bluuebunny/crossref_metadata_2025 huggingface dataset:
Lipid raft components cholesterol and sphingomyelin increase H+/OH− permeability of phosphatidylcholine membranes
Authors: Gensure Rebekah H. , Zeidel Mark L. , Hill Warren G.
Published: August 2006

H+/OH− permeation through lipid bilayers occurs at anomalously high rates and the determinants of proton flux through membranes are poorly understood. Since all life depends on proton gradients, it is important to develop a greater understanding of proton leak phenomena. We have used stopped-flow fluorimetry to probe the influence of two lipid raft components, chol (cholesterol) and SM (sphingomyelin), on H+/OH− and water permeability. Increasing the concentrations of both lipids in POPC (palmitoyl-2-oleoyl phosphatidylcholine) liposomes decreased water permeability in a concentration-dependent manner, an effect that correlated with increased lipid order. Surprisingly, proton flux was increased by increasing the concentration of chol and SM. The chol effect was complex with molar concentrations of 17.9, 33 and 45.7% giving 2.8-fold (P<0.01), 2.2-fold (P<0.001) and 5.1-fold (P<0.001) increases in H+/OH− permeability from a baseline of 2.4×10−2 cm/s. SM at 10 mole% effected a 2.8-fold increase (P<0.01), whereas 20 and 30 mole% enhanced permeability by 3.6-fold (P<0.05) and 4.1-fold respectively (P<0.05). Supplementing membranes containing chol with SM did not enhance H+/OH− permeability. Of interest was the finding that chol addition to soya-bean lipids decreased H+/OH− permeability, consistent with an earlier report [Ira and Krishnamoorthy (2001) J. Phys. Chem. B 105, 1484–1488]. We speculate that the presence of proton carriers in crude lipid extracts might contribute to this result. We conclude that (i) chol and SM specifically and independently increase rates of proton permeation in POPC bilayers, (ii) domains enriched in these lipids or domain interfaces may represent regions with high H+/OH− conductivity, (iii) H+/OH− fluxes are not governed by lipid order and (iv) chol can inhibit or promote H+/OH− permeability depending on the total lipid environment. Theories of proton permeation are discussed in the light of these results.
Characterization of Ca2+ interactions with matrix metallopeptidase-12: implications for matrix metallopeptidase regulation
Authors: Gossas Thomas , Danielson U. Helena
Published: August 2006

Matrix metallopeptidase-12 (MMP-12) binds three calcium ions and a zinc ion, in addition to the catalytic zinc ion. These ions are thought to have a structural role, stabilizing the active conformation of the enzyme. To characterize the importance of Ca2+ binding for MMP-12 activity and the properties of the different Ca2+ sites, the activity as a function of [Ca2+] and the effect of pH was investigated. The enzymatic activity was directly correlated to calcium binding and a Langmuir isotherm for three binding sites described the activity as a function of [Ca2+]. The affinities for two of the binding sites were quantified at several pH values. At pH 7.5, the KD was 0.1 mM for the high-affinity binding site, 5 mM for the intermediate-affinity binding site and >100 mM for the low-affinity binding site. For all three sites, the affinity for calcium decreased with reduced pH, in accordance with the loss of interactions upon protonation of the calcium-co-ordinating aspartate and glutamate carboxylates at acidic pH. The pKa values of the calcium binding sites with the highest and intermediate affinities were determined to be 4.3 and 6.5 respectively. Optimal pH for catalysis was above 7.5. The low-, intermediate- and high-affinity binding sites were assigned on the basis of analysis of three-dimensional-structures of MMP-12. The strong correlation between MMP-12 activity and calcium binding for the physiologically relevant [Ca2+] and pH ranges studied suggest that Ca2+ may be involved in controlling the activity of MMP-12.
Inhibition of hepatocyte nuclear factor 4 transcriptional activity by the nuclear factor κB pathway
Authors: Nikolaidou-Neokosmidou Varvara , Zannis Vassilis I. , Kardassis Dimitris
Published: August 2006

HNF-4 (hepatocyte nuclear factor 4) is a key regulator of liver-specific gene expression in mammals. We have shown previously that the activity of the human APOC3 (apolipoprotein C-III) promoter is positively regulated by the anti-inflammatory cytokine TGFβ (transforming growth factor β) and its effectors Smad3 (similar to mothers against decapentaplegic 3) and Smad4 proteins via physical and functional interactions between Smads and HNF-4. We now show that the pro-inflammatory cytokine TNFα (tumour necrosis factor α) antagonizes TGFβ for the regulation of APOC3 gene expression in hepatocytes. TNFα was a strong inhibitor of the activity of apolipoprotein promoters that harbour HNF-4 binding sites and this inhibition required HNF-4. Using specific inhibitors of TNFα-induced signalling pathways, it was shown that inhibition of the APOC3 promoter by TNFα involved NF-κB (nuclear factor κB). Latent membrane protein 1 of the Epstein–Barr virus, which is an established potent activator of NF-κB as well as wild-type forms of various NF-κB signalling mediators, also inhibited strongly the APOC3 promoter and the transactivation function of HNF-4. TNFα had no effect on the stability or the nuclear localization of HNF-4 in HepG2 cells, but inhibited the binding of HNF-4 to the proximal APOC3 HRE (hormone response element). Using the yeast-transactivator-GAL4 system, we showed that both AF-1 and AF-2 (activation functions 1 and 2) of HNF-4 are inhibited by TNFα and that this inhibition was abolished by overexpression of different HNF-4 co-activators, including PGC-1 (peroxisome-proliferator-activated-receptor-γ co-activator 1), CBP [CREB (cAMP-response-element-binding protein) binding protein] and SRC3 (steroid receptor co-activator 3). In summary, our findings indicate that TNFα, or other factors that trigger an NF-κB response in hepatic cells, inhibit the transcriptional activity of the APOC3 and other HNF-4-dependent promoters and that this inhibition could be accounted for by a decrease in DNA binding and the down-regulation of the transactivation potential of the AF-1 and AF-2 domains of HNF-4.
Membrane binding of zebrafish actinoporin-like protein: AF domains, a novel superfamily of cell membrane binding domains
Authors: Gutiérrez-Aguirre Ion , Trontelj Peter , Maček Peter , Lakey Jeremy H. , Anderluh Gregor
Published: August 2006

Actinoporins are potent eukaryotic pore-forming toxins specific for sphingomyelin-containing membranes. They are structurally similar to members of the fungal fruit-body lectin family that bind cell-surface exposed Thomsen–Friedenreich antigen. In the present study we found a number of sequences in public databases with similarity to actinoporins. They originate from three animal and two plant phyla and can be classified in three families according to phylogenetic analysis. The sequence similarity is confined to a region from the C-terminal half of the actinoporin molecule and comprises the membrane binding site with a highly conserved P-[WYF]-D pattern. A member of this novel actinoporin-like protein family from zebrafish was cloned and expressed in Escherichia coli. It displays membrane-binding behaviour but does not have permeabilizing activity or sphingomyelin specificity, two properties typical of actinoporins. We propose that the three families of actinoporin-like proteins and the fungal fruit-body lectin family comprise a novel superfamily of membrane binding proteins, tentatively called AF domains (abbreviated from actinoporin-like proteins and fungal fruit-body lectins).
Determination of the consensus DNA-binding sequence and a transcriptional activation domain for ESE-2
Authors: Choi Yeon Sook , Sinha Satrajit
Published: August 2006

The ESE (epithelium-specific Ets) subfamily of Ets transcription factors plays an important role in regulating gene expression in a variety of epithelial cell types. Although ESE proteins have been shown to bind to regulatory elements of some epithelial genes, the optimal DNA-binding sequence has not been experimentally ascertained for any member of the ESE subfamily of transcription factors. This has made the identification and validation of their targets difficult. We are studying ESE-2 (Elf5), which is highly expressed in epithelial cells of many tissues including skin keratinocytes. Here, we identify the preferred DNA-binding site of ESE-2 by performing CASTing (cyclic amplification and selection of targets) experiments. Our analysis shows that the optimal ESE-2 consensus motif consists of a GGA core and an AT-rich 5′- and 3′-flanking sequences. Mutational and competition experiments demonstrate that the flanking sequences that confer high DNA-binding affinity for ESE-2 show considerable differences from the known consensus DNA-binding sites of other Ets proteins, thus reinforcing the idea that the flanking sequences may impart recognition specificity for Ets proteins. In addition, we have identified a novel isoform of murine ESE-2, ESE-2L, that is generated by use of a hitherto unreported new exon and an alternate promoter. Interestingly, transient transfection assays with an optimal ESE-2 responsive reporter show that both ESE-2 and ESE-2L are weak transactivators. However, similar studies utilizing GAL4 chimaeras of ESE-2 demonstrate that while the DNA-binding ETS (E twenty-six) domain functions as a repressor, the PNT (pointed domain) of ESE-2 can act as a potent transcriptional activation domain. This novel transactivating property of PNT is also shared by ESE-3, another ESE family member. Identification of the ESE-2 consensus site and characterization of the transcriptional activation properties of ESE-2 shed new light on its potential as a regulator of target genes.
Id2 leaves the chromatin of the E2F4–p130-controlled c-myc promoter during hepatocyte priming for liver regeneration
Authors: Rodríguez José L. , Sandoval Juan , Serviddio Gaetano , Sastre Juan , Morante María , Perrelli Maria-Giulia , Martínez-Chantar María L. , Viña José , Viña Juan R. , Mato José M. , Ávila Matías A. , Franco Luis , López-Rodas Gerardo , Torres Luis
Published: August 2006

The Id (inhibitor of DNA binding or inhibitor of differentiation) helix–loop–helix proteins are involved in the regulation of cell growth, differentiation and cancer. The fact that the molecular mechanisms of liver regeneration are not completely understood prompted us to study the fate of Id2 in proliferating liver. Id2 increases in liver regeneration after partial hepatectomy, following the early induction of its gene. Co-immunoprecipitation shows that Id2 forms a complex with E2F4, p130 and mSin3A in quiescent liver and all these components are present at the c-myc promoter as shown using ChIP (chromatin immunoprecipitation). Activation of c-myc during hepatocyte priming (G0–G1 transition) correlates with the dissociation of Id2 and HDAC (histone deacetylase), albeit p130 remains bound at least until 6 h. Moreover, as the G0–G1 transition progresses, Id2 and HDAC again bind the c-myc promoter concomitantly with the repression of this gene. The time course of c-myc binding to the Id2 promoter, as determined by ChIP assays is compatible with a role of the oncoprotein as a transcriptional inducer of Id2 in liver regeneration. Immunohistochemical analysis shows that Id2 also increases in proliferating hepatocytes after bile duct ligation. In this case, the pattern of Id2 presence in the c-myc promoter parallels that found in regenerating liver. Our results may suggest a control role for Id2 in hepatocyte priming, through a p130 dissociation-independent regulation of c-myc.
Differential expression of a C-terminal splice variant of phosphatidylinositol transfer protein β lacking the constitutive-phosphorylated Ser262 that localizes to the Golgi compartment
Authors: Morgan Clive P. , Allen-Baume Victoria , Radulovic Marko , Li Michelle , Skippen Alison , Cockcroft Shamshad
Published: August 2006

Mammalian PITPβ (phosphatidylinositol transfer protein β) is a 272-amino-acid polypeptide capable of transferring PtdIns, PtdCho and SM (sphingomyelin) between membrane bilayers. It has been reported that Ser262 present in the C-terminus of PITPβ is constitutively phosphorylated and determines Golgi localization. We provide evidence for the expression of an sp (splice) variant of PITPβ (PITPβ-sp2) where the C-terminal 15 amino acids of PITPβ-sp1 are replaced by an alternative C-terminus of 16 amino acids. PITPβ-sp1 is the product of the first 11 exons, whereas PITPβ-sp2 is a product of the first 10 exons followed by the twelfth exon – exon 11 being ‘skipped’. Both splice variants are capable of PtdIns and PtdCho transfer, with PITPβ-sp2 being unable to transport SM. PITPβ is ubiquitously expressed, with the highest amounts of PITPβ found in HL60 cells and in rat liver; HL60 cells express only PITPβ-sp1, whereas rat liver expresses both sp variants in similar amounts. In both cell types, PITPβ-sp1 is constitutively phosphorylated and both the PtdIns and PtdCho forms of PITPβ-sp1 are present. In contrast, PITPβ-sp2 lacks the constitutively phosphorylated Ser262 (replaced with glutamine). Nonetheless, both PITPβ variants localize to the Golgi and, moreover, dephosphorylation of Ser262 of PITPβ-sp1 does not affect its Golgi localization. The presence of PITPβ sp variants adds an extra level of proteome complexity and, in rat liver, the single gene for PITPβ gives rise to seven distinct protein species that can be resolved on the basis of their charge differences.
Interfacial behaviour of bovine testis hyaluronidase
Authors: Belem-Gonçalves Silvia , Tsan Pascale , Lancelin Jean-Marc , Alves Tito L. M. , Salim Vera M. , Besson Françoise
Published: August 2006

The interfacial properties of bovine testicular hyaluronidase were investigated by demonstrating the association of hyaluronidase activity with membranes prepared from bovine testis. Protein adsorption to the air/water interface was investigated using surface pressure-area isotherms. In whichever way the interfacial films were obtained (protein injection or deposition), the hyaluronidase exhibited a significant affinity for the air/water interface. The isotherm obtained 180 min after protein injection into a pH 5.3 subphase was similar to the isotherm obtained after spreading the same amount of protein onto the same subphase, indicating that bovine testicular hyaluronidase molecules adopted a similar arrangement and/or conformation at the interface. Increasing the subphase pH from 5.3 to 8 resulted in changes of the protein isotherms. These modifications, which could correspond to the small pH-induced conformational changes observed by Fourier-transform IR spectroscopy, were discussed in relation to the pH influence on the hyaluronidase activity. Adding hyaluronic acid, the enzyme substrate, to the subphase tested the stability of the interfacial properties of hyaluronidase. The presence of hyaluronic acid in the subphase did not modify the protein adsorption and allowed substrate binding to a preformed film of hyaluronidase at pH 5.3, the optimal pH for the enzyme activity. Such effects of hyaluronic acid were not observed when the subphase was constituted of pure water, a medium where the enzyme activity was negligible. These influences of hyaluronic acid were discussed in relation to the modelled structure of bovine testis hyaluronidase where a hydrophobic region was proposed to be opposite of the catalytic site.
Crystal structure of the SENP1 mutant C603S–SUMO complex reveals the hydrolytic mechanism of SUMO-specific protease
Authors: Xu Zheng , Chau So Fun , Lam Kwok Ho , Chan Ho Yin , Ng Tzi Bun , Au Shannon W. N.
Published: August 2006

SUMO (small ubiquitin-related modifier)-specific proteases catalyse the maturation and de-conjugation processes of the sumoylation pathway and modulate various cellular responses including nuclear metabolism and cell cycle progression. The active-site cysteine residue is conserved among all known SUMO-specific proteases and is not substitutable by serine in the hydrolysis reactions demonstrated previously in yeast. We report here that the catalytic domain of human protease SENP1 (SUMO-specific protease 1) mutant SENP1CC603S carrying a mutation of cysteine to serine at the active site is inactive in maturation and de-conjugation reactions. To further understand the hydrolytic mechanism catalysed by SENP1, we have determined, at 2.8 Å resolution (1 Å=0.1 nm), the X-ray structure of SENP1CC603S–SUMO-1 complex. A comparison of the structure of SENP2–SUMO-1 suggests strongly that SUMO-specific proteases require a self-conformational change prior to cleavage of peptide or isopeptide bond in the maturation and de-conjugation processes respectively. Moreover, analysis of the interface of SENP1 and SUMO-1 has led to the identification of four unique amino acids in SENP1 that facilitate the binding of SUMO-1. By means of an in vitro assay, we further demonstrate a novel function of SENP1 in hydrolysing the thioester linkage in E1-SUMO and E2-SUMO complexes. The results disclose a new mechanism of regulation of the sumoylation pathway by the SUMO-specific proteases.
Functional expression of a biologically active fragment of soluble gp130 as an ELP-fusion protein in transgenic plants: purification via inverse transition cycling
Authors: Lin Meng , Rose-John Stefan , Grötzinger Joachim , Conrad Udo , Scheller Jürgen
Published: August 2006

In murine models of Crohn's disease, rheumatoid arthritis and colon cancer, IL-6 (interleukin-6) signalling via the sIL-6R (soluble IL-6 receptor; termed IL-6 trans-signalling) has been shown to promote the pathology associated with these conditions. These detrimental activities can, however, be selectively blocked by soluble forms of the gp130 (glycoprotein 130) receptor. Although sgp130 (soluble gp130) therefore represents a viable therapeutic modality for the treatment of these conditions, the mass manufacture of such biologics is often expensive. The advent of molecular farming has, however, provided an extremely cost-effective strategy for the engineering of recombinant proteins. Here, we describe the expression and production of a biologically active sgp130 variant that is expressed in transgenic tobacco plants as an ELP (elastin-like peptide)-fusion protein (mini-gp130–ELP). Mini-gp130–ELP consists of the first three domains of gp130 (Ig-like domain and cytokine binding module) fused to 100 repeats of ELP. Expression of mini-gp130–ELP did not affect the growth rate or morphology of the transgenic plants, and purification was achieved using inverse transition cycling. This approach led to an overall yield of 141 μg of purified protein per g of fresh leaf weight. The purified mini-gp130–ELP specifically inhibited sIL-6R-mediated trans-signalling as measured by binding to the IL-6–sIL-6R complex and through its ability to block sIL-6R-mediated activation of STAT3 (signal transducer and activator of transcription 3) phosphorylation and proliferation in human hepatoma cells and murine pre-B-cells. Consequently, the present study validates the potential application of molecular farming in transgenic tobacco plants as a strategy for the expression and purification of therapeutically advantageous biologics such as sgp130.
In vivo contribution of amino acid sulfur to cartilage proteoglycan sulfation
Authors: Pecora Fabio , Gualeni Benedetta , Forlino Antonella , Superti-Furga Andrea , Tenni Ruggero , Cetta Giuseppe , Rossi Antonio
Published: August 2006

Cytoplasmic sulfate for sulfation reactions may be derived either from extracellular fluids or from catabolism of sulfur-containing amino acids and other thiols. In vitro studies have pointed out the potential relevance of sulfur-containing amino acids as sources for sulfation when extracellular sulfate concentration is low or when its transport is impaired such as in DTDST [DTD (diastrophic dysplasia) sulfate transporter] chondrodysplasias. In the present study, we have considered the contribution of cysteine and cysteine derivatives to in vivo macromolecular sulfation of cartilage by using the mouse model of DTD we have recently generated [Forlino, Piazza, Tiveron, Della Torre, Tatangelo, Bonafe, Gualeni, Romano, Pecora, Superti-Furga et al. (2005) Hum. Mol. Genet. 14, 859–871]. By intraperitoneal injection of [35S]cysteine in wild-type and mutant mice and determination of the specific activity of the chondroitin 4-sulfated disaccharide in cartilage, we demonstrated that the pathway by which sulfate is recruited from the intracellular oxidation of thiols is active in vivo. To check whether cysteine derivatives play a role, sulfation of cartilage proteoglycans was measured after treatment for 1 week of newborn mutant and wild-type mice with hypodermic NAC (N-acetyl-L-cysteine). The relative amount of sulfated disaccharides increased in mutant mice treated with NAC compared with the placebo group, indicating an increase in proteoglycan sulfation due to NAC catabolism, although pharmacokinetic studies demonstrated that the drug was rapidly removed from the bloodstream. In conclusion, cysteine contribution to cartilage proteoglycan sulfation in vivo is minimal under physiological conditions even if extracellular sulfate availability is low; however, the contribution of thiols to sulfation becomes significant by increasing their plasma concentration.
Crystal structure of yeast Sis1 peptide-binding fragment and Hsp70 Ssa1 C-terminal complex
Authors: Li Jingzhi , Wu Yunkun , Qian Xinguo , Sha Bingdong
Published: August 2006

Heat shock protein (Hsp) 40 facilitates the critical role of Hsp70 in a number of cellular processes such as protein folding, assembly, degradation and translocation in vivo. Hsp40 and Hsp70 stay in close contact to achieve these diverse functions. The conserved C-terminal EEVD motif in Hsp70 has been shown to regulate Hsp40–Hsp70 interaction by an unknown mechanism. Here, we provide a structural basis for this regulation by determining the crystal structure of yeast Hsp40 Sis1 peptide-binding fragment complexed with the Hsp70 Ssa1 C-terminal. The Ssa1 extreme C-terminal eight residues, G634PTVEEVD641, form a β-strand with the domain I of Sis1 peptide-binding fragment. Surprisingly, the Ssa1 C-terminal binds Sis1 at the site where Sis1 interacts with the non-native polypeptides. The negatively charged residues within the EEVD motif in Ssa1 C-terminal form extensive charge–charge interactions with the positively charged residues in Sis1. The structure-based mutagenesis data support the structural observations.
Transmembrane topology of ceramide synthase in yeast
Authors: Kageyama-Yahara Natsuko , Riezman Howard
Published: August 2006

Ceramide plays a crucial role as a basic building block of sphingolipids, but also as a signalling molecule mediating cell-fate decisions. Three genes, LAG1, LAC1 and LIP1, have been shown to be required for ceramide synthase activity in Saccharomyces cerevisiae [Guillas, Kirchman, Chuard, Pfefferli, Jiang, Jazwinski and Conzelman (2001) EMBO J. 20, 2655–2665; Schorling, Vallee, Barz, Reizman and Oesterhelt (2001) Mol. Biol. Cell 12, 3417–3427; Vallee and Riezman (2005) EMBO J. 24, 730–741]. In the present study, the topology of the Lag1p and Lac1p subunits was investigated. The N- and C-termini of the proteins are in the cytoplasm and eight putative membrane-spanning domains were identified in Lag1p and Lac1p by insertion of glycosylation and factor Xa cleavage sites at various positions. The conserved Lag motif, potentially containing the active site, is most likely embedded in the membrane. We also present evidence that histidine and aspartic acid residues in the Lag motif are essential for the function of Lag1p in vivo.
Cyclo-oxygenase 2 expression impairs serum-withdrawal-induced apoptosis in liver cells
Authors: Fernández-Martínez Amalia , Mollá Belén , Mayoral Rafael , Boscá Lisardo , Casado Marta , Martín-Sanz Paloma
Published: August 2006

We have investigated the mechanism of COX-2 (cyclo-oxygenase 2)-dependent inhibition of apoptosis in liver, a key pathway underlying proliferative actions of COX-2 in liver cancers, cirrhosis, chronic hepatitis C infection and regeneration after partial hepatectomy. Stable expression of COX-2 in CHL (Chang liver) cells induced proliferation, with an increase in the proportion of cells in S-phase, but no other significant changes in cell-cycle distribution. This was associated with a marked inhibition of the apoptotic response to serum deprivation, an effect mimicked by treating empty-vector-transfected control cells (CHL-V cells) with prostaglandin E2 and prevented in COX-2-expressing cells (CHL-C cells) treated with selective inhibitors of COX-2. Serum-deprived CHL-V cells displayed several indicators of activation of intrinsic apoptosis: caspases 9 and 3 activated within 6 h and caspase 8 within 18 h, Bax expression was induced, cytochrome c was released to the cytosol, and PARP-1 [poly(ADP-ribose) polymerase 1] cleavage was evident in nuclei. COX-2 expression blocked these events, concomitant with reduced expression of p53 and promotion of Akt phosphorylation, the latter indicating activation of survival pathways. CHL cells were resistant to stimulation of the extrinsic pathway with anti-Fas antibody. Moreover, in vivo expression of GFP (green fluorescent protein)-labelled COX-2 in mice by hydrodynamics-based transient transfection conferred resistance to caspase 3 activation and apoptosis induced by stimulation of Fas.
Calmodulin interacts with the platelet ADP receptor P2Y1
Authors: Arthur Jane F. , Shen Yang , Mu Fi-Tjen , Leon Catherine , Gachet Christian , Berndt Michael C. , Andrews Robert K.
Published: August 2006

P2Y1 [P2 (purinergic type-2)-receptor 1] is a G-protein-coupled ADP receptor that regulates platelet activation and ADP-induced Ca2+ signalling. Studies using P2Y1-knockout mice, Gq-deficient mice or P2Y1-selective inhibitors have previously identified a key role for P2Y1 in pathophysiological thrombus formation at high shear stress. We provide evidence that a positively charged juxtamembrane sequence within the cytoplasmic C-terminal tail of P2Y1 can bind directly to the cytosolic regulatory protein calmodulin. Deletion by mutagenesis of the calmodulin-binding domain of P2Y1 inhibits intracellular Ca2+ flux in transfected cells. These results suggest that the interaction of calmodulin with the P2Y1 C-terminal tail may regulate P2Y1-dependent platelet aggregation.
Role of long-range elastic energy in relaxor ferroelectrics
Authors: Wang L. F. , Liu J.-M.
Published: August 2006

The dipole configuration of relaxor ferroelectrics (RFs) is investigated by numerically solving the time-dependent Ginzburg-Landau equation based on the dipole defect model. The domain structure of RFs is revealed to consist of dipole ordered clusters embedded in the paraelectric matrix. We demonstrate that the role of long-range elastic energy in RFs is much less important than in normal ferroelectrics, although the shape of the dipole clusters depends on the elastic energy. Based on the numerical results, a phase diagram of temperature-defect density for RFs is constructed, which identifies four distinct phase regimes.
Effect of growth conditions on the magnetic characteristics of GaGdN
Authors: Hite J. K. , Frazier R. M. , Davies R. , Thaler G. T. , Abernathy C. R. , Pearton S. J. , Zavada J. M.
Published: August 2006

GaGdN layers were grown by gas source molecular beam epitaxy with varying crystal quality and Gd concentrations as set by the Gd cell temperature. Magnetic measurements showed ferromagnetic behavior at room temperature, with the saturation magnetization dependent both on Gd concentration and crystalline quality. The Gd concentration was under the detection limit of secondary ion mass spectrometry, and estimated to be on the order of <1017at.∕cm3. As expected at this low dopant concentration, x-ray diffraction measurements showed the films to be single phase. Gd-doped samples codoped with Si to make them conducting with resistivity of 0.04Ωcm showed similar magnetic properties as Gd-doped films without addition of Si.
Experimental demonstration of high quality factor, x-dipole modes in InAs∕InP quantum dot photonic crystal microcavity membranes
Authors: Frédérick Simon , Dalacu Dan , Lapointe Jean , Poole Philip J. , Aers Geof C. , Williams Robin L.
Published: August 2006

The authors study the quality factor Q of the x-dipole mode in single missing hole defect photonic crystal microcavities in InAs∕InP quantum dot membranes as a function of the structural design parameters. Photoluminescence experiments show an optimized Q in excess of 28 000 for a wavelength close to λ=1550nm. This is to be compared with a Q of 57 000 determined by finite difference time domain calculations. The fabrication tolerances necessary to achieve experimental Q values close to those predicted by theory are identified.
Shape induced anomalies in vortex pinning and dynamics of superconducting antidot arrays with spherical cavities
Authors: Filby E. T. , Zhukov A. A. , de Groot P. A. J. , Ghanem M. A. , Bartlett P. N. , Metlushko V. V.
Published: August 2006

Using electrochemical deposition of Pb in the pores of templates prepared by self-assembly from colloidal suspensions of polystyrene latex spheres, well ordered superconducting antidot arrays with spherically shaped holes are fabricated. In contrast to conventional lithographic arrays the samples with spherical cavities demonstrate significantly reduced pinning strength favoring the formation of commensurate states. The ac-flux penetration acquires a hybrid intra- and intervalley regime. For high ac drives an unusual inversion to paramagnetic ac shielding is found at commensurate states.
Plasmonic laser antenna
Authors: Cubukcu Ertugrul , Kort Eric A. , Crozier Kenneth B. , Capasso Federico
Published: August 2006

The authors have demonstrated a surface plasmon device composed of a resonant optical antenna integrated on the facet of a commercial diode laser, termed a plasmonic laser antenna. This device generates enhanced and spatially confined optical near fields. Spot sizes of a few tens of nanometers have been measured at a wavelength ∼0.8μm. This device can be implemented in a wide variety of semiconductor lasers emitting in spectral regions ranging from the visible to the far infrared, including quantum cascade lasers. It is potentially useful in many applications including near-field optical microscopes, optical data storage, and heat-assisted magnetic recording.
All-fiber picosecond laser source based on nonlinear spectral compression
Authors: Rusu M. , Okhotnikov O. G.
Published: August 2006

The authors report the realization of an all-fiber system emitting high-quality ultrashort powerful light pulses at 1060nm. The oscillator-amplifier system is intended for compact visible light generation via frequency conversion. Optical nonlinearity in a fiber amplifier is employed to compress the spectrum of pulses negatively prechirped in a hollow core photonic bandgap fiber. Second-harmonic generation in a periodically poled crystal is demonstrated.
Improvement of low-field magnetoresistance and Curie temperature in the hole doping of double perovskites Sr2FeMoO6 polycrystals
Authors: Lü M. F. , Wang J. P. , Liu J. F. , Hao X. F. , Zhou D. F. , Wu Z. J. , Meng Jian
Published: August 2006

Polycrystalline Sr2FeMoO6 compounds with most vacancies at normal Fe sites were fabricated through Mo hole doping; its effect is similar to Fe3+ by our estimation. Sharp increase of magnetoconductance at low field was evidence of spin-polarized tunneling between the grains. The room temperature low-field magnetoresistivity at optimal doping x=0.03 is 8.5% in 3000Oe and increases to 11.4% in 1T associated with soft magnetic behaviors; furthermore it exhibits a ferromagnetic Curie temperature of 450K, connected with hole doping effect. The improved magnetoresistivity behavior was related to Curie temperature.
Optical generation of high frequency ultrasound using two-dimensional gold nanostructure
Authors: Hou Yang , Kim Jin-Sung , Ashkenazi Shai , O’Donnell Matthew , Guo L. Jay
Published: August 2006

A two-dimensional (2D) gold nanostructure is used to optically generate high frequency ultrasound. The structure consists of 2D arrangements of gold nanoparticles, sandwiched between a transparent substrate and a 4.5μm thick polydimethylsiloxane (PDMS) layer. The acoustic signal displays significant improvements compared to a bulk black PDMS films (the current state of the art) at frequencies from 50to100MHz. The high optical extinction ratio of the gold nanostructure provides a convenient method to construct an integrated transmit/receive optoacoustic array. These results show that a 2D gold nanostructure can be used to produce high frequency arrays for ultrasound imaging.
High differential resistance type-II InAs∕GaSb superlattice photodiodes for the long-wavelength infrared
Authors: Hood Andrew , Hoffman Darin , Nguyen Binh-Minh , Delaunay Pierre-Yves , Michel Erick , Razeghi Manijeh
Published: August 2006

Type-II InAs∕GaSb superlattice photodiodes with a 50% cutoff wavelength ranging from 11to13μm are presented. Optimization of diffusion limited photodiodes provided superlattice structures for improved injection efficiency in direct injection hybrid focal plane array applications. Photodiodes with a cutoff wavelength of 12.9μm exhibit an R0A of ∼7Ωcm2 and a Johnson-limited detectivity of 4.03×1010cmHz1∕2W−1 operating at 77K. Quantum efficiency measurements indicate minority carrier diffusion lengths exceeding 3μm.
Heating and cooling in semiconductor structures by an electric current
Authors: Logvinov G. N. , Velázquez J. E. , Lashkevych I. M. , Gurevich Yu. G.
Published: August 2006

A comprehensive study of the mechanisms of heating and cooling originated by an electrical current in semiconductor devices is reported. The authors studied the Peltier, Joule, and Thomson phenomena self-consistently and found that the magnitudes of all of them were commensurable. A new formulation and interpretation of the Thomson effect are offered. The main conclusion of the present work is that the thermal analysis of any semiconductor device under real working conditions demands the inclusion of all heating and cooling mechanisms simultaneously.
Direct measurement of the linewidth enhancement factor by optical heterodyning of an amplitude-modulated quantum cascade laser
Authors: Aellen Thierry , Maulini Richard , Terazzi Romain , Hoyler Nicolas , Giovannini Marcella , Faist Jérôme , Blaser Stéphane , Hvozdara Lubos
Published: August 2006

A measurement of the linewidth enhancement factor α of a distributed feedback quantum cascade laser is presented. The measurement is based on a heterodyning experiment, in which one of the lasers is modulated at radio frequency. A value of α=0.02±0.20 is obtained for a modulation frequency of 500MHz. As the frequency is decreased, α increases and is consistent with a thermal chirp effect.
Initial oxidation of the Rh(110) surface: Ordered adsorption and surface oxide structures
Authors: Dri C. , Africh C. , Esch F. , Comelli G. , Dubay O. , Köhler L. , Mittendorfer F. , Kresse G. , Dudin P. , Kiskinova M.
Published: August 2006

The initial oxidation of the Rh(110) surface was studied by scanning tunneling microscopy, core level spectroscopy, and density functional theory. The experiments were carried out exposing the Rh(110) surface to molecular or atomic oxygen at temperatures in the 500–700K range. In molecular oxygen ambient, the oxidation terminates at oxygen coverage close to a monolayer with the formation of alternating islands of the (10×2) one-dimensional surface oxide and (2×1)p2mg adsorption phases. The use of atomic oxygen facilitates further oxidation until a structure with a c(2×4) periodicity develops. The experimental and theoretical results reveal that the c(2×4) structure is a “surface oxide” very similar to the hexagonal O–Rh–O trilayer structures formed on the Rh(111) and Rh(100) substrates. Some of the experimentally found adsorption phases appear unstable in the phase diagram predicted by thermodynamics, which might reflect kinetic hindrance. The structural details, core level spectra, and stability of the surface oxides formed on the three basal planes are compared with those of the bulk RhO2 and Rh2O3.
T-shaped microcantilever sensor with reduced deflection offset
Authors: Plaza J. A. , Zinoviev K. , Villanueva G. , Álvarez M. , Tamayo J. , Domínguez C. , Lechuga L. M.
Published: August 2006

The authors have designed and fabricated arrays of microcantilevers with a geometry that shows reduced initial angular offset and angle deviation between the cantilevers of the array. This feature allows to detect the displacement of the cantilevers using the optical beam deflection technique and a single split photodetector. The structure is analytically and numerically simulated to demonstrate its feasibility. In addition, experimental measurements of the angle offset corroborate the offset and the angle deviation reduction. Finally, they illustrate the potential of these micromechanical structures as sensors by measuring a monolayer of single stranded DNA.
Steryl glucoside concentration declines with Cycas micronesica seed age
Authors: Marler Thomas E. , Lee Vivian , Chung J. , Shaw Christopher A.
Published: August 2006

Neurotoxins contained in the seeds of Cycas micronesica K.D. Hill have been implicated in the Guam neurological disease cluster, amyotrophic lateral sclerosis–parkinsonism dementia complex (ALS–PDC). Some of these neurotoxins remain in the washed cycad seed flour that was historically an important part of the Chamorro diet. Of these, variant steryl glucosides have been identified by us as a possible etiological factor in the disease. In vitro and in vivo animal studies have strongly supported a role for these molecules in some forms of neurodegeneration. As part of a series of studies, we have now determined the concentrations of several steryl glucosides and their sterol precursors as affected by the age of C. micronesica seeds. The concentration of these molecules declined with seed age from 2.0 to 30.5 months. Following log-transformation of both axes, the decline was linear. Similarly, concentration of all but one of the molecules declined with age when samples were restricted to gametophyte tissue. Factors suspected of influencing phenotypic plasticity must be addressed when interpreting plant physiology data. Our results confirm for the first time that tissue age must be documented and reported in cycad seed biochemistry studies to remove ambiguities from results. Past studies in this important area of research have failed to account for the potential impact of seed age, rendering previous outcomes and interpretations of cycad neurotoxins in their impact on ALS–PDC ambiguous.
Two AP2 domain containing genes isolated from the cold-hardy Citrus relative Poncirus trifoliata are induced in response to cold
Authors: Şahin-Çevik Mehtap , Moore Gloria A.
Published: August 2006

Poncirus trifoliata (L.) Raf. is a cold-hardy, interfertile Citrus relative able to tolerate temperatures as low as –26°C when cold acclimated. Therefore, it has been used for improving cold tolerance in cold-sensitive commercial citrus varieties. A cold-induced cDNA library was constructed by subtractive hybridisation of non-acclimated and 2-d cold-acclimated P. trifoliata seedlings and many genes induced in response to cold were identified. Two of these cDNAs, PI-B05 and PI-C10, were selected from this library for further characterisation. Full-length cDNA sequences of these genes were obtained by 5′ and 3′ rapid amplification of cDNA ends (RACE). Sequence analysis revealed that PI-B05 contained an apetala2 / ethylene response factor (AP2 / ERF) domain and showed homology with ERF proteins from other plants, some of which are involved in environmental stress-induced gene expression. PI-C10 contained both AP2 / ERF and B3 DNA binding domains and showed homology with other plant proteins in the RAV subfamily of the AP2 / ERF transcription factors, some of which are induced in response to cold and other environmental stresses. Expression patterns of these genes in cold-tolerant P. trifoliata and cold-sensitive pummelo [Citrus grandis (L.) Osb.] in response to cold and drought at different time points were analysed by northern blots. Expression analysis showed that both genes were induced in response to cold, but not under drought conditions in cold-hardy P. trifoliata. However, little or no expression of these genes was detected by northern analysis in cold-sensitive pummelo under cold or drought conditions. The sequence analysis and expression data indicated that these genes may play a role in cold-responsive gene expression in cold-hardy P. trifoliata and could possibly be used for improving cold tolerance in cold-sensitive citrus cultivars.
VvMADS9, a class B MADS-box gene involved in grapevine flowering, shows different expression patterns in mutants with abnormal petal and stamen structures
Authors: Sreekantan Lekha , Torregrosa Laurent , Fernandez Lucie , Thomas Mark R.
Published: August 2006

VvMADS9, a MADS-box gene, from grapevine (Vitis vinifera L.) cultivar Cabernet Sauvignon has been isolated and its expression pattern studied in wild type Cabernet Sauvignon, Mourvèdre, and Bouchalès cultivars and mutants of the latter two genotypes showing abnormal petal / stamen structures. Sequence analysis showed that VvMADS9 was highly similar to PISTILLATA (PI), the class B gene that specifies the identity of petals and stamens in Arabidopsis. The temporal expression pattern of VvMADS9 studied through real-time PCR revealed that its expression was specific to flower development. The low levels of expression in the Mourvèdre mutant and the skewed expression pattern in the Bouchalès mutant as compared to their wild type counterparts suggested that VvMADS9 is involved in normal formation of petals and stamens. Through in situ hybridisation, expression of VvMADS9 was detected in stamens and weak expression on the basal regions of the petals. This suggested a possible role for VvMADS9 in specifying stamen and petal organ identity in grapevine similar to Class B genes in other species. All evidence thus pointed to the conclusion that VvMADS9 is an orthologue of PISTILLATA in grapevine.
Flowing water decreases hydrodynamic signal detection in a fish with an epidermal lateral-line system
Authors: Bassett Daniel K. , Carton Alexander G. , Montgomery John C.
Published: August 2006

The lateral-line system of the common bully, Gobiomorphus cotidianus, is unusual in that it possesses an extensive array of superficial neuromasts. Fish were trained to orientate to a small vibrating bead (50 Hz). By manipulating the amplitude of vibration to determine the threshold level for the behaviour, the hydrodynamic detection capabilities of the common bully were characterised in both still- and flowing-water. In still water, the common bully attained a detection threshold (calculated as the amplitude of water particle displacement at the snout) of 3.3 × 10−5 cm at 50 Hz. Successive elevations in the background flow caused a 10-fold decrease in detection sensitivity. At a background flow of 4.5 cm s–1 the detection threshold increased to 3 × 10−4 cm. These findings demonstrate that a lateral-line system that lacks sub-surface canal neuromasts is most sensitive in still-water conditions (low-noise). However, this system is compromised under flowing-water conditions such that sensitivity is reduced at current velocities >1.5 cm s–1.
Prediction of riverine fish assemblages through the concept of environmental filters
Authors: Chessman Bruce C.
Published: August 2006

Although the taxonomic composition and richness of fish assemblages are important properties to be considered in freshwater bioassessment, conservation and rehabilitation, it can be difficult to establish a natural benchmark for these properties because of widespread human impact and a lack of pristine reference sites or pre-impact data. As an alternative to the reference site approach, the concept of multiple environmental filters was used to predict the assemblages of fish taxa expected in the absence of anthropogenic stress at 85 sites on rivers in north-eastern New South Wales, Australia. The predicted native fish assemblages were compared with the assemblages recorded by backpack and boat electrofishing at each site. The number of native species predicted by the filters model at each site was highly correlated with the observed number of native species (R2 = 0.75; P < 0.001) but the observed number was generally lower. The model had an average sensitivity of 93% and specificity of 87%, but sensitivity and specificity were considerably less for a few species, including some that are known to have suffered historical declines or been translocated outside of their natural ranges. Comparisons between predicted and observed richness and composition can be used to identify areas of high conservation value and areas where native fish assemblages have been adversely affected by anthropogenic impacts.
DNA-mediated anisotropic mechanical reinforcement of a virus
Authors: Carrasco C. , Carreira A. , Schaap I. A. T. , Serena P. A. , Gómez-Herrero J. , Mateu M. G. , de Pablo P. J.
Published: August 2006

In this work, we provide evidence of a mechanism to reinforce the strength of an icosahedral virus by using its genomic DNA as a structural element. The mechanical properties of individual empty capsids and DNA-containing virions of the minute virus of mice are investigated by using atomic force microscopy. The stiffness of the empty capsid is found to be isotropic. Remarkably, the presence of the DNA inside the virion leads to an anisotropic reinforcement of the virus stiffness by ≈3%, 40%, and 140% along the fivefold, threefold, and twofold symmetry axes, respectively. A finite element model of the virus indicates that this anisotropic mechanical reinforcement is due to DNA stretches bound to 60 concavities of the capsid. These results, together with evidence of biologically relevant conformational rearrangements of the capsid around pores located at the fivefold symmetry axes, suggest that the bound DNA may reinforce the overall stiffness of the viral particle without canceling the conformational changes needed for its infectivity.
Familial ALS-superoxide dismutases associate with mitochondria and shift their redox potentials
Authors: Ferri Alberto , Cozzolino Mauro , Crosio Claudia , Nencini Monica , Casciati Arianna , Gralla Edith Butler , Rotilio Giuseppe , Valentine Joan Selverstone , Carrì Maria Teresa
Published: August 2006

Recent studies suggest that the toxicity of familial amyotrophic lateral sclerosis mutant Cu, Zn superoxide dismutase (SOD1) arises from its selective recruitment to mitochondria. Here we demonstrate that each of 12 different familial ALS-mutant SOD1s with widely differing biophysical properties are associated with mitochondria of motoneuronal cells to a much greater extent than wild-type SOD1, and that this effect may depend on the oxidation of Cys residues. We demonstrate further that mutant SOD1 proteins associated with the mitochondria tend to form cross-linked oligomers and that their presence causes a shift in the redox state of these organelles and results in impairment of respiratory complexes. The observation that such a diverse set of mutant SOD1 proteins behave so similarly in mitochondria of motoneuronal cells and so differently from wild-type SOD1 suggests that this behavior may explain the toxicity of ALS-mutant SOD1 proteins, which causes motor neurons to die.