bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA-dependent phosphorylation of Chk1 and Claspin in a human cell-free system
Authors: CLARKE Catriona A. L. , CLARKE Paul R.
Published: June 2005

Cell-cycle checkpoints induced by DNA damage or replication play critical roles in the maintenance of genomic integrity during cell proliferation. Biochemical analysis of checkpoint pathways has been greatly facilitated by the use of cell-free systems made from Xenopus eggs. In the present study, we describe a human cell-free system that reproduces a DNA-dependent checkpoint pathway acting on the Chk1 protein kinase. In this system, double-stranded DNA oligonucleotides induce the phosphorylation of Chk1 at activating sites targeted by ATR [ATM (ataxia telangiectasia mutated)- and Rad3-related] and ATM kinases. Phosphorylation of Chk1 is dependent on the interaction of Claspin, a protein first identified in Xenopus as a Chk1-binding protein. We show that the DNA-dependent binding of Chk1 to Claspin requires two phosphorylation sites, Thr916 and Ser945, which lie within the Chk1-binding domain of Claspin. Using a phosphopeptide derived from the consensus motif of these sites, we show that the interaction of Claspin with Chk1 is required for the ATR/ATM-dependent phosphorylation of Chk1. Using a panel of protein kinase inhibitors, we provide evidence that Chk1 is phosphorylated at an additional site in response to activation of the checkpoint response, probably by autophosphorylation. Claspin is phosphorylated in the Chk1-binding domain in an ATR/ATM-dependent manner and is also targeted by additional kinases in response to double-stranded DNA oligonucleotides. This cell-free system will facilitate further biochemical analysis of the Chk1 pathway in humans.
Plant ribulosamine/erythrulosamine 3-kinase, a putative protein-repair enzyme
Authors: FORTPIED Juliette , GEMAYEL Rita , STROOBANT Vincent , van SCHAFTINGEN Emile
Published: June 2005

FN3K (fructosamine 3-kinase) is a mammalian enzyme that catalyses the phosphorylation of fructosamines, which thereby becomes unstable and detaches from proteins. The homologous mammalian enzyme, FN3K-RP (FN3K-related protein), does not phosphorylate fructosamines but ribulosamines, which are probably formed through a spontaneous reaction of amines with ribose 5-phosphate, an intermediate of the pentose–phosphate pathway and the Calvin cycle. We show in the present study that spinach leaf extracts display a substantial ribulosamine kinase activity (approx. 700 times higher than the specific activity of FN3K in erythrocytes). The ribulosamine kinase was purified approx. 400 times and shown to phosphorylate ribulose-ε-lysine, protein-bound ribulosamines and also, with higher affinity, erythrulose-ε-lysine and protein-bound erythrulosamines. Evidence is presented for the fact that the third carbon of the sugar portion is phosphorylated by this enzyme and that this leads to the formation of unstable compounds decomposing with half-lives of approx. 30 min at 37 °C (ribulosamine 3-phosphates) and 5 min at 30 °C (erythrulosamine 3-phosphates). This decomposition results in the formation of a 2-oxo-3-deoxyaldose and inorganic phosphate, with regeneration of the free amino group. The Arabidopsis thaliana homologue of FN3K/FN3K-RP was overexpressed in Escherichia coli and shown to have properties similar to those of the enzyme purified from spinach leaves. These results indicate that the plant FN3K/FN3K-RP homologue, which appears to be targeted to the chloroplast in many species, is a ribulosamine/erythrulosamine 3-kinase. This enzyme may participate in a protein deglycation process removing Amadori products derived from ribose 5-phosphate and erythrose 4-phosphate, two Calvin cycle intermediates that are potent glycating agents.
Characterizing monoclonal antibody epitopes by filtered gene fragment phage display
Authors: DI NIRO Roberto , FERRARA Fortunato , NOT Tarcisio , BRADBURY Andrew R. M. , CHIRDO Fernando , MARZARI Roberto , SBLATTERO Daniele
Published: June 2005

In the present paper, we describe a novel approach to map monoclonal antibody epitopes, using three new monoclonal antibodies that recognize h-TG2 (human transglutaminase 2) as an example. The target gene was fragmented and cloned upstream of an antibiotic-resistance gene, in the vector pPAO2, to select for in-frame polypeptides. After removal of the antibiotic-resistance gene by Cre/Lox recombination, an antigen fragment phage display library was created and selected against specific monoclonal antibodies. Using the h-TG2 fragment library, we were able to identify epitopes. This technique can also be broadly applied to the study of protein–protein interactions.
Tolerance of the Rieske-type [2Fe-2S] cluster in recombinant ferredoxin BphA3 fromPseudomonassp. KKS102 to histidine ligand mutations
Authors: KIMURA Shigenobu , KIKUCHI Akihiro , SENDA Toshiya , SHIRO Yoshitsugu , FUKUDA Masao
Published: June 2005

BphA3 from Pseudomonas sp. KKS102 is a Rieske-type [2Fe-2S] ferredoxin that transfers electrons from an NADH-dependent oxidoreductase, BphA4, to a biphenyl dioxygenase complex. A high-level expression and purification system for the recombinant BphA3 in Escherichia coli was constructed. Two histidine ligands of the Rieske-type cluster in BphA3, were each replaced with serine, cysteine, asparagine and tyrosine. The single mutants, in which either His44 or His65 was replaced with a cysteine residue (CH and HC mutants respectively), and the double mutant, in which both histidine residues were replaced with cysteine residue (CC mutant), accumulated to high levels in the E. coli cells, while the other single mutants did not. The purified WT (wild-type) protein showed characteristic near-UV and visible absorption and CD spectra of Rieske-type clusters. The X-ray absorption spectra were suggestive of the existence of [2Fe-2S] clusters, with one histidine and three cysteine ligands in the CH and HC mutants, and an [2Fe-2S] cluster with four cysteine ligands in the CC mutant. The BphA4-dependent cytochrome c reductase activities of the mutants were less than 0.3% of that of the WT protein. The redox potential of the WT protein determined by cyclic voltammetry was −180±5 mV compared with the standard hydrogen electrode, and that of the CH mutant was approx. 175 mV lower. The changes in the near-UV and visible absorption spectra of the mutants showed that the reduced iron–sulphur clusters in the mutants were unstable. His44 and His65 in BphA3 can be replaced with cysteine residues, but are required for the stabilization of the reduced form of the cluster.
Relationship between hepatic phenotype and changes in gene expression in cytochrome P450 reductase (POR) null mice
Authors: WANG Xiu Jun , CHAMBERLAIN Mark , VASSIEVA Olga , HENDERSON Colin J. , WOLF C. Roland
Published: June 2005

Cytochrome P450 reductase is the unique electron donor for microsomal cytochrome P450s; these enzymes play a major role in the metabolism of endogenous and xenobiotic compounds. In mice with a liver-specific deletion of cytochrome P450 reductase, hepatic cytochrome P450 activity is ablated, with consequent changes in bile acid and lipid homoeostasis. In order to gain insights into the metabolic changes resulting from this phenotype, we have analysed changes in hepatic mRNA expression using microarray analysis and real-time PCR. In parallel with the perturbations in bile acid levels, changes in the expression of key enzymes involved in cholesterol and lipid homoeostasis were observed in hepatic cytochrome P450 reductase null mice. This was characterized by a reduced expression of Cyp7b1, and elevation of Cyp7a1 and Cyp8b1 expression. The levels of mRNAs for other cytochrome P450 genes, including Cyp2b10, Cyp2c29, Cyp3a11 and Cyp3a16, were increased, demonstrating that endogenous factors play a role in regulating the expression of these proteins and that the increases are due, at least in part, to altered levels of transcripts. In addition, levels of mRNAs encoding genes involved in glycolysis and lipid transport were also increased; the latter may provide an explanation for the increased hepatic lipid content observed in the hepatic null mice. Serum testosterone and oestradiol levels were lowered, accompanied by significantly decreased expression of Hsd3b2 (3β-hydroxy-Δ5-steroid dehydrogenase-2), Hsd3b5 (3β-hydroxy-Δ5-steroid dehydrogenase-5) and Hsd11b1 (11β-hydroxysteroid dehydrogenase type 1), key enzymes in steroid hormone metabolism. These microarray data provide important insights into the control of metabolic pathways by the cytochrome system.
Interaction between the bacterial nucleoid associated proteins Hha and H-NS involves a conformational change of Hha
Authors: GARCÍA Jesús , CORDEIRO Tiago N. , NIETO José M. , PONS Ignacio , JUÁREZ Antonio , PONS Miquel
Published: June 2005

The H-NS family of proteins has been shown to participate in the regulation of a large number of genes in Gram-negative bacteria in response to environmental factors. In recent years, it has become apparent that proteins of the Hha family are essential elements for H-NS-regulated gene expression. Hha has been shown to bind H-NS, although the details for this interaction are still unknown. In the present paper, we report fluorescence anisotropy and NMR studies of the interaction between Hha and H-NS64, a truncated form of H-NS containing only its N-terminal dimerization domain. We demonstrate the initial formation of a complex between one Hha and two H-NS64 monomers in 150 mM NaCl. This complex seems to act as a nucleation unit for higher-molecular-mass complexes. NMR studies suggest that Hha is in equilibrium between two different conformations, one of which is stabilized by binding to H-NS64. A similar exchange is also observed for Hha in the absence of H-NS when temperature is increased to 37 °C, suggesting a key role for intrinsic conformational changes of Hha in modulating its interaction with H-NS.
Grb10 and Grb14: enigmatic regulators of insulin action – and more?
Authors: HOLT Lowenna J. , SIDDLE Kenneth
Published: June 2005

The Grb proteins (growth factor receptor-bound proteins) Grb7, Grb10 and Grb14 constitute a family of structurally related multidomain adapters with diverse cellular functions. Grb10 and Grb14, in particular, have been implicated in the regulation of insulin receptor signalling, whereas Grb7 appears predominantly to be involved in focal adhesion kinase-mediated cell migration. However, at least in vitro, these adapters can bind to a variety of growth factor receptors. The highest identity within the Grb7/10/14 family occurs in the C-terminal SH2 (Src homology 2) domain, which mediates binding to activated receptors. A second well-conserved binding domain, BPS [between the PH (pleckstrin homology) and SH2 domains], can act to enhance binding to the IR (insulin receptor). Consistent with a putative adapter function, some non-receptor-binding partners, including protein kinases, have also been identified. Grb10 and Grb14 are widely, but not uniformly, expressed in mammalian tissues, and there are various isoforms of Grb10. Binding of Grb10 or Grb14 to autophosphorylated IR in vitro inhibits tyrosine kinase activity towards other substrates, but studies on cultured cell lines have been conflicting as to whether Grb10 plays a positive or negative role in insulin signalling. Recent gene knockouts in mice have established that Grb10 and Grb14 act as inhibitors of intracellular signalling pathways regulating growth and metabolism, although the phenotypes of the two knockouts are distinct. Ablation of Grb14 enhances insulin action in liver and skeletal muscle and improves whole-body tolerance, with little effect on embryonic growth. Ablation of Grb10 results in disproportionate overgrowth of the embryo and placenta involving unidentified pathways, and also impacts on hepatic glycogen synthesis, and probably on glucose homoeostasis. This review discusses the extent to which previous studies in vitro can account for the observed phenotype of knockout animals, and considers evidence that aberrant function of Grb10 or Grb14 may contribute to disorders of growth and metabolism in humans.
Characterization of quantum algorithms by quantum process tomography using quadrupolar spins in solid-state nuclear magnetic resonance
Authors: Kampermann H. , Veeman W. S.
Published: June 2005

NMR quantum computing with qubit systems represented by nuclear spins (I=12) in small molecules in liquids has led to the most successful experimental quantum information processors so far. We use the quadrupolar spin-32 sodium nuclei of a NaNO3 single crystal as a virtual two-qubit system. The large quadrupolar coupling in comparison with the environmental interactions and the usage of strongly modulating pulses allow us to manipulate the system fast enough and at the same time keeping the decoherence reasonably slow. The experimental challenge is to characterize the “calculation” behavior of the quantum processor by process tomography which is here adapted to the quadrupolar spin system. The results of a selection of quantum gates and algorithms are presented as well as a detailed analysis of experimental results.
Exciton dissociation dynamics in model donor-acceptor polymer heterojunctions. I. Energetics and spectra
Authors: Bittner Eric R. , Ramon John Glenn Santos , Karabunarliev Stoyan
Published: June 2005

In this paper we consider the essential electronic excited states in parallel chains of semiconducting polymers that are currently being explored for photovoltaic and light-emitting diode applications. In particular, we focus upon various type II donor-acceptor heterojunctions and explore the relation between the exciton binding energy to the band offset in determining the device characteristic of a particular type II heterojunction material. As a general rule, when the exciton binding energy is greater than the band offset at the heterojunction, the exciton will remain the lowest-energy excited state and the junction will make an efficient light-emitting diode. On the other hand, if the offset is greater than the exciton binding energy, either the electron or hole can be transferred from one chain to the other. Here we use a two-band exciton to predict the vibronic absorption and emission spectra of model polymer heterojunctions. Our results underscore the role of vibrational relaxation and suggest that intersystem crossings may play some part in the formation of charge-transfer states following photoexcitation in certain cases.
Measurement of rock-core capillary pressure curves using a single-speed centrifuge and one-dimensional magnetic-resonance imaging
Authors: Chen Quan , Balcom Bruce J.
Published: June 2005

Capillary pressure curves are widely used in materials, soil, and environmental sciences, and especially in the petroleum industry. The traditional (Hassler–Brunner) interpretation of centrifugal capillary pressure data is based on several assumptions. These assumptions are known to lead to significant errors in the measurement of capillary pressure curves. In this work, we propose a new “single-shot” method to measure the capillary pressure curve of a long sedimentary rock core using a single-speed centrifuge experiment and magnetic-resonance imaging to directly determine the water saturation distribution along the length of the sample. Since only a single moderate centrifuge speed is employed, the effect of gravity can be ignored and the outlet boundary condition of the core plug was maintained. The capillary pressure curve obtained by the single-shot method is remarkably consistent with results determined with conventional mercury-intrusion methods. The proposed method is much faster and more precise than traditional centrifuge methods.
A minimal proteinlike lattice model: An alpha-helix motif
Authors: Pokarowski Piotr , Droste Karol , Kolinski Andrzej
Published: June 2005

A simple protein model of a four-helix bundle motif on a face-centered cubic lattice has been studied. Total energy of a conformation includes attractive interactions between hydrophobic residues, repulsive interactions between hydrophobic and polar residues, and a potential that favors helical turns. Using replica exchange Monte Carlo simulations we have estimated a set of parameters for which the native structure is a global minimum of conformational energy. Then we have shown that all the above types of interactions are necessary to guarantee the cooperativity of folding transition and to satisfy the thermodynamic hypothesis.
Theoretical study of the electronic structure of the lower states of the [Cr2Cl9]3− and [Mo2Cl9]3− ions
Authors: Tanaka Kiyoshi , Sekiya Masahiro , Tawada Yoshihiro , Miyoshi Eisaku
Published: June 2005

The electronic structure of the lower states of a trigonal Cr3+ pair and Mo3+ pair, which occur in the Cs3M2Cl9 crystal (M=Cr,Mo), were studied by theoretical calculations carried out according to several methods: multireference singly and doubly excited configuration interaction, second-order configuration interaction, and multireference coupled-pair approximation. We employed a model of a [M2Cl9]3− anion embedded in a cage of point charges, which were arranged so as to simulate the anion in the crystal. The model core potential was utilized, where the relativistic effect was included for Mo. Results of the Cr complex showed that there were no direct bonds between the Cr metals. The lower electronic spectra of the [Cr2Cl9]3− ion were interpreted in terms of the electronic spectra of [CrCl6]3−. The lowest state of simultaneous excitation in both metals was considered. The [Mo2Cl9]3− ion exhibited a single direct bond between the metals. Reflecting this single bond, the observed singlet-triplet splitting was much larger than that in the case of Cr and the calculated splitting was in good agreement with the observed one. We account for the electronic spectra of the [Mo2Cl9]3− complex, which exhibited quite different features in the electronic excitation spectra in comparison with those of the Cr complex.
Observation of a spin one native defect in as-grown high-purity semi-insulating 4H SiC
Authors: Zvanut M. E. , Wang Haiyan , Richards Mpumelelo , Konovalov V. V.
Published: June 2005

Electron paramagnetic resonance measurements of high-purity semi-insulating 4H SiC reveals a spectrum characteristic of an S=1 defect, which appears only after exposure to light with a wavelength less than 690 nm. Analysis of the hyperfine structure of the spectrum suggests that the defect is an intrinsic pair or defect∕impurity complex. The center is stable in an inert ambient up to temperatures of 1200 °C, but a 1-h, 1600 °C anneal reduces the concentration by at least an order of magnitude. Because the spectrum is not affected by removal of the excitation light, it is concluded that the center is the ground state of an S=1 defect. A study of the angular dependence of the spectrum shows that g=2.0052, ∣D∣=(329±14)×10−4cm−1, and ∣E∣<19×10−4cm−1.
Tunable electrochromic photonic crystals
Authors: Kuai Su-Lan , Bader Georges , Ashrit P. V.
Published: June 2005

Photonic crystals based on the electrochromic phenomenon have been fabricated and proposed for band gap tuning. Electrochromic tungsten trioxide (WO3) inverse opals have been fabricated by polystyrene colloidal crystal templating. The WO3 matrix was obtained through a dip-infiltrating sol-gel process, with subsequent removal of the polymer microspheres by calcination. Scanning electron micrographs confirm the ordering of the hexagonal macroporous structure. The reflection spectra show two pronounced Bragg diffraction peaks. By inserting lithium into the crystals, the first reflection peak shifts gradually toward shorter wavelength for 36 nm, while the second reflection peak shifts toward longer wavelength for about 28 nm. This should be of great interest for photonic device applications.
Exponential convergence of coupled diffusion processes
Authors: Zhang Fuxi
Published: June 2005

The coupled diffusion process, which describes Brownian motors, is an important model in the physics related to biophenomena. We address the exponential convergence of the Markov semigroup of a coupled diffusion process, and show the spectral gap inequality and Log-Sobolev inequality by comparing them with those of related diffusion processes. At the end of the paper, we provide sufficient conditions for a coupled diffusion process to converge exponentially.
Self-consistent global model with multi-step ionizations in inductively coupled plasmas
Authors: Lee Min-Hyong , Chung Chin-Wook
Published: June 2005

Modified particle and power balance equations including multi-step ionizations are derived and solved in a self-consistent manner. According to the modified balance equations, the electron temperature (Te) decreases with the electron density (ne) to balance between the generation and the loss of an electron-ion pair. The multi-step ionizations give rise to the decrease in the collisional energy loss per electron-ion pair created (εc) so that the electron density is rapidly increased compared to when only single step ionization is considered. The effect of neutral pressure on the multi-step ionizations is presented and discussed.
Efficient organic solar cells based on a double p-i-n architecture using doped wide-gap transport layers
Authors: Drechsel J. , Männig B. , Kozlowski F. , Pfeiffer M. , Leo K. , Hoppe H.
Published: June 2005

The use of doped wide-gap charge transport layers with high conductivity and low absorption in the visible range enables one to achieve high internal quantum efficiencies and to optimize the devices with respect to optical interference effects. Here, it is shown that this architecture is particularly useful for stacking several cells on top of each other. The doping eases the recombination of the majority carriers at the interface between the cells, whereas the recombination centers are hidden for excitons and minority carriers. By stacking two p-i-n cells both with a phthalocyanine-fullerene blend as photoactive layer, a power efficiency of up to 3.8% at simulated AM1.5 illumination as compared to 2.1% for the respective single p-i-n cell has been achieved. Numerical simulations of the optical field distribution based on the transfer-matrix formalism are applied for optimization. The concept paves the way to even higher efficiencies by stacking several p-i-n cells with different photoactive materials that together cover the full visible spectrum.
Phospho-tellurite glasses containing heavy metal oxides for ultrabroad band fiber Raman amplifiers
Authors: Murugan G. Senthil , Suzuki Takenobu , Ohishi Yasutake
Published: June 2005

Multicomponent phospho-tellurite glasses containing heavy metal oxides and alkaline earth oxides have been fabricated. These glasses have thermal stabilities as high as 224 °C, which make them suitable for various fiber devices applications. The Raman intensities and cross sections of these glasses are compared relative to silica. These glasses show superior relative Raman cross sections than silica and conventional tellurite glasses. The presence of heavy metal oxides and alkaline earth oxides makes the Raman bands due to TeO2 and P2O5 continuous and one such glass has continuous Raman bandwidths exceeding 700cm−1. Thus, these glasses could be potential candidates for ultrawide band fiber Raman amplifiers.
Field emission properties of macroscopic single-walled carbon nanotube strands
Authors: Liu Chang , Tong Yu , Cheng Hui-Ming , Golberg Dmitri , Bando Yoshio
Published: June 2005

Centimeter-long strands of well-aligned single-walled carbon nanotubes (SWNT) synthesized by a hydrogen–argon arc discharge method were employed for the investigation of their field emission properties. These macroscopically long aligned SWNT strands showed advantages of low turn on electric field, high current density, good emission stability, and easy manipulation over the disoriented SWNT samples. The field enhancement factor of the strand is basically linearly proportional to its macro aspect ratio when the microstructure of the emission tip is kept unchanged. The present SWNT strands can be valuable candidates for the applications as electron-emitting sources in various electronic devices.
Silicon waveguide-integrated optical power monitor with enhanced sensitivity at 1550nm
Authors: Bradley J. D. B. , Jessop P. E. , Knights A. P.
Published: June 2005

We describe the fabrication and operation of an optical power monitor, monolithically integrated with a silicon-on-insulator rib waveguide. The device consists of a p+-v-n+ structure with a detection volume coincident with the single-mode supporting waveguide. Detection of optical signals at wavelengths around 1550nm is significantly enhanced by the introduction of midband-gap generation centers, which provide partial absorption of the infrared light. The most efficient device extracted 19% of optical power from the waveguide and showed a responsivity of 3mA∕W. These devices are fabricated using current standard processing technology and are fully compatible with silicon waveguide technology and integrated operational amplifier circuits.
Extreme bendability of single-walled carbon nanotube networks transferred from high-temperature growth substrates to plastic and their use in thin-film transistors
Authors: Hur Seung-Hyun , Park O Ok , Rogers John. A.
Published: June 2005

In this paper we describe printing methods for transferring single-walled carbon nanotubes (SWNTs) from high-temperature growth substrates to flexible, low-cost plastic supports. Thin-film transistors (TFTs) built with networks of transferred SWNTs grown by chemical vapor deposition show good performance—mobilities and on∕off current ratios similar to those of devices fabricated on the growth substrates for a wide range of channel lengths. Bending tests on these TFTs show that their output current varies only in a narrow (±5%) range, even for bend radii that induce surface strains larger than 1%. Similar structures evaluated under sharp folding, with strains larger than 20%, show that the SWNT networks are operational even under extreme bending conditions. This level of mechanical robustness, the good electrical performance, and optical transparency make transferred SWNT networks an attractive type of electronic material for applications in macroelectronics, sensors, and other systems that require wide area coverage and unusual substrates.
Detection of spin coupling in iron nanoparticles with small angle neutron scattering
Authors: Ijiri Y. , Kelly C. V. , Borchers J. A. , Rhyne J. J. , Farrell D. F. , Majetich S. A.
Published: June 2005

Aggregates of monodisperse iron-based nanoparticles were investigated by small-angle neutron scattering. The field dependence of the scattering intensity showed marked differences for particles depending on size and degree of oxidation. The angular dependence of the intensity indicated magnetic regions within an oxidized sample with spins perpendicular to the applied field, which dominated the scattering at the diffraction peak. The unexpected results are interpreted in terms of an iron core that is exchange coupled to an iron oxide shell.
Not over Your Dead Bodies! A Lacanian Interpretation of Urban Planning Discourse and Practice
Authors: Hillier Jean , Gunder Michael
Published: June 2005

This paper examines aspects of Lacanian critical social theory in terms of its appropriateness for understanding urban planning. We tell a story from planning practice in Western Australia which we then analyse by introducing Lacan's notion of the master signifier and the sets of knowledges, values and practices which master signifiers embody. We then apply the Lacanian concepts of desire and jouissance, followed by an exploration of the Lacanian four discourses and the speech acts, or language games, of the planner and the ‘planned’. We conclude by estimating the potential value of Lacanian analysis for understanding planning praxis.
The City in the Country: Wilderness Gentrification and the Rent Gap
Authors: Darling Eliza
Published: June 2005

In this paper I explore the efficacy of applying Neil Smith's theory of the rent gap to rural gentrification in New York State's Adirondack Park, making three central claims. In the first place, although the underlying impetus for both rural and urban gentrification (namely, the maximization of profit on the part of a variety of gentrifying agents from individual owner-occupants to large-scale developers) is essentially the same, some fundamental differences between the determination of what constitutes ‘undercapitalized’ ground rent in the city and the wilderness leads to subsequent differences in the geographical expression of gentrification in each area. In the second, the unique land-management practices instituted by the State of New York in this region have set up the conditions for a singular type of disinvestment not typically found in the city, rendering disinvestment a central aspect of Adirondack gentrification but in a different way than the disinvestment which anchors Smith's argument. Finally, I argue that the ‘postproductivist’ theories which have recently gained currency in the extant rural gentrification literature are not applicable to the empirical realities of Adirondack land use, suggesting that rural areas themselves may be sufficiently differentiated to render the idea of an overarching, homogeneous ‘rural gentrification’ suspect and pointing to the need for a more refined and specific set of labels to indicate a variety of landscape-specific gentrification models in the hinterlands.
Dynamic reassembly of peptide RADA16 nanofiber scaffold
Authors: Yokoi Hidenori , Kinoshita Takatoshi , Zhang Shuguang
Published: June 2005

Nanofiber structures of some peptides and proteins as biological materials have been studied extensively, but their molecular mechanism of self-assembly and reassembly still remains unclear. We report here the reassembly of an ionic self-complementary peptide RADARADARADARADA (RADA16-I) that forms a well defined nanofiber scaffold. The 16-residue peptide forms stable β-sheet structure and undergoes molecular self-assembly into nanofibers and eventually a scaffold hydrogel consisting of >99.5% water. In this study, the nanofiber scaffold was sonicated into smaller fragments. Circular dichroism, atomic force microscopy, and rheology were used to follow the kinetics of the reassembly. These sonicated fragments not only quickly reassemble into nanofibers that were indistinguishable from the original material, but their reassembly also correlated with the rheological analyses showing an increase of scaffold rigidity as a function of nanofiber length. The disassembly and reassembly processes were repeated four times and, each time, the reassembly reached the original length. We proposed a plausible sliding diffusion model to interpret the reassembly involving complementary nanofiber cohesive ends. This reassembly process is important for fabrication of new scaffolds for 3D cell culture, tissue repair, and regenerative medicine.
Nitric oxide synthase II suppresses the growth and metastasis of human cancer regardless of its up-regulation of protumor factors
Authors: Le Xiangdong , Wei Daoyan , Huang Suyun , Lancaster Jack R. , Xie Keping
Published: June 2005

Inducible nitric oxide (NO) synthase (NOS) II has been implicated in macrophage-mediated antitumor activity. However, use of the NOS II gene in cancer therapy is problematic because of the double-edged nature of NO action. Herein we show that adenoviral vectors mediated effective NOS II gene transfer into various human tumors. Production of NO significantly up-regulated multiple angiogenic molecules. However, the NO-producing tumor cells did not form tumors or metastases in ectopic or orthotopic xenograft nude mouse models. The dramatic loss of malignancy was due to NO-mediated apoptosis. We also generated a series of adenoviral vectors harboring mutant NOS II genes that expressed mutant NOS II proteins with defined levels of enzymatic activity. Tumor cells transduced with these NOS II genes produced NO at different levels, which directly correlated with the antitumor activity
in vitro
and
in vivo
. This demonstration using a relevant biological system shows that NO produces dose-dependent antitumor activity
in vitro
and
in vivo
, regardless of its up-regulation of protumor factors.
Characterization of two avian MHC-like genes reveals an ancient origin of the CD1 family
Authors: Miller Marcia M. , Wang Carren , Parisini Emilio , Coletta Ricardo D. , Goto Ronald M. , Lee Stella Y. , Barral Duarte C. , Townes Maria , Roura-Mir Carme , Ford Heide L. , Brenner Michael B. , Dascher Christopher C.
Published: June 2005

Many of the genes that comprise the vertebrate adaptive immune system are conserved across wide evolutionary time scales. Most notably, homologs of the mammalian MHC gene family have been found in virtually all jawed vertebrates, including sharks, bony fishes, reptiles, and birds. The CD1 family of antigen-presenting molecules are related to the MHC class I family but have evolved to bind and present lipid antigens to T cells. Here, we describe two highly divergent nonclassical MHC class I genes found in the chicken (Gallus gallus) that have sequence homology to the mammalian CD1 family of proteins. One of the chicken CD1 genes expresses a full-length transcript, whereas the other has multiple splice variants. Both Southern blot and single nucleotide polymorphism analysis indicates that chicken CD1 is relatively nonpolymorphic. Moreover, cross-hybridizing bands are present in other bird species, suggesting broad conservation in the avian class. Northern analysis of chicken tissue shows a high level of CD1 expression in the bursa and spleen. In addition, molecular modeling predicts that the potential antigen-binding pocket is probably hydrophobic, a universal characteristic of CD1 molecules. Genomic analysis indicates that the CD1 genes are located on chicken chromosome 16 and maps to within 200 kb of the chicken MHCBlocus, suggesting that CD1 genes diverged from classical MHC genes while still linked to the major histocompatibility complex locus. The existence of CD1 genes in an avian species suggests that the origin of CD1 extends deep into the evolutionary history of terrestrial vertebrates.
Actin polymerization kinetics, cap structure, and fluctuations
Authors: Vavylonis Dimitrios , Yang Qingbo , O'Shaughnessy Ben
Published: June 2005

Polymerization of actin proteins into dynamic structures is essential to eukaryotic cell life, motivating many
in vitro
experiments measuring polymerization kinetics of individual filaments. Here, we model these kinetics, accounting for all relevant steps revealed by experiment: polymerization, depolymerization, random ATP hydrolysis, and release of phosphate (P
i
). We relate filament growth rates to the dynamics of ATP–actin and ADP–P
i
–actin caps that develop at filament ends. At the critical concentration of the barbed end,
c
crit
, we find a short ATP cap and a long fluctuation-stabilized ADP–P
i
cap. We show that growth rates and the critical concentration at the barbed end are intimately related to cap structure and dynamics. Fluctuations in filament lengths are described by the length diffusion coefficient,
D
. Recently Fujiwara
et al.
[Fujiwara, I., Takahashi, S., Takaduma, H., Funatsu, T. & Ishiwata, S. (2002)
Nat. Cell Biol.
4, 666–673] and Kuhn and Pollard [Kuhn, J. & Pollard, T. D. (2005)
Biophys. J.
88, 1387–1402] observed large length fluctuations slightly above
c
crit
, provoking speculation that growth may proceed by oligomeric rather than monomeric on–off events. For the single-monomer growth process, we find that
D
exhibits a pronounced peak below
c
crit
, due to filaments alternating between capped and uncapped states, a mild version of the dynamic instability of microtubules. Fluctuations just above
c
crit
are enhanced but much smaller than those reported experimentally. Future measurements of
D
as a function of concentration can help identify the origin of the observed fluctuations.
Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A
Authors: Zambon Alexander C. , Zhang Lingzhi , Minovitsky Simon , Kanter Joan R. , Prabhakar Shyam , Salomonis Nathan , Vranizan Karen , Dubchak Inna , Conklin Bruce R. , Insel Paul A.
Published: June 2005

Although a substantial number of hormones and drugs increase cellular cAMP levels, the global impact of cAMP and its major effector mechanism, protein kinase A (PKA), on gene expression is not known. Here we show that treatment of murine wild-type S49 lymphoma cells for 24 h with 8-(4-chlorophenylthio)-cAMP (8-CPT-cAMP), a PKA-selective cAMP analog, alters the expression of ≈4,500 of ≈13,600 unique genes. By contrast, gene expression was unaltered in Kin
-
S49 cells (that lack PKA) incubated with 8-CPT-cAMP. Changes in mRNA and protein expression of several cell-cycle regulators accompanied cAMP-induced G
1
-phase cell-cycle arrest of wild-type S49 cells. Within 2 h, 8-CPT-cAMP altered expression of 152 genes that contain evolutionarily conserved cAMP-response elements within 5 kb of transcriptional start sites, including the circadian clock gene
Per1
. Thus, cAMP through its activation of PKA produces extensive transcriptional regulation in eukaryotic cells. These transcriptional networks include a primary group of cAMP-response element-containing genes and secondary networks that include the circadian clock.
Reading depends on writing, in Chinese
Authors: Tan Li Hai , Spinks John A. , Eden Guinevere F. , Perfetti Charles A. , Siok Wai Ting
Published: June 2005

Language development entails four fundamental and interactive abilities: listening, speaking, reading, and writing. Over the past four decades, a large body of evidence has indicated that reading acquisition is strongly associated with a child's listening skills, particularly the child's sensitivity to phonological structures of spoken language. Furthermore, it has been hypothesized that the close relationship between reading and listening is manifested universally across languages and that behavioral remediation using strategies addressing phonological awareness alleviates reading difficulties in dyslexics. The prevailing view of the central role of phonological awareness in reading development is largely based on studies using Western (alphabetic) languages, which are based on phonology. The Chinese language provides a unique medium for testing this notion, because logographic characters in Chinese are based on meaning rather than phonology. Here we show that the ability to read Chinese is strongly related to a child's writing skills and that the relationship between phonological awareness and Chinese reading is much weaker than that in reports regarding alphabetic languages. We propose that the role of logograph writing in reading development is mediated by two possibly interacting mechanisms. The first is orthographic awareness, which facilitates the development of coherent, effective links among visual symbols, phonology, and semantics; the second involves the establishment of motor programs that lead to the formation of long-term motor memories of Chinese characters. These findings yield a unique insight into how cognitive systems responsible for reading development and reading disability interact, and they challenge the prominent phonological awareness view.
Robust hepatitis C virus infectionin vitro
Authors: Zhong Jin , Gastaminza Pablo , Cheng Guofeng , Kapadia Sharookh , Kato Takanobu , Burton Dennis R. , Wieland Stefan F. , Uprichard Susan L. , Wakita Takaji , Chisari Francis V.
Published: June 2005

The absence of a robust cell culture model of hepatitis C virus (HCV) infection has severely limited analysis of the HCV life cycle and the development of effective antivirals and vaccines. Here we report the establishment of a simple yet robust HCV cell culture infection system based on the HCV JFH-1 molecular clone and Huh-7-derived cell lines that allows the production of virus that can be efficiently propagated in tissue culture. This system provides a powerful tool for the analysis of host-virus interactions that should facilitate the discovery of antiviral drugs and vaccines for this important human pathogen.
Vortices and flow reversal due to suction slots
Authors: Ovenden Nicholas C , Smith Frank T
Published: June 2005

Suction into small two- or three-dimensional surface slots inside an otherwise planar boundary-layer is examined theoretically through a combined analytical and computational approach. Increasing suction strength leads to enhanced nonlinear structures with flow reversals or trailing vortices.
Investigations into resting-state connectivity using independent component analysis
Authors: Beckmann Christian F , DeLuca Marilena , Devlin Joseph T , Smith Stephen M
Published: June 2005

Inferring resting-state connectivity patterns from functional magnetic resonance imaging (fMRI) data is a challenging task for any analytical technique. In this paper, we review a probabilistic independent component analysis (PICA) approach, optimized for the analysis of fMRI data, and discuss the role which this exploratory technique can take in scientific investigations into the structure of these effects. We apply PICA to fMRI data acquired at rest, in order to characterize the spatio-temporal structure of such data, and demonstrate that this is an effective and robust tool for the identification of low-frequency resting-state patterns from data acquired at various different spatial and temporal resolutions. We show that these networks exhibit high spatial consistency across subjects and closely resemble discrete cortical functional networks such as visual cortical areas or sensory–motor cortex.
Estimation of the transmission time of stimulus-locked responses: modelling and stochastic phase resetting analysis
Authors: Tass Peter A
Published: June 2005

A model of two coupled phase oscillators is studied, where both oscillators are subject to random forces but only one oscillator is repetitively stimulated with a pulsatile stimulus. A pulse causes a reset, which is transmitted to the other oscillator via the coupling. The transmission time of the cross-trial (CT) averaged responses, i.e. the difference in time between the maxima of the CT averaged responses of both oscillators differs from the time difference between the maxima of the oscillators' resets. In fact, the transmission time of the CT averaged responses directly corresponds to the phase difference in the stable synchronized state with integer multiples of the oscillators' mean period added to it. With CT averaged responses it is impossible to reliably estimate the time elapsing, owing to the stimulus' action being transmitted between the two oscillators.
Bilinear dynamical systems
Authors: Penny W , Ghahramani Z , Friston K
Published: June 2005

In this paper, we propose the use of bilinear dynamical systems (BDS)s for model-based deconvolution of fMRI time-series. The importance of this work lies in being able to deconvolve haemodynamic time-series, in an informed way, to disclose the underlying neuronal activity. Being able to estimate neuronal responses in a particular brain region is fundamental for many models of functional integration and connectivity in the brain. BDSs comprise a stochastic bilinear neurodynamical model specified in discrete time, and a set of linear convolution kernels for the haemodynamics. We derive an expectation-maximization (EM) algorithm for parameter estimation, in which fMRI time-series are deconvolved in an E-step and model parameters are updated in an M-Step. We report preliminary results that focus on the assumed stochastic nature of the neurodynamic model and compare the method to Wiener deconvolution.
Validation ofq-ball imaging with a diffusion fibre-crossing phantom on a clinical scanner
Authors: Perrin Muriel , Poupon Cyril , Rieul Bernard , Leroux Patrick , Constantinesco André , Mangin Jean-François , LeBihan Denis
Published: June 2005

Magnetic resonance (MR) diffusion imaging provides a valuable tool used for inferring structural anisotropy of brain white matter connectivity from diffusion tensor imaging. Recently, several high angular resolution diffusion models were introduced in order to overcome the inadequacy of the tensor model for describing fibre crossing within a single voxel. Among them,q-ball imaging (QBI), inherited from theq-space method, relies on a spherical Radon transform providing a direct relationship between the diffusion-weighted MR signal and the orientation distribution function (ODF). Experimental validation of these methods in a model system is necessary to determine the accuracy of the methods and to optimize them. A diffusion phantom made up of two textile rayon fibre (comparable in diameter to axons) bundles, crossing at 90°, was designed and dedicated toex vivo q-ball validation on a clinical scanner. Normalized ODFs were calculated inside regions of interest corresponding to monomodal and bimodal configurations of underlying structures. Three-dimensional renderings of ODFs revealed monomodal shapes for voxels containing single-fibre population and bimodal patterns for voxels located within the crossing area. Principal orientations were estimated from ODFs and were compared witha prioristructural fibre directions, validating efficiency of QBI for depicting fibre crossing. In the homogeneous regions, QBI detected the fibre angle with an accuracy of 19° and in the fibre-crossing region with an accuracy of 30°.
Comparison of Escherichia coli isolates implicated in human urinary tract infection and avian colibacillosis
Authors: Rodriguez-Siek Kylie E. , Giddings Catherine W. , Doetkott Curt , Johnson Timothy J. , Fakhr Mohamed K. , Nolan Lisa K.
Published: June 2005

Since avian pathogenicEscherichia coli(APEC) and human uropathogenicE. coli(UPEC) may encounter similar challenges when establishing infection in extraintestinal locations, they may share a similar content of virulence genes and capacity to cause disease. In the present study, 524 APEC and 200 UPEC isolates were compared by their content of virulence genes, phylogenetic group, and other traits. The two groups showed substantial overlap in terms of their serogroups, phylogenetic groups and virulence genotypes, including their possession of certain genes associated with large transmissible plasmids of APEC. Based on these results, the propensity of both groups to cause extraintestinal infections, and a well-documented ability of avianE. colito spread to human beings, the potential for APEC to act as human UPEC or as a reservoir of virulence genes for UPEC should be considered. However, significant differences in the prevalence of the traits occurred across the two groups, suggesting that if APEC are involved in human urinary tract infections, they are not involved in all of them.
Plasma membrane H+ and K+ transporters are involved in the weak-acid preservative response of disparate food spoilage yeasts
Authors: Macpherson Neil , Shabala Lana , Rooney Henrietta , Jarman Marcus G. , Davies Julia M.
Published: June 2005

The food spoilage yeastsZygosaccharomyces bailiiandSaccharomyces cerevisiaehave been proposed to resist weak-acid preservative stress by different means;Z. bailiiby limiting influx of preservative combined with its catabolism,S. cerevisiaeby active extrusion of the preservative weak-acid anion and H+. Measurement of H+extrusion by exponential-phaseZ. bailiicells suggest that, in common withS. cerevisiae, this yeast uses a plasma membrane H+-ATPase to expel H+when challenged by weak-acid preservative (benzoic acid). Simultaneous measurement ofZ. bailiinet H+and K+fluxes showed that net K+influx accompanies net H+efflux during acute benzoic acid stress. Such ionic coupling is known forS. cerevisiaein short-term preservative stress. Both yeasts significantly accumulated K+on long-term exposure to benzoic acid. Analysis ofS. cerevisiaeK+transporter mutants revealed that loss of the high affinity K+uptake systemTrk1confers sensitivity to growth in preservative. The results suggest that cation accumulation is an important factor in adaptation to weak-acid preservatives by spoilage yeasts and thatZ. bailiiandS. cerevisiaeshare hitherto unsuspected adaptive responses at the level of plasma membrane ion transport.