bluuebunny/crossref_metadata_2025 huggingface dataset:
Boron-doped a-Si:H∕c-Si interface passivation: Degradation mechanism
Authors: De Wolf Stefaan , Kondo Michio
Published: September 2007

The authors report that for a-Si:H∕c-Si heterostructure solar cell fabrication the presence of a boron-doped a-Si:H(p+) overlayer may cause H2 effusion from a (few nanometers) thin underlying intrinsic a-Si:H(i) film at moderate temperatures. This phenomenon is in agreement with losses in the electronic passivation quality of c-Si∕a-Si:H(i)∕a-Si:H(p+) structures occurring during low temperature (⩽260°C) postdeposition annealing. Consequently, it is argued that such passivation degradation is due to Si–H rupture in the a-Si:H(i) film, likely resulting in Si dangling bond defects, mediated by the presence of the doped layer.
Large room-temperature magnetocaloric effects in Fe0.8Mn1.5As
Authors: Sun N. K. , Ma S. , Zhang Q. , Du J. , Zhang Z. D.
Published: September 2007

In Fe0.8Mn1.5As compound, an external magnetic field induces a metamagnetic transition from an antiferromagnetic phase to a ferrimagnetic phase above Ts=285K, leading to large magnetocaloric effects around room temperature. Instead of showing inverse magnetocaloric effects, the sign of the entropy change ΔSM in the compound is unexpectedly negative, revealing a different mechanism. The maximum value of ΔSM is 6.2J∕kgK at 287.5K for a magnetic field change of 5T. The study on systems with antiferromagnetism-related metamagnetic transitions may open an important field in searching good materials for room-temperature magnetic refrigeration.
Observation of microslip dynamics at high-speed microcontacts
Authors: Borovsky Brian , Booth Adam , Manlove Erin
Published: September 2007

The high-speed tribological properties of microscale contacts are studied using an indenter probe and quartz crystal microbalance. Elastic and dissipative shear forces are monitored as a function of contact radius for sapphire/gold interfaces with an adsorbed octadecanethiol monolayer. We observe shear force transitions understood as taking the interface from slipping to stuck conditions. They relate this behavior to the presence of interfacial microslip. Dynamic modeling shows that our observations are consistent with an interface that, when sliding, experiences full slip during half of each cycle. We discuss the implications for this technique as a sensitive probe of sliding friction.
Single photon emission based on coherent state preparation
Authors: Ester P. , Lackmann L. , Michaelis de Vasconcellos S. , Hübner M. C. , Zrenner A. , Bichler M.
Published: September 2007

The authors report here on deterministic single photon emission after coherent optical state preparation in the p-shell of a single InGaAs∕GaAs quantum dot. In the approach, they use p-shell Rabi flopping followed by relaxation to the s-shell ground state with subsequent spontaneous single photon emission. Pulsed photon correlation experiments show complete suppression of the correlation peak at zero time delay and hence demonstrate clean single photon emission.
Vertical dielectric-sandwiched thin metal layer for compact, low-loss long range surface plasmon waveguiding
Authors: Sun Zhijun
Published: September 2007

In this letter, the author proposes a long range surface plasmon waveguide structure of a vertically standing thin metal layer sandwiched between finite-width dielectric layers to achieve both compact and low-loss photonic waveguiding. Rounded 90° bends in such waveguides, with radii of curvature on the scale of the incident wavelength, are studied. The author analyzes waveguiding modes of such waveguides at the straight and bend parts, and also the coupling of surface plasmon waves between them. The analyses are verified with numerical simulations. High transmission of surface plasmon waves through the bends is demonstrated.
Three-dimensional atomic-scale mapping of Pd in Ni1−xPdxSi∕Si(100) thin films
Authors: Kim Yeong-Cheol , Adusumilli Praneet , Lauhon Lincoln J. , Seidman David N. , Jung Soon-Yen , Lee Hi-Deok , Alvis Roger L. , Ulfig Rob M. , Olson Jesse D.
Published: September 2007

Atom-probe tomography was utilized to map the three-dimensional distribution of Pd atoms in nickel monosilicide thin films on Si(100). A solid-solution Ni0.95Pd0.05 film on a Si(100) substrate was subjected to rapid thermal processing plus steady-state annealing to simulate the thermal processing experienced by NiSi source and drain contacts in standard complementary metal-oxide-semiconductor processes. Pd is found to segregate at the (Ni0.95Pd0.05)Si∕Si(100) heterophase interface, which may provide a previously unrecognized contribution to monosilicide stabilization. The silicide-Si heterophase interface was reconstructed in three dimensions on an atomic scale and its chemical roughness was evaluated.
Donor/acceptor doping and electrical tailoring in ZnO quantum dots
Authors: Ye Z. Z. , Zeng Y. J. , Lu Y. F. , Lin S. S. , Sun L. , Zhu L. P. , Zhao B. H.
Published: September 2007

The authors report on donor/acceptor doping in ZnO quantum dots (QDs) grown by a metal-organic chemical vapor deposition method. The Ga donor and N acceptor, as identified by x-ray photoelectron spectroscopy (XPS), are introduced into ZnO QDs. They demonstrate, with a combination of valence band XPS and scanning tunneling microscopy, that the electrical properties as well as Fermi level of the ZnO QDs can be well tuned by the donor/acceptor doping. In addition, photoluminescence from the ZnO QDs with quantum confinement effect is observed.
Two dimensional simulation on immunoassay for a biosensor with applying electrothermal effect
Authors: Yang Chih-Kai , Chang Jeng-Shian , Chao Sheng D. , Wu Kuang-Chong
Published: September 2007

For diffusion-limited proteins, the diffusion boundary layer on the reacting surface hinders the binding reaction. The authors performed finite-element simulations of the electrothermal effect on the reaction kinetics of C-reactive protein (CRP)–anti-CRP. The induced vortices stir the flow and enhance the transport rate of analytes. They attribute the enhancement to the reduction of the thickness of diffusion boundary layer. Significant interference patterns of the votices are observed by varying the position of the reacting surface. These patterns are utilized to optimize the enhancement factor, yielding 5.166 and 3.744 times for association and dissociation, respectively, under voltage (15Vrms) and frequency (100kHz).
Magnetic domain configurations of epitaxial chromium dioxide (CrO2) nanostructures
Authors: Zou Xiaojing , Xiao Gang
Published: September 2007

Magnetic domain structures of submicrometric epitaxial CrO2 fabricated using selective-area growth technique were studied by magnetic force microscopy. In-plane, lamellar domain structure with fragmented walls aligned along the magnetic easy axis direction is observed, indicating the existence of a large magnetocrystalline anisotropy. A classical model for ferromagnetic materials with a uniaxial anisotropy was used to explain this domain configuration. Estimates of the domain wall energy density and exchange stiffness constant for CrO2 were obtained.
Biocompatible, Polyampholyte Microgel Particles
Authors: Bradley Melanie , Vincent Brian , Burnett Gary
Published: September 2007

Biocompatible, polyampholyte microgel particles have been prepared by the acid hydrolysis of t-butyl groups within (2-diethylamino)ethyl methacrylate-co-t-butyl methacrylate microgel particles to give (2-diethylamino)ethyl methacrylate-co-methacrylic acid microgel particles. The hydrodynamic diameter and electrophoretic mobility of both the pre-hydrolyzed and post-hydrolyzed microgel particles have been investigated as a function of pH for three microgel dispersions differing in their monomer compositions. The swelling properties and isoelectric point pH are shown to depend on the monomer composition.
Real-Time Detection of Antigen–Antibody Reactions by Imaging Ellipsometry
Authors: Chamritski Irina , Clarkson Mark , Franklin Jeff , Li Shi Wei
Published: September 2007

In the field of proteomics the quantification of the affinity of an antibody to its partners and the evaluation of its specific binding is an important issue. With an imaging ellipsometer the interaction of an antibody with immobilized antigens on a model microarray is observed in a time-resolved and label-free manner. Imaging ellipsometry was developed for real-time monitoring of the biomolecule interaction between an antigen in solution and an antibody immobilized on a silicon surface. Proteins were immobilized by the formation of carboxy-alkyl monolayers on silicon substrates, where a biotin-labelled antibody was immobilized by a biotin–streptavidin linkage. Anti-human IgG bound specifically to human antibody and protein A, similarly anti-goat IgG bound to goat antibody. No binding was observed between anti-rabbit IgG and goat antibody. All stages of the formation of the antigen–antibody complex were imaged by imaging ellipsometry. By monitoring changes in y, the mole fraction θ of the antigen–antibody binding was determined. Immunological reactions of two different antigen–antibody combinations were fitted by the Langmuir adsorption equation, and affinity constants for two reactions were calculated.
Direct Measurement of Mechanical and Adhesive Properties of Living Cells Using Surface Forces Apparatus
Authors: Banquy Xavier , Rabanel Jean-Michel , Hildgen Patrice , Giasson Suzanne
Published: September 2007

The adhesive and mechanical properties of living cells assembled into a monolayer on two different substrates were investigated using the surface forces apparatus (SFA) technique. The force measurements allowed elastic and bending moduli of the cells plated on substrates to be determined. The moduli are in good agreement with data reported in the literature for single cells determined using atomic force microscopy. Results confirm that the nature of the cell–substrate interactions can mediate cell mechanical and adhesive properties.
Kinetic Investigations on Microwave-Assisted Statistical Terpolymerizations of 2-Oxazoline Monomers
Authors: Hoogenboom Richard , Wiesbrock Frank , Leenen Mark A. M. , van der Loop Michel , van Nispen Sjoerd F. G. M. , Schubert Ulrich S.
Published: September 2007

The microwave-assisted statistical terpolymerization of 2-oxazolines via a living cationic ring-opening polymerization mechanism is discussed. Kinetic investigations on the terpolymerizations of combinations of 2-methyl-2-oxazoline, 2-ethyl-2-oxazoline, 2-nonyl-2-oxazoline, and 2-phenyl-2-oxazoline were performed by heating separate polymerization mixtures for different predefined times. The resulting polymer solutions were analyzed by gas chromatography and size exclusion chromatography, demonstrating the living character of the statistical terpolymerizations. In addition, the monomer distribution throughout the polymer chains is discussed based on the linear first order kinetic plots of the separate monomers in the terpolymerizations. The observed differences in monomer distribution are expected to influence the polymer properties, which will be the focus of future investigations.
Bisamidoximes: Synthesis and Complexation with Iron(III)
Authors: Johnson James E. , Carvallo Carol , Dolliver Debra D. , Sanchez Natalia , Garza Vilma , Canseco Diana C. , Eggleton Gordon L. , Fronczek Frank R.
Published: September 2007

Bisamidoximes have been synthesized by the reaction of 4-methylbenzohydroximoyl chloride with 1,2-diaminoethane, 1,3-diaminopropane, 1,4-diaminobutane, and 3,3′-diamino-N-methyl-dipropylamine. A monoamidoxime and a trisamidoxime were also prepared in the present work by the reaction of 4-methylbenzohydroximoyl chloride with N,N-dimethylethylenediamine and tris(2-aminoethyl)amine. Single crystal X-ray structures of three of the bisamidoximes have shown that the two amidoxime moieties have the Z configuration in all three compounds. Job’s method of continuous variations showed that three of the bisamidoximes prepared in this work form 1:1 complexes with iron(iii) and therefore are acting as tetradentate ligands.
Increased Valence or Electronic Hypervalence for Symmetrical Three-Centre Molecular Orbital Configurations
Authors: Harcourt Richard D.
Published: September 2007

With ψ1 = y + k1a + b, ψ2 = y – b, and ψ3 = y – k3a + b as Y–A and A–B bonding, non-bonding, and antibonding three-centre molecular orbitals for a symmetrical Y–A–B type bonding unit with overlapping atomic orbitals y, a, and b, it is deduced that the maximum value for the A atom valence, (VA = Vab + Vay), is (a) 4(3 – 2√2) = 0.6863 for the one-electron and five-electron configurations Φ(1) = (ψ1)1 and Φ(5) = (ψ1)2ψ2)2(ψ3)1; (b) 8(3 – 2√2) = 1.3726 for the two-electron and four-electron configurations Φ(2) = (ψ1)2 and Φ(4) = (ψ1)2(ψ2)2; and (c) 4/3 for the three-electron configuration Φ(3) = (ψ1)2(ψ2)1. Thus for each of the three-centre molecular orbital configurations, the A-atom can exhibit increased valence, or electronic hypervalence, relative to the valence for an A-atom in a two-centre molecular orbital configuration. When k1 ≠ 0 for Φ(1) and k3 ≠ 0 for Φ(5), the A-atom odd-electron charge is not equal to zero. This odd-electron charge is available for (fractional) electron-pair bonding to a fourth atom X, to give an additional contribution, Va, to the valence. The resulting maximum value for the A-atom valence (VA = Vab + Vay + Va) is equal to 1.2020 for each of Φ(1) and Φ(5). A-atom valencies are calculated for the three-centre bonding units for several molecules and ions. The expressions for VA = Vab + Vay were derived with atomic orbital overlap integrals omitted. The present paper shows how the theory is modified when these integrals are included.
The effects of UV-B radiation on photosynthesis in relation to Photosystem II photochemistry, thermal dissipation and antioxidant defenses in winter wheat (Triticum aestivum L.) seedlings at different growth temperatures
Authors: Yang Shu-Hua , Wang Li-Jun , Li Shao-Hua , Duan Wei , Loescher Wayne , Liang Zhen-Chang
Published: September 2007

To study the UV-B effect on photosynthesis in winter wheat at different day/night temperatures, biologically effective UV-B radiation at 4.2 (LUVB) and 10.3 (HUVB) kJ m–2 d–1 was provided on the seedlings at 25/20°C or 10/5°C. UV-B radiation inhibited net photosynthesis rate (Pn) by enhanced intensity and decreased temperature without change of intercellular CO2 concentrations (Ci). Decreased maximal quantum yield of Photosystem II (Fv/Fm) and increased minimum fluorescence (Fo) were observed in HUVB at both temperatures and LUVB at 10/5°C. HUVB increased total pool size (VAZ) of xanthophyll cycle pigments, but decreased the de-epoxidation state (DEPS) of these pigments at both temperatures, while LUVB only decreased DEPS at 10/5°C. The activities of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR) and the redox states of ascorbate and glutathione (AsA/DAsA and GSH/GSSG) were enhanced at 25/20°C, while there were increased SOD and CAT, unaltered APX activities and AsA/DHA, as well as decreased GR activity and GSH/GSSG in LUVB and HUVB at 10/5°C. UV-B radiation resulted in higher H2O2 and thiobarbituric acid reactive substance (TBARS) concentrations at 10/5°C than 25/20°C. It appears that low temperature alone did not influence photosynthesis but aggravated UV-B induced photoinhibition, which was associated with PSII photochemistry rather than stomatal limitation. Xanthophyll cycle pigments failed to provide photoprotection through thermal dissipation. The antioxidant system was up-regulated in LUVB and HUVB at 25/20°C, but was impaired at 10/5°C. Low temperature intensified UV-B induced photoinhibition and damage by weakening the antioxidant system.
N-protein mobilisation associated with the leaf senescence process in oilseed rape is concomitant with the disappearance of trypsin inhibitor activity
Authors: Etienne Philippe , Desclos Marie , Le Gou Lucie , Gombert Julie , Bonnefoy Josette , Maurel Karine , Le Dily Frédérik , Ourry Alain , Avice Jean-Christophe
Published: September 2007

Brassica napus L. (oilseed rape) is an important crop plant characterised by low nitrogen (N) use efficiency. This is mainly due to a weak N recycling from leaves that is related to incomplete protein degradation. Assuming that protease inhibitors are involved throughout protein mobilisation, the goal of this study was to determine their role in the control of N mobilisation associated with leaf senescence. Results showed that a 19-kDa polypeptide exhibiting trypsin inhibitor (TI) activity presented an increased gradient from the older to the younger leaves. According to the SAG12/Cab gene expression profile, which is an indicator of leaf senescence, mature leaves of nitrate-deprived plants presented an earlier initiation of senescence and a decrease in protein concentration when compared with nitrate-replete plants. This coincided with disappearance of both TI activity and a reduction in the transcript level of the BnD22 gene (encoding a protein sharing homology with Künitz protease inhibitor). In young leaves of N-deprived plants, initiation of senescence was delayed; soluble protein concentration was maintained while both TI activity and BnD22 transcripts were high. This indicates that in oilseed rape growing under nitrate deprivation, the more efficient N recycling from mature leaves contributes to the maintenance of growth in young leaves. The data suggest a significant role for protease inhibitors in the regulation of proteolytic processes associated with N mobilisation during leaf senescence.
Elastic properties of the forisome
Authors: Warmann Stephen A. , Pickard William F. , Shen Amy Q.
Published: September 2007

Forisomes are elongate Ca2+-responsive contractile protein bodies and act as flow blocking gates within the phloem of legumes. Because an understanding of their mechanical properties in vitro underpins understanding of their physiology in vivo, we undertook, using a microcantilever method, microscopic tensile tests (incremental stress-relaxation measurements) on forisomes from Canavalia gladiata (Jacq.) DC Akanata Mame and Vicia faba L. Witkiem Major. Viscoelastic properties of forisomes in their longitudinal direction were investigated before and after Ca2+-induced contraction, but in the radial direction only before contraction. Forisomes showed mechanical properties typical of a biological material with a unidirectional fibrous structure, i.e. the modulus of elasticity in the direction of their fibers is much greater than in the radial direction. Creep data were collected in all tensile tests and fit with a three parameter viscoelastic model. The pre-contraction longitudinal elastic moduli of the forisomes were not differentiable between the two species (V. faba, 660 ± 360 kPa; C. gladiata, 600 ± 360 kPa). Both species showed a direction-dependent mechanical response: the elastic modulus was dramatically smaller in the radial direction than in the longitudinal direction, suggesting a weak protein cross-linking amongst longitudinal protein fibers. Activation of forisomes decreased forisome stiffness longitudinally, as evidenced by the loss of toe-region in the stress strain curve, suggesting that the forisome may have dispersed or disordered its protein structure in a controlled fashion. Contractile forces generated by single forisomes undergoing activation were also measured for V. faba (510 ± 390 nN) and C. gladiata (570 ± 310 nN).
Actin filaments modulate hypoosmotic-responsive K+ efflux channels in specialised cells of developing bean seed coats
Authors: Zhang Wen-Hao , Patrick John W. , Tyerman Stephen D.
Published: September 2007

In developing bean (Phaseolus vulgaris L.) seeds, nutrients move in the symplasm from sieve elements to ground-parenchyma cells where they are transported across the plasma membrane into the seed apoplasm. Release of nutrients to the seed apoplasm is related to the osmotic conditions of the apoplasm. A hypoosmotic solution, resulting from enhanced uptake of nutrients by cotyledons, stimulates nutrient release from seed coat to the apoplasm. We investigated hypoosmotic nutrient release by examining the ionic membrane currents that respond to hypoosmotic treatment in protoplasts derived from three important cell types that occur at the seed coat–cotyledonary boundary. A non-selective but predominantly K+ efflux current that displayed a distinct time-dependent inactivation was elicited by membrane depolarisation under hypoosmotic conditions only in ground-parenchyma protoplasts. Hypoosmotic treatment had little effect on whole-cell ionic currents in protoplasts derived from coat chlorenchyma cells and cotyledon dermal cells. The inactivating K+ efflux current was elicited under isosmotic conditions by treatment with cytochalasin D, which disrupts actin filaments. Hypoosmotic treatment and cytochalasin D failed to induce the K+ current in ground-parenchyma protoplasts in the presence of the actin stabiliser, phalloidin. The net efflux of K+ from intact seed coats was enhanced by hypoosmotic treatment and cytochalasin D, and the stimulation of K+ efflux induced by the hypoosmotic treatment and cytochalasin D was abolished by phalloidin. A bursting Cl– channel previously described showed a similar pattern of responses. These results suggest that hypoosmotic-dependent KCl efflux from seed coats is mediated by the inactivating K+ outward current and bursting Cl– channel, and that actin filaments act as components of the transduction process that is a function of cell volume.
Endogenous auxin regulates the sensitivity of Dendrobium (cv. Miss Teen) flower pedicel abscission to ethylene
Authors: Rungruchkanont Karnchana , Ketsa Saichol , Chatchawankanphanich Orawan , van Doorn Wouter G.
Published: September 2007

Dendrobium flower buds and flowers have an abscission zone at the base of the pedicel (flower stalk). Ethylene treatment of cv. Miss Teen inflorescences induced high rates of abscission in flower buds but did not affect abscission once the flowers had opened. It is not known if auxin is a regulator of the abscission of floral buds and open flowers. The hypotheses that auxin is such a regulator and is responsible for the decrease in ethylene sensitivity were tested. Severed inflorescences bearing 4–8 floral buds and 4–6 open flowers were used in all tests. The auxin antagonists 2,3,5-triiodobenzoic acid (TIBA, an inhibitor of auxin transport) or 2-(4-chlorophenoxy)-2-methyl propionic acid (CMPA, an inhibitor of auxin action) were applied to the stigma of open flowers. Both chemicals induced high flower abscission rates, even if the inflorescences were not treated with ethylene. The effects of these auxin antagonists virtually disappeared when the inflorescences were treated with 1-methylcyclopropene (1-MCP), indicating that the abscission induced by the auxin antagonists was due to ethylene. Removal of the open flowers at the distal end of the pedicel hastened the time to abscission of the remaining pedicel, and also resulted in an increase in ethylene sensitivity. Indole-3-acetic acid (IAA) in lanolin, placed on the cut surface of the pedicel, replaced the effect of the removed flower. Treatments that promoted abscission of open flowers up-regulated a gene encoding a β-1,4-glucanase (Den-Cel1) in the abscission zone (AZ). The abundance of Den-Cel1 mRNA was highly correlated with β-1,4-glucanase activity in the AZ. The results show that auxin is an endogenous regulator of floral bud and flower abscission and suggest that auxin might explain, at least partially, why pedicel abscission of Dendrobium cv. Miss Teen changes from very ethylene-sensitive to ethylene-insensitive.
Functional genomics in chickpea: an emerging frontier for molecular-assisted breeding
Authors: Coram Tristan E. , Mantri Nitin L. , Ford Rebecca , Pang Edwin C. K.
Published: September 2007

Chickpea is a valuable and important agricultural crop, but yield potential is limited by a series of biotic and abiotic stresses, including Ascochyta blight, Fusarium wilt, drought, cold and salinity. To accelerate molecular breeding efforts for the discovery and introgression of stress tolerance genes into cultivated chickpea, functional genomics approaches are rapidly growing. Recently a series of genetic tools for chickpea have become available that have allowed high-powered functional genomics studies to proceed, including a dense genetic map, large insert genome libraries, expressed sequence tag libraries, microarrays, serial analysis of gene expression, transgenics and reverse genetics. This review summarises the development of these genomic tools and the achievements made in initial and emerging functional genomics studies. Much of the initial research focused on Ascochyta blight resistance, and a resistance model has been synthesised based on the results of various studies. Use of the rich comparative genomics resources from the model legumes Medicago truncatula and Lotus japonicus is also discussed. Finally, perspectives on the future directions for chickpea functional genomics, with the goal of developing elite chickpea cultivars, are discussed.
Generalization of distance to higher dimensional objects
Authors: Plotkin Steven S.
Published: September 2007

The measurement of distance between two objects is generalized to the case where the objects are no longer points but are one-dimensional. Additional concepts such as nonextensibility, curvature constraints, and noncrossing become central to the notion of distance. Analytical and numerical results are given for some specific examples, and applications to biopolymers are discussed.
A structural gap in Dpo4 supports mutagenic bypass of a major benzo[
a
]pyrene dG adduct in DNA through template misalignment
Authors: Bauer Jacob , Xing Guangxin , Yagi Haruhiko , Sayer Jane M. , Jerina Donald M. , Ling Hong
Published: September 2007

Erroneous replication of lesions in DNA by DNA polymerases leads to elevated mutagenesis. To understand the molecular basis of DNA damage-induced mutagenesis, we have determined the x-ray structures of the Y-family polymerase, Dpo4, in complex with a DNA substrate containing a bulky DNA lesion and incoming nucleotides. The DNA lesion is derived from an environmentally widespread carcinogenic polycyclic aromatic hydrocarbon, benzo[
a
]pyrene (BP). The potent carcinogen BP is metabolized to diol epoxides that form covalent adducts with cellular DNA. In the present study, the major BP diol epoxide adduct in DNA, BP-
N
2
-deoxyguanosine (BP–dG), was placed at a template–primer junction. Three ternary complexes reveal replication blockage, extension past a mismatched lesion, and a −1 frameshift mutation. In the productive structures, the bulky adduct is flipped/looped out of the DNA helix into a structural gap between the little finger and core domains. Sequestering of the hydrophobic BP adduct in this new substrate-binding site permits the DNA to exhibit normal geometry for primer extension. Extrusion of the lesion by template misalignment allows the base 5′ to the adduct to serve as the template, resulting in a −1 frameshift. Subsequent strand realignment produces a mismatched base opposite the lesion. These structural observations, in combination with replication and mutagenesis data, suggest a model in which the additional substrate-binding site stabilizes the extrahelical nucleotide for lesion bypass and generation of base substitutions and −1 frameshift mutations.
TRRAP and GCN5 are used by c-Myc to activate RNA polymerase III transcription
Authors: Kenneth Niall S. , Ramsbottom Ben A. , Gomez-Roman Natividad , Marshall Lynne , Cole Philip A. , White Robert J.
Published: September 2007

Activation of RNA polymerase (pol) II transcription by c-Myc generally involves recruitment of histone acetyltransferases and acetylation of histones H3 and H4. Here, we describe the mechanism used by c-Myc to activate pol III transcription of tRNA and 5S rRNA genes. Within 2 h of its induction, c-Myc appears at these genes along with the histone acetyltransferase GCN5 and the cofactor TRRAP. At the same time, occupancy of the pol III-specific factor TFIIIB increases and histone H3 becomes hyperacetylated, but increased histone H4 acetylation is not detected at these genes. The rapid acetylation of histone H3 and promoter assembly of TFIIIB, c-Myc, GCN5, and TRRAP are followed by recruitment of pol III and transcriptional induction. The selective acetylation of histone H3 distinguishes pol III activation by c-Myc from mechanisms observed in other systems.
Myocardial ischemia results in tetrahydrobiopterin (BH
4
) oxidation with impaired endothelial function ameliorated by BH
4
Authors: Dumitrescu Cristian , Biondi Roberto , Xia Yong , Cardounel Arturo J. , Druhan Lawrence J. , Ambrosio Giuseppe , Zweier Jay L.
Published: September 2007

Coronary vasodilation is impaired in the postischemic heart with a loss of endothelial nitric oxide synthase (eNOS) activity, but the mechanisms underlying ischemia-induced eNOS dysfunction are not understood. For nitric oxide (NO) synthesis, eNOS requires the redox-sensitive cofactor tetrahydrobiopterin (BH
4
); however, the role of BH
4
in ischemia-induced endothelial dysfunction remains unknown. Therefore, isolated rat hearts were subjected to varying durations of ischemia, and the alterations in NOS-dependent vasodilation were measured and correlated with assays of eNOS activity and cardiac BH
4
concentrations. Ischemia time-dependently decreased cardiac BH
4
content with 85, 95, or 97% irreversible degradation after 30, 45, or 60 min of ischemia, respectively. Paralleling the decreases in BH
4
, reductions of eNOS activity were seen of 58, 86, or 92%, and NOS-derived superoxide production was greatly increased. Addition of 10 μM BH
4
enhanced eNOS activity in nonischemic hearts and partially restored activity after ischemia. It also suppressed NOS-derived superoxide production. Impaired coronary flow during postischemic reperfusion was improved by BH
4
infusion. Thus, BH
4
depletion contributes to postischemic eNOS dysfunction, and BH
4
treatment is effective in partial restoration of endothelium-dependent coronary flow. Supplementation of BH
4
may therefore be an important therapeutic approach to reverse endothelial dysfunction in postischemic tissues.
Analysis of ryanodine receptor clusters in rat and human cardiac myocytes
Authors: Soeller Christian , Crossman David , Gilbert Ray , Cannell Mark B.
Published: September 2007

Single rat ventricular myocytes and human ventricle tissue sections were labeled with antibodies against the ryanodine receptor (RyR) and α-actinin to examine the 3D distribution of RyRs with confocal microscopy. Image contrast was maximized by refractive index matching and deconvolution. The RyR label formed discrete puncta representing clusters of RyRs or “couplons” around the edges of the myofilaments with a nearest-neighbor spacing of 0.66 ± 0.06 μm in rat and 0.78 ± 0.07 μm in human. Each bundle of myofibrils was served by approximately six couplons, which supplied a cross-sectional area of ≈0.6 μm
2
in rat and ≈0.8 μm
2
in human. Although the couplons were in reasonable registration with z-lines, there were discontinuities in the longitudinal position of sarcomeres so that dislocations in the order of RyR clusters occurred. There was ≈53% longitudinal registration of RyR clusters, suggesting a nonrandom placement of couplons around the sarcomere. These data can explain the spherical propagation of Ca
2+
waves and provide quantitative 3D data sets needed for accurate modeling of cardiac Ca
2+
-induced Ca
2+
release. By quantifying labeling intensity in rat ventricular myocytes, a lower limit of 78 RyRs per cluster (on average) was obtained. By modeling the couplon as a disk wrapping around a t-tubule and fitting cluster images, 95% of couplons contained between 120 and 260 RyRs (assuming that RyRs are tight packed with a spacing of 29 nm). Assuming similar labeling efficiency in human, from the fluorescence intensity alone we estimate that human ventricular myocytes contain ≈30% fewer RyRs per couplon than rat.
Proteasomal selection of multiprotein complexes recruited by LIM homeodomain transcription factors
Authors: Güngör Cenap , Taniguchi-Ishigaki Naoko , Ma Hong , Drung Alexander , Tursun Baris , Ostendorff Heather P. , Bossenz Michael , Becker Catherina G. , Becker Thomas , Bach Ingolf
Published: September 2007

Complexes composed of multiple proteins regulate most cellular functions. However, our knowledge about the molecular mechanisms governing the assembly and dynamics of these complexes in cells remains limited. The
in vivo
activity of LIM homeodomain (LIM-HD) proteins, a class of transcription factors that regulates neuronal development, depends on the high-affinity association of their LIM domains with cofactor of LIM homeodomain proteins (LIM-HDs) (CLIM, also known as Ldb or NLI). CLIM cofactors recruit single-stranded DNA-binding protein 1 (SSDP1, also known as SSBP3), and this interaction is important for the activation of the LIM-HD/CLIM protein complex
in vivo
. Here, we identify a cascade of specific protein interactions that protect LIM-HD multiprotein complexes from proteasomal degradation. In this cascade, CLIM stabilizes LIM-HDs, and SSDP1 stabilizes CLIM. Furthermore, we show that stabilizing cofactors prevent binding of ubiquitin ligases to multiple protein interaction domains in LIM-HD recruited protein complexes. Together, our results indicate a combinatorial code that selects specific multiprotein complexes via proteasomal degradation in cells with broad implications for the assembly and specificity of multiprotein complexes.
Maintenance of imprinting and nuclear architecture in cycling cells
Authors: Teller Kathrin , Solovei Irina , Buiting Karin , Horsthemke Bernhard , Cremer Thomas
Published: September 2007

Dynamic gene repositioning has emerged as an additional level of epigenetic gene regulation. An early example was the report of a transient, spatial convergence (≤2 μm) of oppositely imprinted regions (“kissing”), including the Angelman syndrome/Prader–Willi syndrome (AS/PWS) locus and the Beckwith–Wiedemann syndrome locus in human lymphocytes during late S phase. It was argued that kissing is required for maintaining opposite imprints in cycling cells. Employing 3D-FISH with a BAC contig covering the AS/PWS region, light optical, serial sectioning, and quantitative 3D-image analysis, we observed that both loci always retained a compact structure and did not form giant loops. Three-dimensional distances measured among various, homologous AS/PWS segments in 393 human lymphocytes, 132 human fibroblasts, and 129 lymphoblastoid cells fromGorilla gorillarevealed a wide range of distances at any stage of interphase and in G0. At late S phase, 4% of nuclei showed distances ≤2 μm, 49% showed distances >6 μm, and 18% even showed distances >8 μm. A similar distance variability was found forHomo sapiens(HSA) 15 centromeres in a PWS patient with a deletion of the maternal AS/PWS locus and for the Beckwith–Wiedemann syndrome loci in human lymphocytes. A transient kiss during late S phase between loci widely separated at other stages of the cell cycle seems incompatible with known global constraints of chromatin movements in cycling cells. Further experiments suggest that the previously observed convergence of AS/PWS loci during late S phase was most likely a side effect of the convergence of nucleolus organizer region-bearing acrocentric human chromosomes, including HSA 15.
Biosynthesis of 2-methylbacteriohopanepolyols by an anoxygenic phototroph
Authors: Rashby Sky E. , Sessions Alex L. , Summons Roger E. , Newman Dianne K.
Published: September 2007

Sedimentary 2-methyhopanes have been used as biomarker proxies for cyanobacteria, the only known bacterial clade capable of oxygenic photosynthesis and the only group of organisms found thus far to produce abundant 2-methylbacteriohopanepolyols (2-MeBHPs). Here, we report the identification of significant quantities of 2-MeBHP in two strains of the anoxygenic phototroph
Rhodopseudomonas palustris
. Biosynthesis of 2-MeBHP can occur in the absence of O
2
, deriving the C-2 methyl group from methionine. The relative abundance of 2-MeBHP varies considerably with culture conditions, ranging from 13.3% of total bacteriohopanepolyol (BHP) to trace levels of methylation. Analysis of intact BHPs reveals the presence of methylated bacteriohopane-32,33,34,35-tetrol but no detectable methylation of 35-aminobacteriohopane-32,33,34-triol. Our results demonstrate that an anoxygenic photoautotroph is capable of generating 2-MeBHPs and show that the potential origins of sedimentary 2-methylhopanoids are more diverse than previously thought.
MicroRNA regulation of cyclooxygenase-2 during embryo implantation
Authors: Chakrabarty Anindita , Tranguch Susanne , Daikoku Takiko , Jensen Kevin , Furneaux Henry , Dey Sudhansu K.
Published: September 2007

The implantation process is complex, requiring reciprocal interactions between implantation-competent blastocysts and the receptive uterus. Because microRNAs (miRNAs) have major roles in regulating gene expression, we speculated that they participate in directing the highly regulated spatiotemporally expressed genetic network during implantation. Here, we show that two miRNAs, mmu-miR-101a and mmu-miR-199a*, are spatiotemporally expressed in the mouse uterus during implantation coincident with expression of
cyclooxygenase-2
, a gene critical for implantation. More interestingly, our
in vitro
gain- and loss-of-function experiments show that
cyclooxygenase-2
expression is posttranscriptionally regulated by these two miRNAs. We report on miRNA-mediated regulation of uterine gene expression in the context of implantation. We believe that many other critical genes related to this process are also regulated by miRNAs. Thus, elucidating the physiological roles of uterine miRNAs will help us better understand the genetic control of implantation, the gateway to a successful pregnancy.
Structural basis for evasion of IgA immunity by
Staphylococcus aureus
revealed in the complex of SSL7 with Fc of human IgA1
Authors: Ramsland Paul A. , Willoughby Natasha , Trist Halina M. , Farrugia William , Hogarth P. Mark , Fraser John D. , Wines Bruce D.
Published: September 2007

Infection by
Staphylococcus aureus
can result in severe conditions such as septicemia, toxic shock, pneumonia, and endocarditis with antibiotic resistance and persistent nasal carriage in normal individuals being key drivers of the medical impact of this virulent pathogen. In both virulent infection and nasal colonization,
S. aureus
encounters the host immune system and produces a wide array of factors that frustrate host immunity. One in particular, the prototypical staphylococcal superantigen-like protein SSL7, potently binds IgA and C5, thereby inhibiting immune responses dependent on these major immune mediators. We report here the three-dimensional structure of the complex of SSL7 with Fc of human IgA1 at 3.2 Å resolution. Two SSL7 molecules interact with the Fc (one per heavy chain) primarily at the junction between the Cα2 and Cα3 domains. The binding site on each IgA chain is extensive, with SSL7 shielding most of the lateral surface of the Cα3 domain. However, the SSL7 molecules are positioned such that they should allow binding to secretory IgA. The key IgA residues interacting with SSL7 are also bound by the leukocyte IgA receptor, FcαRI (CD89), thereby explaining how SSL7 potently inhibits IgA-dependent cellular effector functions mediated by FcαRI, such as phagocytosis, degranulation, and respiratory burst. Thus, the ability of
S. aureus
to subvert IgA-mediated immunity is likely to facilitate survival in mucosal environments such as the nasal passage and may contribute to systemic infections.
DNA evidence for historic population size and past ecosystem impacts of gray whales
Authors: Alter S. Elizabeth , Rynes Eric , Palumbi Stephen R.
Published: September 2007

Ecosystem restoration may require returning threatened populations of ecologically pivotal species to near their former abundances, but it is often difficult to estimate historic population size of species that have been heavily exploited. Eastern Pacific gray whales play a key ecological role in their Arctic feeding grounds and are widely thought to have returned to their prewhaling abundance. Recent mortality spikes might signal that the population has reached long-term carrying capacity, but an alternative is that this decline was due to shifting climatic conditions on Arctic feeding grounds. We used a genetic approach to estimate prewhaling abundance of gray whales and report DNA variability at 10 loci that is typical of a population of ≈76,000–118,000 individuals, approximately three to five times more numerous than today's average census size of 22,000. Coalescent simulations indicate these estimates may include the entire Pacific metapopulation, suggesting that our average measurement of ≈96,000 individuals was probably distributed between the eastern and currently endangered western Pacific populations. These levels of genetic variation suggest the eastern population is at most at 28–56% of its historical abundance and should be considered depleted. If used to inform management, this would halve acceptable human-caused mortality for this population from 417 to 208 per year. Potentially profound ecosystem impacts may have resulted from a decline from 96,000 gray whales to the current population. At previous levels, gray whales may have seasonally resuspended 700 million cubic meters of sediment, as much as 12 Yukon Rivers, and provided food to a million sea birds.
Visualizing the dynamics of p21
Waf1/Cip1
cyclin-dependent kinase inhibitor expression in living animals
Authors: Ohtani Naoko , Imamura Yuko , Yamakoshi Kimi , Hirota Fumiko , Nakayama Rika , Kubo Yoshiaki , Ishimaru Naozumi , Takahashi Akiko , Hirao Atsushi , Shimizu Takatsune , Mann David J. , Saya Hideyuki , Hayashi Yoshio , Arase Seiji , Matsumoto Mitsuru , Kazuki Nakao , Hara Eiji
Published: September 2007

Although the role of
p21

Waf1/Cip1

gene expression is well documented in various cell culture studies, its
in vivo
roles are poorly understood. To gain further insight into the role of
p21

Waf1/Cip1

gene expression
in vivo
, we attempted to visualize the dynamics of
p21

Waf1/Cip1

gene expression in living animals. In this study, we established a transgenic mice line (p21-
p
-luc) expressing the firefly luciferase under the control of the
p21

Waf1/Cip1

gene promoter. In conjunction with a noninvasive bioluminescent imaging technique, p21-
p
-luc mice enabled us to monitor the endogenous
p21

Waf1/Cip1

gene expression
in vivo
. By monitoring and quantifying the
p21

Waf1/Cip1

gene expression repeatedly in the same mouse throughout its entire lifespan, we were able to unveil the dynamics of
p21

Waf1/Cip1

gene expression in the aging process. We also applied this system to chemically induced skin carcinogenesis and found that the levels of
p21

Waf1/Cip1

gene expression rise dramatically in benign skin papillomas, suggesting that
p21

Waf1/Cip1

plays a preventative role(s) in skin tumor formation. Surprisingly, moreover, we found that the level of
p21

Waf1/Cip1

expression strikingly increased in the hair bulb and oscillated with a 3-week period correlating with hair follicle cycle progression. Notably, this was accompanied by the expression of p63 but not p53. This approach, together with the analysis of
p21

Waf1/Cip1

knockout mice, has uncovered a novel role for the
p21

Waf1/Cip1

gene in hair development. These data illustrate the unique utility of bioluminescence imaging in advancing our understanding of the timing and, hence, likely roles of specific gene expression in higher eukaryotes.
Sense of Place, Quality of Life and Local Socioeconomic Context: Evidence from the Survey of English Housing, 2002/03
Authors: Mohan John , Twigg Liz
Published: September 2007

This paper explores associations between local socioeconomic context and perceptions of neighbourhood quality of life, using a multilevel modelling approach to analyse data from the 2002/03 Survey of English Housing. A range of individual, property and area variables is successively introduced, the aim being to determine which of these has the greatest influence on the probability of being dissatisfied with one's neighbourhood. Several variables relating to property type and characteristics were derived and a set of ecological independent variables was used that is different from those deployed in previous analyses. Using a multilevel approach, the analysis determines the spatial scale at which variance is most concentrated—namely, the primary sampling unit (PSU). The relationship between tenure and property type is broken down and it is shown that social renting per se is not necessarily associated with greater dissatisfaction, although there is an association between private renting and greater satisfaction, probably reflecting the age and social profile of private renters. In respect of ecological indicators, increased levels of deprivation were associated with a raised probability of expressing neighbourhood satisfaction, as was settlement size, which is consistent with earlier work on quality of life. Conclusions are drawn concerning the use of studies of this kind to monitor trends in neighbourhood satisfaction.
Ecology of Sound: The Sonic Order of Urban Space
Authors: Atkinson Rowland
Published: September 2007

Sound provides an often-ignored element of our conceptualisation of the urban fabric. The power of music, sound and noise to denote place and demarcate space is used here to develop the idea of a sonic ecology. The paper attempts to map the relative order of this unseen city and to theorise its spatial and temporal patterning. The sonic ecology, a relatively persistent and chronologically ordered quality to sound in urban space, is used as a means of examining the distribution of sound and to weigh the broader social impact of these qualities. The ambient soundscape of the street is made up of a shifting aural terrain, a resonant metropolitan fabric, which may exclude or subtly guide us in our experience of the city, thus highlighting an invisible yet highly affecting and socially relevant area of urban enquiry.
The Performance of Public-sector Housing in Kolkata, India, in the Post-reform Milieu
Authors: Sengupta Urmi , Tipple Allan G.
Published: September 2007

The public sector has been a prominent actor in the urban housing sector in the State of West Bengal for the past three decades. Reform measures introduced since 1990 have led to a shift in the mode of public housing delivery from direct provision to providing housing in the market model. The concept of private-sector participation in construction and finance has emerged as a natural response to meet the colossal demand for housing within government's dwindling budgetary capacity and a need for a catalyst to boost macroeconomic conditions. Paradoxically, the public-sector agencies are leading the reform initiatives by assuming the role of a real estate developer. The paper reviews the housing output in Kolkata in the pre- and post-reform eras in terms of housing quantity, quality, price and affordability. It is argued that new reforms have been successful in stimulating the overall housing market, but more targeted programmes are needed to improve the supply, quality and affordability for low-income families in the city.