ precursor formation in Drosophila development. Most of the models were capable of generating expression patterns for the gene Enhancer of split that were compatible with experimental observations for wild type and two Notch mutants. We further examined factors differentiating the neural fate among cells in a proneural cluster, and found two opposite driving forces that bias the choice between middle cells and the peripheral cells. Therefore, it is possible to build numerical models from mutant screening and to study mechanisms behind the complicated network.

Contact:  cherri@sinica.edu.tw

Supplementary information: Supplementary data are available at Bioinformatics online.
TOPAAS, a Tomato and Potato Assembly Assistance System for Selection and Finishing of Bacterial Artificial Chromosomes
Authors: Peters Sander A. , van Haarst Jan C. , Jesse Taco P. , Woltinge Dennis , Jansen Kim , Hesselink Thamara , van Staveren Marjo J. , Abma-Henkens Marleen H.C. , Klein-Lankhorst René M.
Published: March 2006

We have developed the software package Tomato and Potato Assembly Assistance System (TOPAAS), which automates the assembly and scaffolding of contig sequences for low-coverage sequencing projects. The order of contigs predicted by TOPAAS is based on read pair information; alignments between genomic, expressed sequence tags, and bacterial artificial chromosome (BAC) end sequences; and annotated genes. The contig scaffold is used by TOPAAS for automated design of nonredundant sequence gap-flanking PCR primers. We show that TOPAAS builds reliable scaffolds for tomato (Solanum lycopersicum) and potato (Solanum tuberosum) BAC contigs that were assembled from shotgun sequences covering the target at 6- to 8-fold coverage. More than 90% of the gaps are closed by sequence PCR, based on the predicted ordering information. TOPAAS also assists the selection of large genomic insert clones from BAC libraries for walking. For this, tomato BACs are screened by automated BLAST analysis and in parallel, high-density nonselective amplified fragment length polymorphism fingerprinting is used for constructing a high-resolution BAC physical map. BLAST and amplified fragment length polymorphism analysis are then used together to determine the precise overlap. Assembly onto the seed BAC consensus confirms the BACs are properly selected for having an extremely short overlap and largest extending insert. This method will be particularly applicable where related or syntenic genomes are sequenced, as shown here for the Solanaceae, and potentially useful for the monocots Brassicaceae and Leguminosea.
Abundantly and Rarely Expressed Lhc Protein Genes Exhibit Distinct Regulation Patterns in Plants
Authors: Klimmek Frank , Sjödin Andreas , Noutsos Christos , Leister Dario , Jansson Stefan
Published: March 2006

We have analyzed gene regulation of the Lhc supergene family in poplar (Populus spp.) and Arabidopsis (Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar (Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting-like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.
How does activation loop phosphorylation modulate catalytic activity in the cAMP‐dependent protein kinase: A theoretical study
Authors: Cheng Yuhui , Zhang Yingkai , McCammon J. Andrew
Published: March 2006

Phosphorylation mediates the function of many proteins and enzymes. In the catalytic subunit of cAMP‐dependent protein kinase, phosphorylation of Thr 197 in the activation loop strongly influences its catalytic activity. In order to provide theoretical understanding about this important regulatory process, classical molecular dynamics simulations and ab initio QM/MM calculations have been carried out on the wild‐type PKA–Mg2 ATP–substrate complex and its dephosphorylated mutant, T197A. It was found that pThr 197 not only facilitates the phosphoryl transfer reaction by stabilizing the transition state through electrostatic interactions but also strongly affects its essential protein dynamics as well as the active site conformation.
Computer‐aided NMR assay for detecting natively folded structural domains
Authors: Hondoh Takayuki , Kato Atsushi , Yokoyama Shigeyuki , Kuroda Yutaka
Published: March 2006

Structural genomics projects require strategies for rapidly recognizing protein sequences appropriate for routine structure determination. For large proteins, this strategy includes the dissection of proteins into structural domains that form stable native structures. However, protein dissection essentially remains an empirical and often a tedious process. Here, we describe a simple strategy for rapidly identifying structural domains and assessing their structures. This approach combines the computational prediction of sequence regions corresponding to putative domains with an experimental assessment of their structures and stabilities by NMR and biochemical methods. We tested this approach with nine putative domains predicted from a set of 108 Thermus thermophilus HB8 sequences using PASS, a domain prediction program we previously reported. To facilitate the experimental assessment of the domain structures, we developed a generic 6‐hour His‐tag‐based purification protocol, which enables the sample quality evaluation of a putative structural domain in a single day. As a result, we observed that half of the predicted structural domains were indeed natively folded, as judged by their HSQC spectra. Furthermore, two of the natively folded domains were novel, without related sequences classified in the Pfam and SMART databases, which is a significant result with regard to the ability of structural genomics projects to uniformly cover the protein fold space.
Identification of phosphorylation sites in glycine N‐methyltransferase from rat liver
Authors: Luka Zigmund , Ham Amy‐Joan L. , Norris Jeremy L. , Yeo Eui‐Ju , Yermalitsky Valery , Glenn Byron , Caprioli Richard M. , Liebler Daniel C. , Wagner Conrad
Published: March 2006

Previous studies have shown that rat glycine N‐methyltransferase (GNMT) is phosphorylated in vivo, and could be phosphorylated in vitro on serine residues with a significant increase of enzyme activity, but no phosphorylation sites were identified. In this work the identification of the specific phosphorylation sites of rat GNMT is reported. Three different preparations of rat GNMT were analyzed: (1) purified from liver by standard methods of protein purification, (2) prepared from isolated hepatocytes and from liver tissue by immunoprecipitation, and (3) recombinant protein expressed in Escherichia coli. We measured the molecular weights of protein isoforms using electrospray mass spectrometry and used liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) of peptides resulting from tryptic and chymotryptic digests. We also performed chemical analysis of phosphoamino acids and protein sequencing. In all samples, the phosphorylated serine residues 71, 182, and 241 were found. In GNMT prepared from liver tissue and hepatocytes an S9 additional residue was found to be phosphorylated. In hepatocytes and in recombinant GNMT S139 was detected. Serine 9 was also identified as a target for cAMP‐dependent protein kinase in vitro. The positions of these phosphorylated residues in the tertiary structure of GNMT indicate their possible effect on enzyme conformation and activity.
Repeat protein architectures predicted by a continuum representation of fold space
Authors: Hausrath Andrew C. , Goriely Alain
Published: March 2006

It is an open question whether nature has utilized all possible protein folds. For a simple protein architecture, the helical repeats, we report a method to address this question based on a mapping between the set of repetitive curves and a space of parameters specifying the curve. The exploration of the parameter space for a particular architecture enables a systematic exploration of the fold space for that protein architecture. In a planar subspace of the parameter space of helical repeats we have identified points corresponding to both naturally occurring folds and potential folds not observed so far.
Crystal structure of the DUF16 domain of MPN010 from Mycoplasma pneumoniae
Authors: Shin Dong Hae , Kim Jeong‐Sun , Yokota Hisao , Kim Rosalind , Kim Sung‐Hou
Published: March 2006

We have determined the crystal structure of the DUF16 domain of unknown function encoded by the gene MPN010 of Mycoplasma pneumoniae at 1.8 Å resolution. The crystal structure revealed that this domain is composed of two separated homotrimeric coiled‐coils. The shorter one consists of 11 highly conserved residues. The sequence comprises noncanonical heptad repeats that induce a right‐handed coiled‐coil structure. The longer one is composed of approximately nine heptad repeats. In this coiled‐coil structure, there are three distinguishable regions that confer unique structural properties compared with other known homotrimeric coiled‐coils. The first part, containing one stutter, is an unusual phenylalanine‐rich region that is not found in any other coiled‐coil structures. The second part is a highly conserved glutamine‐rich region, frequently found in other trimeric coiled‐coil structures. The last part is composed of prototype heptad repeats. The phylogenetic analysis of the DUF16 family together with a secondary structure prediction shows that the DUF16 family can be classified into five subclasses according to N‐terminal sequences. Based on the structural comparison with other coiled‐coil structures, a probable molecular function of the DUF16 family is discussed.
Stagonospora nodorum: cause of stagonospora nodorum blotch of wheat
Authors: SOLOMON PETER S. , LOWE ROHAN G. T. , TAN KAR‐CHUN , WATERS ORMONDE D. C. , OLIVER RICHARD P.
Published: March 2006

Stagonospora nodorum is an important pathogen of wheat and related cereals, causing both a leaf and glume blotch. This review summarizes recent advances in our understanding of taxonomy, control and pathogenicity of this species.

Taxonomy:   Stagonospora (syn. Septoria) nodorum (Berk.) Castell. and Germano [teleomorph: Phaeosphaeria (syn. Leptosphaeria) nodorum (Müll.) Hedjar.], kingdom Fungi, phylum Ascomycota, subphylum Euascomycota, class Dothideomycetes, order Pleosporales, family Phaeosphaeriaceae, genus Phaeosphaeria, species nodorum.

Host range:   Wheat, Triticum aestivum, T. durum, Triticale, are the main hosts but other cereals and wild grasses have been reported to harbour S. nodorum. Disease symptoms are lens‐shaped necrotic lesions on leaves, girdling necrosis on stems (especially the nodes, hence ‘nodorum’) and lesions on glumes. Mature lesions produce pycnidia scattered throughout the lesions, especially as tissue senesces.

Useful websites:   http://ocid.nacse.org/research/deephyphae/htmls/asco_taxlist_spat.html (taxonomic information), http://ohioline.osu.edu/ac‐fact/0002.html (disease information), http://wwwacnfp.murdoch.edu.au/ (ACNFP homepage), http://www.broad.mit.edu/annotation/fungi/stagonospora_nodorum/index.html (genome sequence homepage), http://cogeme.ex.ac.uk/efungi/ (genome sequence annotation and analysis).
A combination of a transforming growth factor-β antagonist and an inhibitor of cyclooxygenase is an effective treatment for murine pulmonary tuberculosis
Authors: Hernández-Pando R , Orozco-Esteves H , Maldonado H A , Aguilar-León D , Vilchis-Landeros M M , Mata-Espinosa D A , Mendoza V , López-Casillas F
Published: March 2006

Transforming growth factor-beta (TGF-β) and prostaglandins (PG) regulate the cell-mediated immune response, so it has been proposed that they affect the progression of pulmonary tuberculosis. Here we report that the administration of soluble betaglycan, a potent TGF-β antagonist, and niflumic acid, a PG synthesis inhibitor, during the chronic phase of experimental murine tuberculosis enhanced Th1 and decreased Th2 cytokines, increased the expression of iNOS and reduced pulmonary inflammation, fibrosis and bacillary load. This immunotherapeutic approach resulted in significant control of the disease comparable to that achieved by anti-microbial treatment alone. Importantly, the combination of immunotherapy and anti-microbials resulted in an accelerated clearance of bacilli from the lung. These results confirm that TGF-β and PG have a central pathophysiological role in the progression of pulmonary tuberculosis in the mouse and suggest that the addition of immunotherapy to conventional anti-microbial drugs might result in improved treatment of the disease.
Presence of IgE+ cells in human placenta is independent of malaria infection or chorioamnionitis
Authors: Rindsjö E , Varli I Hulthén , Ofori M F , Lundquist M , Holmlund U , Papadogiannakis N , Scheynius A
Published: March 2006

We have shown previously that numerous IgE+ macrophage-like cells are present in the villous stroma of full term placenta and that there was no difference in the amount of IgE+ cells between allergic and non-allergic mothers. The presence of such an abundant number of IgE+ cells in the placenta in allergic as well as non-allergic women suggests that the IgE is of some importance for a successful pregnancy outcome. Here we have investigated the IgE-pattern in 59 placentas from second and third trimesters from Sweden with different degrees of chorioamnionitis and 27 full term placentas from Ghana with and without malaria parasites. The immunohistochemical staining pattern for IgE looked similar to our previous study, with the IgE located on Hofbauer-like cells. We could not find any difference in the amount or distribution of IgE+ cells between malaria-infected and non-infected placentas, nor between different degrees of chorioamnionitis. The IgE score in the placenta did not correlate with the levels of IgE in maternal serum or plasma. However, the IgE score was significantly higher in second- compared to third-trimester placentas (P = 0·03). This might reflect a maturation time-point in the fetus and in the intrauterine environment during the second trimester, or it might be associated with the increased number of intrauterine fetal deaths in the second trimester.
Miller’s seminal studies on the role of thymus in immunity
Authors: Ribatti D , Crivellato E , Vacca A
Published: March 2006

The thymus is one of the two primary lymphoid organs. It is responsible for the provision of T lymphocytes to the entire body, and provides a unique microenvironment in which T cell precursors (thymocytes) undergo development, differentiation and clonal expansion. This review article summarizes the seminal work of the Australian scientist Francis Albert Pierre Miller concerning the description for the first time of the crucial role of the thymus for normal development of the immune system.