bluuebunny/crossref_metadata_2025 huggingface dataset:
Heterotypic interactions among NACHT domains: implications for regulation of innate immune responses
Authors: DAMIANO Jason S. , OLIVEIRA Vasco , WELSH Kate , REED John C.
Published: June 2004

Proteins of the NACHT [NAIP (neuronal apoptosis inhibitory protein), CIITA (MHC class II transcription activator), HET-E (incompatibility locus protein from Podospora anserina) and TP1 (telomerase-associated protein)] family may serve as critical pathogen-sensing and signal-transducing molecules within the innate immune system. In the present paper, we show that CLAN [CARD (caspase-recruitment domain), LRR (leucine-rich repeat) and NACHT domain-containing protein], a NACHT-containing protein originally demonstrated to bind and activate pro-caspase 1, is also capable of influencing the functions of other members of the NACHT family. Through heterotypic NACHT-domain interactions, CLAN was found to associate with Nod1, Nod2 and NAC [nucleotide-binding domain and CARD-containing protein; NALP1 (NACHT, LRR and PYRIN protein 1)] when co-expressed in HEK-293T (human embryonic kidney) cells. NF-κB (nuclear factor κB) reporter assays demonstrated that co-expression of either full-length CLAN or the NACHT domain of CLAN significantly inhibited NF-κB activation induced by Nod1 or Nod2 overexpression. In addition, co-expression of CLAN or the NACHT domain of CLAN with Nod1 or Nod2 inhibited the ability of these proteins to generate active IL-1β (interleukin 1β) through their association with pro-caspase 1. The NACHT domain of CLAN was demonstrated by co-immunoprecipitation experiments to bind all NACHT domains that were tested, including the NACHT domains from CLAN itself, Nod1, Nod2, cryopyrin, NAC, PAN2 {PAAD [pyrin, AIM (absent-in-melanoma), ASC (apoptosis-associated speck-like protein containing a CARD) and death-domain-like]- and NACHT-containing protein} and NAIP (neuronal apoptosis inhibitory protein). Finally, monocyte-expressed CLAN was found to associate with Nod2 following exposure to bacterial peptidoglycan, implying a regulatory role for interaction of these NACHT proteins in the innate immune response. These studies suggest that by mediating hetero-oligomerization, NACHT domains provide a means by which various NACHT-containing proteins may interact, creating protein-interaction networks that potentially modulate immune responses to invading pathogens.
Channelling of substrate promiscuity of the skeletal-muscle ADP-ribosyl cyclase isoform
Authors: BACHER Ingrid , ZIDAR Andreas , KRATZEL Martin , HOHENEGGER Martin
Published: June 2004

The novel Ca2+-mobilizing second messengers cADPr (cyclic ADP-ribose) and NAADP (nicotinic acid–adenine dinucleotide phosphate) are both synthesized by ADP-ribosyl cyclases. Using HSR (heavy sarcoplasmic reticulum) fractions from rabbit skeletal muscle, NAADP-induced Ca2+ release was observed. In the present paper, we show in HSR membranes the formation of authentic cADPr, cGDPr (cyclic GDP-ribose) and NAADP. The cyclization reaction to form cADPr and cGDPr as well as the base-exchange reaction to form NAADP were strictly dependent on pH. Although the formation of cGDPr is optimized at pH 6, the synthesis of NAADP was most pronounced at a pH below 5. A novel regulation mechanism is provided for nicotinic acid, the co-substrate for NAADP synthesis. Nicotinic acid had virtually no influence on the cyclization reaction, but increased the affinity of NADP at an acidic pH and had the opposite effect at alkaline pH. Nicotinamide, the side product of cADPr synthesis, is an inhibitor of the cyclization reaction (IC50, 0.7±0.1 mM) and was 30-fold more potent at suppressing the base-exchange reaction. Although the synthesis of NAADP was highly sensitive to nicotinamide inhibition, this was not via a competition with the nicotinic-acid-binding site. In contrast with the ecto-ADP-ribosyl cyclase (CD38), the cyclization and base-exchange reaction of the skeletal muscle isoform was inhibited by Cu2+ and Zn2+, while other bivalent cations such as Ca2+, Mg2+ and Mn2+ had virtually no effect. These findings allow for the prediction of a novel ADP-ribosyl cyclase isoform in skeletal muscle HSR, other than CD38. Hence the enzymic prerequisite for cADPr- and NAADP-mediated Ca2+ signalling is present.
The sulphur oxygenase reductase from Acidianus ambivalens is a multimeric protein containing a low-potential mononuclear non-haem iron centre
Authors: URICH Tim , BANDEIRAS Tiago M. , LEAL Sónia S. , RACHEL Reinhard , ALBRECHT Till , ZIMMERMANN Peter , SCHOLZ Corinna , TEIXEIRA Miguel , GOMES Cláudio M. , KLETZIN Arnulf
Published: June 2004

The SOR (sulphur oxygenase reductase) is the initial enzyme in the sulphur-oxidation pathway of Acidianus ambivalens. Expression of the sor gene in Escherichia coli resulted in active, soluble SOR and in inclusion bodies from which active SOR could be refolded as long as ferric ions were present in the refolding solution. Wild-type, recombinant and refolded SOR possessed indistinguishable properties. Conformational stability studies showed that the apparent unfolding free energy in water is approx. 5 kcal·mol−1 (1 kcal=4.184 kJ), at pH 7. The analysis of the quaternary structures showed a ball-shaped assembly with a central hollow core probably consisting of 24 subunits in a 432 symmetry. The subunits form homodimers as the building blocks of the holoenzyme. Iron was found in the wild-type enzyme at a stoichiometry of one iron atom/subunit. EPR spectroscopy of the colourless SOR resulted in a single isotropic signal at g=4.3, characteristic of high-spin ferric iron. The signal disappeared upon reduction with dithionite or incubation with sulphur at elevated temperature. Thus both EPR and chemical analysis indicate the presence of a mononuclear iron centre, which has a reduction potential of −268 mV at pH 6.5. Protein database inspection identified four SOR protein homologues, but no other significant similarities. The spectroscopic data and the sequence comparison led to the proposal that the Acidianus ambivalens SOR typifies a new type of non-haem iron enzyme containing a mononuclear iron centre co-ordinated by carboxylate and/or histidine ligands.
Participation of the proteasomal lid subunit Rpn11 in mitochondrial morphology and function is mapped to a distinct C-terminal domain
Authors: RINALDI Teresa , PICK Elah , GAMBADORO Alessia , ZILLI Stefania , MAYTAL-KIVITY Vered , FRONTALI Laura , GLICKMAN Michael H.
Published: June 2004

Substrates destined for degradation by the 26 S proteasome are labelled with polyubiquitin chains. Rpn11/Mpr1, situated in the lid subcomplex, partakes in the processing of these chains or in their removal from substrates bound to the proteasome. Rpn11 also plays a role in maintaining mitochondrial integrity, tubular structure and proper function. The recent finding that Rpn11 participates in proteasome-associated deubiquitination focuses interest on the MPN+ (Mpr1, Pad1, N-terminal)/JAMM (JAB1/MPN/Mov34) metalloprotease site in its N-terminal domain. However, Rpn11 damaged at its C-terminus (the mpr1-1 mutant) causes pleiotropic effects, including proteasome instability and mitochondrial morphology defects, resulting in both proteolysis and respiratory malfunctions. We find that overexpression of WT (wild-type) RPN8, encoding a paralogous subunit that does not contain the catalytic MPN+ motif, corrects proteasome conformations and rescues cell cycle phenotypes, but is unable to correct defects in the mitochondrial tubular system or respiratory malfunctions associated with the mpr1-1 mutation. Transforming mpr1-1 with various RPN8–RPN11 chimaeras or with other rpn11 mutants reveals that a WT C-terminal region of Rpn11 is necessary, and more surprisingly sufficient, to rescue the mpr1-1 mitochondrial phenotype. Interestingly, single-site mutants in the catalytic MPN+ motif at the N-terminus of Rpn11 lead to reduced proteasome-dependent deubiquitination connected with proteolysis defects. Nevertheless, these rpn11 mutants suppress the mitochondrial phenotypes associated with mpr1-1 by intragene complementation. Together, these results point to a unique role for the C-terminal region of Rpn11 in mitochondrial maintenance that may be independent of its role in proteasome-associated deubiquitination.
Hypochlorite and superoxide radicals can act synergistically to induce fragmentation of hyaluronan and chondroitin sulphates
Authors: REES Martin D. , HAWKINS Clare L. , DAVIES Michael J.
Published: June 2004

Activated phagocytes release the haem enzyme MPO (myeloperoxidase) and also generate superoxide radicals (O2•−), and hence H2O2, via an oxidative burst. Reaction of MPO with H2O2 in the presence of chloride ions generates HOCl (the physiological mixture of hypochlorous acid and its anion present at pH 7.4). Exposure of glycosaminoglycans to a MPO–H2O2–Cl− system or reagent HOCl generates long-lived chloramides [R-NCl-C(O)-R′] derived from the glycosamine N-acetyl functions. Decomposition of these species by transition metal ions gives polymer-derived amidyl (nitrogen-centred) radicals [R-N•-C(O)-R′], polymer-derived carbon-centred radicals and site-specific strand scission. In the present study, we have shown that exposure of glycosaminoglycan chloramides to O2•− also promotes chloramide decomposition and glycosaminoglycan fragmentation. These processes are inhibited by superoxide dismutase, metal ion chelators and the metal ion-binding protein BSA, consistent with chloramide decomposition and polymer fragmentation occurring via O2•−-dependent one-electron reduction, possibly catalysed by trace metal ions. Polymer fragmentation induced by O2•− [generated by the superoxide thermal source 1, di-(4-carboxybenzyl)hyponitrite] was demonstrated to be entirely chloramide dependent as no fragmentation occurred with the native polymers or when the chloramides were quenched by prior treatment with methionine. EPR spin-trapping experiments using 5,5-dimethyl1-pyrroline-N-oxide and 2-methyl-2-nitrosopropane have provided evidence for both O2•− and polymer-derived carbon-centred radicals as intermediates. The results obtained are consistent with a mechanism involving one-electron reduction of the chloramides to yield polymer-derived amidyl radicals, which subsequently undergo intramolecular hydrogen atom abstraction reactions to give carbon-centred radicals. The latter undergo fragmentation reactions in a site-specific manner. This synergistic damage to glycosaminoglycans induced by HOCl and O2•− may be of significance at sites of inflammation where both oxidants are generated concurrently.
The mosaic receptor sorLA/LR11 binds components of the plasminogen-activating system and platelet-derived growth factor-BB similarly to LRP1 (low-density lipoprotein receptor-related protein), but mediates slow internalization of bound ligand
Authors: GLIEMANN Jørgen , HERMEY Guido , NYKJÆR Anders , PETERSEN Claus M. , JACOBSEN Christian , ANDREASEN Peter A.
Published: June 2004

The type-1 receptor sorLA/LR11, a member of the Vps10p-domain receptor family that also contains domains characterizing members of the LDL (low-density lipoprotein) receptor family, has been shown to induce increased uPAR (urokinase receptor) expression as well as enhanced migration and invasion activities in smooth muscle cells in the presence of PDGF-BB (platelet-derived growth factor-BB). Here we show that sorLA interacts with both components of the plasminogen activating system and PDGF-BB similarly to LRP1 (LDL receptor-related protein/α2-macroglobulin receptor), which is an important clearance receptor with established functions in controlling uPAR expression as well as PDGF-BB signalling. In contrast with LRP1, sorLA does not interact with α2-macroglobulin, which is a binding protein for several growth factors, including PDGF-BB. By using LRP1-deficient cells transfected with sorLA, we demonstrate that sorLA-bound ligand is internalized at a much lower rate than LRP1-bound ligand, and that sorLA is inefficient in regulating cell surface uPAR expression, which depends on rapid internalization of the ternary complex between urokinase-type plasminogen activator, its type-1 inhibitor, and uPAR. Thus, although overlapping with regard to binding profiles, sorLA is substantially less efficient as a clearance receptor than LRP1. We propose that sorLA can divert ligands away from LRP1 and thereby inhibit both their clearance and signalling events mediated by LRP1.
Functional and biochemical characterization of a recombinant Arabidopsis thaliana 3-deoxy-D-manno-octulosonate 8-phosphate synthase
Authors: WU Jing , PATEL Mayur A. , SUNDARAM Appavu K. , WOODARD Ronald W.
Published: June 2004

An open reading frame, encoding for KDOPS (3-deoxy-D-manno-octulosonate 8-phosphate synthase), from Arabidopsis thaliana was cloned into a T7-driven expression vector. The protein was overexpressed in Escherichia coli and purified to homogeneity. Recombinant A. thaliana KDOPS, in solution, displays an apparent molecular mass of 76 kDa and a subunit molecular mass of 31.519 kDa. Unlike previously studied bacterial KDOPSs, which are tetrameric, A. thaliana KDOPS appears to be a dimer in solution. The optimum temperature of the enzyme is 65 °C and the optimum pH is 7.5, with a broad peak between pH 6.5 and 9.5 showing 90% of maximum activity. The enzyme cannot be inactivated by EDTA or dipicolinic acid treatment, nor it can be activated by a series of bivalent metal ions, suggesting that it is a non-metallo-enzyme, as opposed to the initial prediction that it would be a metallo-enzyme. Kinetic studies showed that the enzyme follows a sequential mechanism with Km=3.6 μM for phosphoenolpyruvate and 3.8 μM for D-arabinose 5-phosphate and kcat=5.9 s−1 at 37 °C. On the basis of the characterization of A. thaliana KDOPS and phylogenetic analysis, plant KDOPSs may represent a new, distinct class of KDOPSs.
Murine cystathionine γ-lyase: complete cDNA and genomic sequences, promoter activity, tissue distribution and developmental expression
Authors: ISHII Isao , AKAHOSHI Noriyuki , YU Xiao-Nian , KOBAYASHI Yuriko , NAMEKATA Kazuhiko , KOMAKI Gen , KIMURA Hideo
Published: June 2004

Cystathionine γ-lyase (CSE) is the last key enzyme in the trans-sulphuration pathway for biosynthesis of cysteine from methionine. Cysteine could be provided through diet; however, CSE has been shown to be important for the adequate supply of cysteine to synthesize glutathione, a major intracellular antioxidant. With a view to determining physiological roles of CSE in mice, we report the sequence of a complete mouse CSE cDNA along with its associated genomic structure, generation of specific polyclonal antibodies, and the tissue distribution and developmental expression patterns of CSE in mice. A 1.8 kb full-length cDNA containing an open reading frame of 1197 bp, which encodes a 43.6 kDa protein, was isolated from adult mouse kidney. A 35 kb mouse genomic fragment was obtained by λ genomic library screening. It contained promoter regions, 12 exons, ranging in size from 53 to 579 bp, spanning over 30 kb, and exon/intron boundaries that were conserved with rat and human CSE. The GC-rich core promoter contained canonical TATA and CAAT motifs, and several transcription factor-binding consensus sequences. The CSE transcript, protein and enzymic activity were detected in liver, kidney, and, at much lower levels, in small intestine and stomach of both rats and mice. In developing mouse liver and kidney, the expression levels of CSE protein and activity gradually increased with age until reaching their peak value at 3 weeks of age, following which the expression levels in liver remained constant, whereas those in kidney decreased significantly. Immunohistochemical analyses revealed predominant CSE expression in hepatocytes and kidney cortical tubuli. These results suggest important physiological roles for CSE in mice.
SUT1-promoted sterol uptake involves the ABC transporter Aus1 and the mannoprotein Dan1 whose synergistic action is sufficient for this process
Authors: ALIMARDANI Parissa , RÉGNACQ Matthieu , MOREAU-VAUZELLE Carole , FERREIRA Thierry , ROSSIGNOL Tristan , BLONDIN Bruno , BERGÈS Thierry
Published: June 2004

Efficient sterol influx in the yeast Saccharomyces cerevisiae is restricted to anaerobiosis or to haem deficiency resulting from mutations. Constitutive expression of SUT1, an hypoxic gene encoding a transcriptional regulator, induces sterol uptake in aerobiosis. A genome-wide approach using DNA microarray was used to identify the mediators of SUT1 effects on aerobic sterol uptake. A total of 121 ORFs (open reading frames) were significantly and differentially expressed after SUT1 overexpression, 61 down-regulated and 60 up-regulated. Among these genes, the role of the putative ABC transporter (ATP-binding-cassette transporter) Aus1, and of the cell-wall mannoprotein Dan1, was characterized better. These two genes play an essential role in aerobic sterol uptake, since their deletion compromised the SUT1 effects, but individual overexpression of either of these genes in a wild-type background was not sufficient for this process. However, constitutive co-expression of AUS1 and DAN1 in a wild-type background resulted in sterol influx in aerobiosis. These results suggest that the corresponding proteins may act synergistically in vivo to promote sterol uptake.
A new class (penaeidin class 4) of antimicrobial peptides from the Atlantic white shrimp (Litopenaeus setiferus) exhibits target specificity and an independent proline-rich-domain function
Authors: CUTHBERTSON Brandon J. , BÜLLESBACH Erika E. , FIEVET Julie , BACHÈRE Evelyne , GROSS Paul S.
Published: June 2004

A highly pure, chemically defined representative of a new class of antimicrobial peptide from the Atlantic white shrimp (Litopenaeus setiferus), penaeidin class 4 [Pen4-1 (penaeidin class 4 isoform 1)], was produced synthetically. Chemical synthesis was achieved by native ligation from two separate domains yielding a bioactive peptide that reflected the characteristics of native penaeidin. Synthetic Pen4-1 proved to be an effective antimicrobial peptide, particularly against the broad-spectrum pathogen Fusarium oxysporum, exhibiting a complex effect on reproductive growth at inhibitory concentrations resulting in the suppression of spore formation. Pen4-1 exhibits unique features [not previously observed for penaeidins from the Pacific white shrimp (L. vannamei)], including target-species specificity against Gram-positive bacteria, indicating a potential partitioning of antimicrobial function among this family of peptides. The proline-rich domain of penaeidin class 4 alone was an active antimicrobial peptide, having the same target range as the full-length Pen4-1. These findings indicate that the proline-rich domain of penaeidin is sufficient to confer target specificity and that divergence in this domain between classes can result in a gain in antimicrobial function as observed for the proline-rich domain of Pen4-1.
Substrate-specifying determinants of the nucleotide pyrophosphatases/phosphodiesterases NPP1 and NPP2
Authors: CIMPEAN Anisoara , STEFAN Cristiana , GIJSBERS Rik , STALMANS Willy , BOLLEN Mathieu
Published: June 2004

The nucleotide pyrophosphatases/phosphodiesterases NPP1 and NPP2/autotaxin are structurally related eukaryotic ecto-enzymes, but display a very different substrate specificity. NPP1 releases nucleoside 5′-monophosphates from various nucleotides, whereas NPP2 mainly functions as a lysophospholipase D. We have used a domain-swapping approach to map substrate-specifying determinants of NPP1 and NPP2. The catalytic domain of NPP1 fused to the N- and C-terminal domains of NPP2 was hyperactive as a nucleotide phosphodiesterase, but did not show any lysophospholipase D activity. In contrast, chimaeras of the catalytic domain of NPP2 and the N- and/or C-terminal domains of NPP1 were completely inactive. These data indicate that the catalytic domain as well as both extremities of NPP2 contain lysophospholipid-specifying sequences. Within the catalytic domain of NPP1 and NPP2, we have mapped residues close to the catalytic site that determine the activities towards nucleotides and lysophospholipids. We also show that the conserved Gly/Phe-Xaa-Gly-Xaa-Xaa-Gly (G/FXGXXG) motif near the catalytic site is required for metal binding, but is not involved in substrate-specification. Our data suggest that the distinct activities of NPP1 and NPP2 stem from multiple differences throughout the polypeptide chain.
Progress in allogeneic bone marrow and peripheral blood stem cell transplantation for multiple myeloma: a comparison between transplants performed 1983–93 and 1994–98 at European Group for Blood and Marrow Transplantation centres
Authors: Gahrton G. , Svensson H. , Cavo M. , Apperley J. , Bacigalupo A. , Björkstrand B. , Bladé J. , Cornelissen J. , De Laurenzi A. , Facon T. , Ljungman P. , Michallet M. , Niederwieser D. , Powles R. , Reiffers J. , Russell N. H. , Samson D. , Schaefer U. W. , Schattenberg A. , Tura S. , Verdonck L. F. , Vernant J. P. , Willemze R. , Volin for the European Group for Blood L. ,   Marrow Transplantation (EBMT)
Published: June 2004

Out of 690 allogeneic matched sibling donor transplants for multiple myeloma reported to the European Group for Blood and Marrow Transplantation (EBMT) registry, 334 were performed during the period 1983–93 (all with bone marrow) and 356 during 1994–98 [223 with bone marrow and 133 with peripheral blood stem cells (PBSCs)]. The median overall survival was 10 months for patients transplanted during the earlier time period and 50 months for patients transplanted with bone marrow during the later period. The use of PBSCs was associated with earlier engraftment but no significant survival benefit compared to bone marrow transplants during the same time period. The improvement in survival since 1994 was the result of a significant reduction in transplant‐related mortality, which was 38%, 21% and 25% at 6 months and 46%, 30% and 37% at 2 years during the earlier period, and the later period with bone marrow and PBSCs respectively. Reasons for the reduced transplant‐related mortality appeared to be fewer deaths owing to bacterial and fungal infections and interstitial pneumonitis, in turn a result of earlier transplantation and less prior chemotherapy. Better supportive treatment and more frequent use of cytokines may also play a role. The improvement in survival was not directly related to the increased use of PBSCs.
Alpha‐Glucosylrutin: ein hochwirksames Flavonoid zum Schutz vor oxidativem Streß
Authors: Wolber Rainer , Stäb Franz , Max Heiner , Wehmeyer Annegret , Hadshiew Ina , Wenck Horst , Rippke Frank , Wittern Klaus‐Peter
Published: June 2004

Das Bioflavonoid alpha‐Glucosylrutin (AGR) findet aufgrund seiner starken antioxidativen Wirksamkeit und hohen epidermalen Bioverfügbarkeit zunehmend Verwendung im dermato‐kosmetischen Bereich. Bioflavonoide sind sekundäre Pflanzenstoffe (Phytamine) mit einer gemeinsamen chemischen Grundstruktur und einem breit gefächerten Wirkungsspektrum, vor allem aber der Fähigkeit, reaktive Sauerstoffspezies (reactive oxygen species, ROS) zu neutralisieren. ROS beeinflussen und schädigen die Zelle sowohl durch direkte zytotoxische Effekte (Membrandestruktion durch Induktion radikalischer Kettenreaktionen, Mutationen nukleärer und mitochondrialer DNA etc.) als auch indirekt durch Modifikation intrazellulärer Signaltransduktionskaskaden, die entzündliche und proliferative Prozesse regulieren. Die ausgezeichnete antioxidative Wirksamkeit von AGR konnte durch verschiedene experimentelle in‐vitro‐ und in‐vivo‐Untersuchungen bestätigt werden. Weiterführende klinische Studien belegen eindeutig die Wirksamkeit einer prophylaktischen Anwendung von AGR bei dermatologischen Krankheitsbildern wie der polymorphen Lichtdermatose (PLD), bei denen oxidativer Streß von pathogenetischer Relevanz ist. Auch in anderen dermato‐kosmetischen Indikationsbereichen wie der vorzeitigen (lichtbedingten) Hautalterung scheint eine vorbeugende Behandlung mit AGR vielversprechend zu sein. In allen durchgeführten in‐vivo‐Untersuchungen zeigte sich zudem, daß AGR in den verwendeten Konzentrationen ein sehr gut hautverträglicher Wirkstoff für die medizinische Hautpflege ist.
Improvement of the dielectric and ferroelectric properties in superlattice structure of Pb(Zr,Ti)O3 thin films grown by a chemical  solution route
Authors: Pontes F. M. , Longo E. , Leite E. R. , Varela J. A.
Published: June 2004

Making heterolayered perovskite materials constitutes an approach for the creation of better dielectric and ferroelectric properties. In the experiment reported here, heterolayered PZT40/PZT60 films were grown on Pt/Ti/SiO2/Si (100) by a chemical solution deposition. The dielectric constant of the heterolayered thin film was significantly enhanced compared with that of pure PZT40 and PZT60 thin films. A dielectric constant of 701 at 100 kHz was observed for a stacking periodicity of six layers having a total thickness of 150 nm. The heterolayered film exhibited greater remanent polarization than PZT60 and PZT40 films. The values of remanent polarization were 7.9, 18.5, and 31 μC/cm2, respectively, for pure PZT60, PZT40, and heterolayered thin films, suggesting that the superior dielectric and ferroelectric properties of the heterolayered thin film resulted from a cooperative interaction between the ferroelectric phases made from alternating tetragonal and rhombohedral phases of PZT, simulating the morphotropic phase boundary of this system.
Ballistic transport in InSb∕InAlSb antidot lattices
Authors: Chen Hong , Heremans J. J. , Peters J. A. , Goel N. , Chung S. J. , Santos M. B.
Published: June 2004

We investigate magnetotransport properties of antidot lattices fabricated on high-mobility InSb∕InAlSb heterostructures. The temperature dependencies of the ballistic magnetoresistance peaks due to the antidot lattice are studied, and compared with mobility and density data over the same temperature range. A scattering time particular to antidot lattices is deduced, with a linear dependence on temperature between 0.4 and 50K, attributed to acoustic phonon scattering. The mobility does not vary substantially over this temperature range, whereas above ∼60K a quadratic dependence of inverse mobility on temperature is noticed, attributed to optical phonon scattering. The very weak temperature dependence of the width of the ballistic magnetoresistance peaks indicates negligible thermal smearing for electrons in the InSb quantum well, a result of the small electron effective mass.
Size-dependent oxygen-related electronic states in silicon nanocrystals
Authors: Biteen J. S. , Lewis N. S. , Atwater H. A. , Polman A.
Published: June 2004

Silicon nanocrystals embedded in SiO2 were isolated with a selective etching procedure, and the isolated nanocrystals’ excitonic emission energy was studied during controlled oxidation. Nanocrystals having initial diameters, d0, of ∼2.9–3.4nm showed a photoluminescence (PL) blueshift upon oxidatively induced size reduction, as expected from models of quantum confinement. Oxidation of smaller Si nanocrystals (d0∼2.5–2.8nm) also initially resulted in a PL blueshift, but a redshift in the PL was then observed after growth of ∼0.3 monolayers of native oxide. This decrease in excitonic emission energy during oxidation is consistent with the theoretically predicted formation of an oxygen-related excitonic recombination state.
Isotopically pure C13 layer as a stress sensor in a diamond anvil cell
Authors: Qiu Wei , Velisavljevic Nenad , Baker Paul A. , Vohra Yogesh K. , Weir Samuel T.
Published: June 2004

Isotopically pure C13 homoepitaxial diamond layer of 20±5microns thickness was grown on top of a brilliant cut diamond anvil by a microwave plasma chemical vapor deposition process for application as a stress sensor. This isotopically pure diamond tip was then used in conjunction with a natural abundance C12 diamond anvil to generate high pressure on a soft sample containing carbon nanotubes to 100GPa. The C13 diamond Raman signal remained a distinct single peak showing that the mean normal stress experienced by this thin layer is uniform to the highest pressure. The stress-induced shift of the C13 layer is related to the quasihydrostatic pressure in the sample chamber using a ruby pressure sensor and shows a remarkably linear behavior to extreme pressures.
Thermophysical property measurements using time-resolved photothermal deflection spectrometry with step optical excitation
Authors: Zhao Jianhua , Zhou Jianqin , Shen Jun
Published: June 2004

This letter reports the theoretical and experimental results of thermophysical property measurements using our recently developed time-resolved photothermal deflection spectrometry (PDS) with step optical excitation. One-dimensional heat conduction boundary conditions of the third kind were derived, and a theoretical model with the boundary conditions was proposed. Both thermal diffusivity and effusivity of two well-known samples were precisely measured simultaneously by fitting experimental data to the theory. Thermal conductivity and unit volume specific heat then can be deduced. Moreover, time-resolved PDS with step optical excitation has the advantages of simpler experimental apparatus and less time consuming measurement, compared with the traditional periodically modulated PDS.
Axial high-temperature superconducting gradiometer with a flexibleflux transformer
Authors: Bick M. , Leslie K. E. , Binks R. A. , Tilbrook D. L. , Lam S. K. H. , Gnanarajan R. , Du J. , Foley C. P.
Published: June 2004

An axial first-order gradiometer is formed by coupling the input coil of a flexible high-temperature superconducting flux transformer inductively to a directly coupled superconducting quantum interference device magnetometer. The transformer is patterned in a single-layer YBa2Cu3O7−x film on a flexible Hastelloy tape. The tape is bent such that the two outer pickup loops of the transformer are facing each other while perpendicular to the magnetometer plane resulting in a gradiometer baseline of 35mm. A superconducting shield is mechanically adjusted to reduce the gradiometer response to uniform fields applied perpendicularly to both the magnetometer plane and the plane of the transformer pickup loops, by a factor of typically 7000.
The use of guided surface acoustic resonances in the determination of the thin film elastic tensor
Authors: Wittkowski T. , Distler G. , Jung K. , Hillebrands B. , Comins J. D.
Published: June 2004

A Brillouin light scattering investigation of thin supported films shows that the measurement of resonances within the continuum of excitations together with the dispersion of discrete surface acoustic modes such as the Rayleigh and Sezawa waves, yields valuable additional information. In the present study, an analysis of the combined data results in the precise determination of four independent components of the film elastic tensor of elastically anisotropic, polycrystalline tungsten carbide (W2C) films for which the single crystal elastic constants are not known.
Mobility studies of field-effect transistor structures basedon anthracene single crystals
Authors: Aleshin A. N. , Lee J. Y. , Chu S. W. , Kim J. S. , Park Y. W.
Published: June 2004

The charge carrier transport in anthracene single crystals has been studied by means of field-effect transistor (FET) structure. The FET mobility (μFET) revealed the nonmonotonous, reliant on gate-voltage (Vg), temperature dependence with the maximum μFET∼0.02cm2∕Vs at T∼170–180K and Vg∼−30V. At temperatures below 180K the mobility decreases and becomes thermally activated with the Vg-dependent activation energy Ea∼40–70meV governed by shallow traps. The space-charge-limited current is the dominant transport mechanism in FET structures based on anthracene single crystals.
Nonlinear self-modulation and subharmonic acoustic spectroscopyfor damage detection and location
Authors: Solodov I. , Wackerl J. , Pfleiderer K. , Busse G.
Published: June 2004

A self-modulation mode of nonlinear acoustic vibrations of cracked defects has been analyzed and observed experimentally. Spectral patterns of the self-modulation are attributed to the sum-frequency type resonance in a multi-degree-of-freedom system and include a subharmonic spectrum as a particular case. Both the subharmonic and self-modulation modes demonstrate a high localization around the defect and provide opportunities for early detection and recognition of damaged areas.
Optimization of mid-infrared InAs∕GaSb type-II superlattices
Authors: Haugan H. J. , Szmulowicz F. , Brown G. J. , Mahalingam K.
Published: June 2004

The effect of small changes in GaSb layer width on the photoresponse spectrum of 20.5ÅInAs∕InSb-interfaces∕XÅ GaSb type-II superlattice (SL) suitable for mid-infrared detection was investigated. By decreasing the GaSb width X from 27 to 18Å, the cut-off wavelength was increased from 4.03 to 4.55μm. This decrease of the SL band gap and other effects of the design changes on photoresponse spectrum with narrower GaSb layers are explained by a nonperturbative, modified envelope function approximation calculation that includes the interface coupling of heavy, light, and spin–orbit holes resulting from the in-plane asymmetry at InAs∕GaSb interfaces.
Positive exchange bias in ferromagnetic La0.67Sr0.33MnO3∕SrRuO3 bilayers
Authors: Ke X. , Rzchowski M. S. , Belenky L. J. , Eom C. B.
Published: June 2004

Epitaxial La0.67Sr0.33MnO3(LSMO)∕SrRuO3(SRO) ferromagnetic bilayers have been grown on (001)SrTiO3(STO) substrates by pulsed laser deposition with atomic layer control. We observe a shift in the magnetic hysteresis loop of the LSMO layer in the same direction as the applied biasing field (positive exchange bias). The effect is not present above the Curie temperature of the SRO layer (TcSRO), and its magnitude increases rapidly as the temperature is lowered below TcSRO. The direction of the shift is consistent with an antiferromagnetic exchange coupling between the ferromagnetic LSMO layer and the ferromagnetic SRO layer. We propose that atomic layer charge transfer modifies the electronic state at the interface, resulting in the observed antiferromagnetic interfacial exchange coupling.
Carbon nanotube electron source based ionization vacuum gauge
Authors: Dong Changkun , Myneni Ganapati R.
Published: June 2004

The results of fabrication and performance of an ionization vacuum gauge using a carbon nanotube electron source are presented. The electron source was constructed with multiwall nanotubes, which were grown using thermal chemical vapor deposition. The electron emission of the source was stable in vacuum pressure up to 10−7Torr, which is better than the metal field emitters. The measurement linearity of the gauge was better than ±10% from 10−6 to 10−10Torr. The gauge sensitivity of 4Torr−1 was achieved under 50μA electron emission in nitrogen. The gauge is expected to find applications in vacuum measurements from 10−7Torr to below 10−11Torr.
Investigations on V-defects in quaternary AlInGaN epilayers
Authors: Liu J. P. , Wang Y. T. , Yang H. , Jiang D. S. , Jahn U. , Ploog K. H.
Published: June 2004

The characteristics of V-defects in quaternary AlInGaN epilayers and their correlation with fluctuations of the In distribution are investigated. The geometric size of the V-defects is found to depend on the In composition of the alloy. The V-defects are nucleated within the AlInGaN layer and associated with threading dislocations. Line scan cathodoluminescence (CL) shows a redshift of the emission peak and an increase of the half width of the CL spectra as the electron beam approaches the apex of the V-defect. The total redshift decreases with decreasing In mole fraction in the alloy samples. Although the strain reduction may partially contribute to the CL redshift, indium segregation is suggested to be responsible for the V-defect formation and has a main influence on the respective optical properties.
High pressure Raman spectroscopic study of structural polymorphismin cyclohexane
Authors: Pravica Michael G. , Shen Yongrong , Nicol Malcolm F.
Published: June 2004

We have performed a Raman spectroscopic study of cyclohexane at high pressures up to 40GPa at ambient temperature and present evidence for one or two new phases of cyclohexane which appear around 10 and between 25 and 37GPa. The R1 and R2 lines of a ruby in the cyclohexane sample were well-resolved to our highest pressure, and the sample was highly transparent. Because cyclohexane is nonpolar, relatively inert, and a liquid at room temperature, it is an excellent and easy-to-use pressure medium, especially for reactive materials. At 40GPa, we heated the sample to 200 °C for several hours and then performed Raman measurements while decreasing pressure at ambient temperature. The material remained in its original liquid form demonstrating that the molecule is remarkably resilient.
Turbulence of second sound waves in superfluid He II
Authors: Brazhnikov M. Yu. , Efimov V. B. , Kolmakov G. V. , Levchenko A. A. , Lebedeva E. V. , Mezhov-Deglin L. P.
Published: June 2004

We communicate the results of numerical studies of acoustic turbulence in a system of slightly dissipating, nonlinear second sound waves in superfluid He II. It is shown that at sufficiently high amplitude of the external driving force a power-like energy distribution over frequency is formed in the system of second sound waves. This distribution is attributed to formation of the acoustic turbulence regime in the system. The interval of frequencies in which the distribution has a power-like form is expanded to high frequencies with increasing amplitude of the driving force. The energy distribution inside this interval is close to Eω∼ω2. It is shown that the distribution of energy Eω depends on the value of the nonlinearity coefficient of the second sound but does not depend on the sign of the coefficient, i.e., the coherent structures (shock waves) do not contribute to the statistical properties of the turbulent state.
Static vortices in long Josephson junctions of exponentially varying width
Authors: Semerdjieva E. G. , Boyadjiev T. L. , Shukrinov Yu. M.
Published: June 2004

A numerical simulation is carried out for static vortices in a long Josephson junction with an exponentially varying width. At specified values of the parameters the corresponding boundary-value problem admits more than one solution. Each solution (distribution of the magnetic flux in the junction) is associated to a Sturm–Liouville problem, the smallest eigenvalue of which can be used, in a first approximation, to assess the stability of the vortex against relatively small spatiotemporal perturbations. The change in width of the junction leads to a renormalization of the magnetic flux in comparison with the case of a linear one-dimensional model. The influence of the model parameters on the stability of the states of the magnetic flux is investigated in detail, particularly that of the shape parameter. The critical curve of the junction is constructed from pieces of the critical curves for the different magnetic flux distributions having the highest critical currents for the given magnetic field.
Composition dependence of the low-temperature magnetic ordering and the hyperfine interactions in Fe–N austenite
Authors: Timoshevskii A. N. , Yanchitsky B. Z. , Bakai A. S.
Published: June 2004

The electronic structure of two model structures of stoichiometry Fe8N with different types of ordering of the nitrogen atoms are calculated using the ab initio FLAPW method. To first approximation these structures can be treated as a prototype of Fe–N austenite. The influence of the nitrogen atoms on the electronic structure and magnetic properties of γ iron and on the components of the Mössbauer spectrum is investigated, permitting a detailed interpretation of the experimental data. The dependence of the exchange integral on the concentration of nitrogen atoms is obtained, clarifying the influence of nitrogen on the magnetic properties of fcc iron. The effective interatomic interaction potentials of nitrogen atoms in fcc iron in six coordination spheres is calculated using the ab initio FLAPW method and the cluster expansion technique. The potentials thus obtained are used in a Monte Carlo investigation of the temperature dependence of the short-range order in the Fe–N system. The temperature dependence of the heat capacity and short-range order parameters is calculated. It is established that a transition from the disordered state to the nitride Fe4N is observed at 830 K.
Size effect in the fluorescence spectra of polysilanes embedded in mesoporous materials
Authors: Ostapenko N. , Kotova N. , Telbiz G. , Suto S. , Watanable A.
Published: June 2004

The low-temperature fluorescence and excitation spectra (T=5–150 K) are investigated for the silicon–organic photoconductors poly(di-n-hexylsilane) (PDHS) and poly(methylphenylsilane) (PMPS) embedded in pores of the mesoporous materials MSM-41 and SBA-15, with pore diameters of 2.8 and 5.8 nm, respectively. It is found that the fluorescence spectra of the polymer nanostructures depend on the pore size and are substantially different from the spectra of films. New bands in the visible region, with maxima at 410 nm for PDHS and at 460 nm for PMPS, are observed for the first time in the fluorescence spectra of the 2.8 nm nantostructures. It is assumed that the new bands in the fluorescence spectrum are due to the formation of defect states as a result of a substantial change in the conformation of the polymer chains near the surface of the pores. The change in symmetry of the polymer chains near such defects gives rise to a new band with maximum at 300 nm in the excitation spectrum of PDHS. The defect nature of the new fluorescence bands is confirmed by temperature studies and also by the vanishing of these bands when the pore size is increased to 5.8 nm.
The louse-borne human pathogen
Bartonella quintana
is a genomic derivative of the zoonotic agent
Bartonella henselae
Authors: Alsmark Cecilia M. , Frank A. Carolin , Karlberg E. Olof , Legault Boris-Antoine , Ardell David H. , Canbäck Björn , Eriksson Ann-Sofie , Näslund A. Kristina , Handley Scott A. , Huvet Maxime , La Scola Bernard , Holmberg Martin , Andersson Siv G. E.
Published: June 2004

We present the complete genomes of two human pathogens,
Bartonella quintana
(1,581,384 bp) and
Bartonella henselae
(1,931,047 bp). The two pathogens maintain several similarities in being transmitted by insect vectors, using mammalian reservoirs, infecting similar cell types (endothelial cells and erythrocytes) and causing vasculoproliferative changes in immunocompromised hosts. A primary difference between the two pathogens is their reservoir ecology. Whereas
B. quintana
is a specialist, using only the human as a reservoir,
B. henselae
is more promiscuous and is frequently isolated from both cats and humans. Genome comparison elucidated a high degree of overall similarity with major differences being
B. henselae
specific genomic islands coding for filamentous hemagglutinin, and evidence of extensive genome reduction in
B. quintana
, reminiscent of that found in
Rickettsia prowazekii
. Both genomes are reduced versions of chromosome I from the highly related pathogen
Brucella melitensis
. Flanked by two rRNA operons is a segment with similarity to genes located on chromosome II of
B. melitensis
, suggesting that it was acquired by integration of megareplicon DNA in a common ancestor of the two
Bartonella
species. Comparisons of the vector-host ecology of these organisms suggest that the utilization of host-restricted vectors is associated with accelerated rates of genome degradation and may explain why human pathogens transmitted by specialist vectors are outnumbered by zoonotic agents, which use vectors of broad host ranges.
Beta oscillations in a large-scale sensorimotor cortical network: Directional influences revealed by Granger causality
Authors: Brovelli Andrea , Ding Mingzhou , Ledberg Anders , Chen Yonghong , Nakamura Richard , Bressler Steven L.
Published: June 2004

Previous studies have shown that synchronized beta frequency (14-30 Hz) oscillations in the primary motor cortex are involved in maintaining steady contractions of contralateral arm and hand muscles. However, little is known about the role of postcentral cortical areas in motor maintenance and their patterns of interaction with motor cortex. We investigated the functional relations of beta-synchronized neuronal assemblies in pre- and postcentral areas of two monkeys as they pressed a hand lever during the wait period of a visual discrimination task. By using power and coherence spectral analysis, we identified a beta-synchronized large-scale network linking pre- and postcentral areas. We then used Granger causality spectra to measure directional influences among recording sites. In both monkeys, strong Granger causal influences were observed from primary somatosensory cortex to both motor cortex and inferior posterior parietal cortex, with the latter area also exerting Granger causal influences on motor cortex. Granger causal influences from motor cortex to postcentral sites, however, were weak in one monkey and not observed in the other. These results are the first, to our knowledge, to demonstrate in awake monkeys that synchronized beta oscillations bind multiple sensorimotor areas into a large-scale network during motor maintenance behavior and carry Granger causal influences from primary somatosensory and inferior posterior parietal cortices to motor cortex.
Induction of interferon-stimulated gene expression and antiviral responses require protein deacetylase activity
Authors: Chang Hao-Ming , Paulson Matthew , Holko Michelle , Rice Charles M. , Williams Bryan R. G. , Marié Isabelle , Levy David E.
Published: June 2004

Histone deacetylase (HDAC) activity, commonly correlated with transcriptional repression, was essential for transcriptional induction of IFN-stimulated genes (ISG). Inhibition of HDAC function led to global impairment of ISG expression, with little effect on basal expression. HDAC function was not required for signal transducer and activator of transcription tyrosine phosphorylation, nuclear translocation, or assembly on chromatin, but it was needed for full activity of the signal transducer and activator of transcription transactivation domain. HDAC function was also required for gene induction driven by the IFN regulatory factor 3 transcription factor activated by virus infection, and it was essential for establishment of an antiviral response against Flaviviridae, Rhabdoviridae, and Picornaviridae. Requirement for HDAC function in transcriptional activation may represent a general mechanism for rapid stimulation of ISG transcription.
Microarray analysis of transposition targets in
Escherichia coli
: The impact of transcription
Authors: Manna Dipankar , Breier Adam M. , Higgins N. Patrick
Published: June 2004

Transposable elements have influenced the genetic and physical composition of all modern organisms. Defining how different transposons select target sites is critical for understanding the biochemical mechanism of this type of recombination and the impact of mobile genes on chromosome structure and function. Phage Mu replicates in Gram-negative bacteria using an extremely efficient transposition reaction. Replicated copies are excised from the chromosome and packaged into virus particles. Each viral genome plus several hundred base pairs of host DNA covalently attached to the prophage right end is packed into a virion. To study Mu transposition preferences, we used DNA microarray technology to measure the abundance of >4,000
Escherichia coli
genes in purified Mu phage DNA. Insertion hot- and cold-spot genes were found throughout the genome, reflecting >1,000-fold variation in utilization frequency. A moderate preference was observed for genes near the origin compared to terminus of replication. Large biases were found at hot and cold spots, which often include several consecutive genes. Efficient transcription of genes had a strong negative influence on transposition. Our results indicate that local chromosome structure is more important than DNA sequence in determining Mu target-site selection.