bluuebunny/crossref_metadata_2025 huggingface dataset:
Highly efficient solid-state neutron scintillators based on hybrid sol-gel nanocomposite materials
Authors: Kesanli Banu , Hong Kunlun , Meyer Kent , Im Hee-Jung , Dai Sheng
Published: November 2006

This research highlights opportunities in the formulation of neutron scintillators that not only have high scintillation efficiencies but also can be readily cast into two-dimensional detectors. Series of transparent, crack-free monoliths were prepared from hybrid polystyrene-silica nanocomposites in the presence of arene-containing alkoxide precursor through room temperature sol-gel processing. The monoliths also contain lithium-6 salicylate as a target material for neutron-capture reactions and amphiphilic scintillator solution as a fluorescent sensitizer. Polystyrene was functionalized by trimethoxysilyl group in order to enable the covalent incorporation of aromatic functional groups into the inorganic sol-gel matrices for minimizing macroscopic phase segregation and facilitating lithium-6 doping in the sol-gel samples. Neutron and alpha responses of these hybrid polystyrene-silica monoliths were explored.
Voltage decay time of a liquid crystal cell submitted to a large difference of potential
Authors: Freire F. C. M. , Alexe-Ionescu A. L. , Scalerandi M. , Barbero G.
Published: November 2006

The voltage decay time of a nematic liquid crystal cell submitted to a large difference of electrical potential is theoretically investigated. The authors show that ions are responsible for a current transient in the electrical circuit containing the cell. The analysis is performed by solving the equations of continuity for the ions and the equation of Poisson for the electrical potential. The results of the authors’ numerical analysis are compared with the experimental data and a good agreement is found. From the best fit of the experimental data the authors obtain the ionic mobility and the bulk density of ions, in thermodynamical equilibrium.
Investigation of spectral diffusion in ribonuclease by photolabeling of intrinsic aromatic amino acids
Authors: Somoza Mark M. , Ponkratov Vladimir V. , Friedrich Josef
Published: November 2006

Spectral diffusion dynamics in ribonuclease A was observed via the broadening of photochemical holes burned into the absorption spectrum of intrinsic tyrosine residues. Unlike previous results based on hole burning of chromophores in the pockets of heme proteins, where spectral diffusion develops according to a power law in time, the dynamics in ribonuclease follow a logarithmic law. The results suggest that the experiment preferentially labels the tyrosines located on the surface of the protein where the two-level system dynamics of the glass host matrix exert a strong influence.
Acoustic method for levitation of small living animals
Authors: Xie W. J. , Cao C. D. , Lü Y. J. , Hong Z. Y. , Wei B.
Published: November 2006

Ultrasonic levitation of some small living animals such as ant, ladybug, and young fish has been achieved with a single-axis acoustic levitator. The vitality of ant and ladybug is not evidently influenced during the acoustic levitation, whereas that of the young fish is reduced because of the inadequacy of water supply. Numerical analysis shows that the sound pressures on the ladybug’s surface almost reach the incident pressure amplitude p0 due to sound scattering. It is estimated that 99.98% of the acoustic energy is reflected away from the ladybug. The acoustic radiation pressure pa on the ladybug’s surface is only 1%–3% of p0, which plays a compression role on the central region and a suction role on the peripheral region.
Influence of contact stiffnesses on the micromechanical characteristics of dense particulate systems subjected to shearing
Authors: Antony S. J. , Moreno-Atanasio R. , Hassanpour A.
Published: November 2006

When characterizing fine particles experimentally, it is a common practice to only measure the normal stiffness between particles and to assume that it is equal to the tangential stiffness. The impact of variations in the stiffness measurements upon the bulk characteristics of particulate systems remains unclear. Using computer simulations, the authors show that the variations in the contact stiffness ratio affect the micromechanical characteristics of nonspherical particulate systems more dominantly than the spherical particulate systems. Hence, attention must be paid to measure both the normal and tangential contact stiffnesses when characterizing nonspherical fine particulates to estimate their assembly characteristics.
Beating the maximum cooling limit with graded thermoelectric materials
Authors: Bian Zhixi , Shakouri Ali
Published: November 2006

The maximum cooling temperature of a uniform thermoelectric material is limited by its nondimensional figure of merit ZT. Conventionally cascaded stages or materials with a larger figure of merit are needed to obtain a higher cooling temperature. In this letter, the authors prove that the maximum cooling in an optimally graded single-stage device could be much larger than the value predicted based on the highest local ZT of the material. The cooling enhancement is attributed to the redistribution of the Joule heating and Peltier cooling profiles along the current and heat flow directions.
Spatially resolved thickness analysis of microscale structures using micro-Raman spectroscopy
Authors: Wu Xiaoming , Ren Tianling , Liu Litian , Yu Jianyuan
Published: November 2006

A novel method, by using micro-Raman spectroscopy, is developed to measure the thickness of microelectromechanical system structures with high spatial resolution. When a microscale structure is heated by a laser, the temperature rise of the structure depends on the structure thickness and material properties. Therefore, the structure thickness can be measured using Raman shift, which is a function of temperature. Micro-Raman spectrometer is capable of measuring the thickness distribution of microscale structures with micron spatial resolution. This technique is evaluated by characterizing the thickness distribution of a single-crystal silicon (c-Si) membrane. The measured thickness distributions are verified by scanning electron microscope measurement.
Thienyl analog of 1-(3-methoxycarbonyl)propyl-1-phenyl-[6,6]-methanofullerene for bulk heterojunction photovoltaic devices in combination with polythiophenes
Authors: Popescu Lacramioara M. , van ’t Hof Patrick , Sieval Alexander B. , Jonkman Harry T. , Hummelen Jan C.
Published: November 2006

An analog of 1-(3-methoxycarbonyl)propyl-1-phenyl-[6,6]-methanofullerene (PCBM) was designed with the aim of improving miscibility with polythiophene donors, especially poly(3-hexyl thiophene) (P3HT). In the title compound the phenyl group from PCBM is replaced by a thienyl group, it is named 1-(3-methoxycarbonyl)propyl-1-thienyl-[6,6]-methanofullerene (ThCBM). In this letter, experimental studies of the morphology, charge transport, and solar cell performance in blends of P3HT:ThCBM are reported. This may open a route for the design of more specific fullerene based acceptor materials, which may optimize the morphology of bulk heterojunction photovoltaic devices with respect to their transport.
Enhancing the germination of three fodder shrubs (Atriplex amnicola, A. nummularia, A. undulata; Chenopodiaceae): implications for the optimisation of field establishment
Authors: Stevens J. C. , Barrett-Lennard E. G. , Dixon K. W.
Published: November 2006

Saltbush (Atriplex) species are widely grown in Australia as saltland pastures. Direct seeding practices for saltbush currently result in asynchronous and unreliable seedling establishment (5% successful establishment is not uncommon from field-sown seed). In part this may stem from a limited understanding of Atriplex seed germination requirements. This paper presents findings with 3 Atriplex species, A. amnicola (Paul G. Wilson.), A. nummularia (Lindl.), and A. undulata (D. Dietr), each of which differs in germination characteristics. For A. amnicola, the presence of light (and artificial substitution of light by 1000 ppm gibberellic acid) improved germination under controlled conditions and resulted in a 4-fold increase (70% total emergence) in field emergence of seedlings. For A. undulata, removing bracteoles increased germination under controlled conditions (~15%), with a 1.5-fold improvement in field seedling emergence (55% final emergence); however, seed priming or gibberellic acid application had no significant effect. In contrast, for A. nummularia, bracteole removal and light had minor positive effects on germination under controlled conditions, but this did not translate into improved emergence in soil or in the field. Under –0.5 MPa NaCl stress, application of gibberellic acid, salicylic acid, or kinetin to the germination medium significantly increased the final germination percentage of A. amnicola seeds (58, 16, and 14%, respectively) and improved the rate at which seeds germinated. All plant signalling compounds significantly increased final germination percentage and germination rate of A. undulata, albeit with a <10% increase at –0.5 MPa NaCl. Priming seeds with plant signalling compounds had similar effects on seed germination under low water potentials compared to direct treatment of the germination media. The effects of seed priming on Atriplex seedling emergence from saline soils varied among species. Priming with water significantly increased emergence percentage of A. amnicola but had no effect on A. nummularia and A. undulata. Gibberellic acid improved A. amnicola germination parameters only, whereas salicylic acid and kinetin improved the rate of emergence in all 3 species at various levels of salinity. This study suggests that a basic understanding of seed dormancy and germination requirements has the potential to substantially improve field emergence of saltbush species.
Selection of field pea (Pisum sativum L.) cultivar and growing site improves germination and uniformity for sprout production
Authors: Fowler C. J. F. , Turner D. W. , Siddique K. H. M.
Published: November 2006

Uniform imbibition and germination of field pea (Pisum sativum L.) seeds is very important for sprout production for human consumption. The imbibition and germination of 3 cultivars of field pea, Dunwa, Dundale, and Helena, each grown at Mullewa, Merredin, and Scaddan in the grainbelt of Western Australia, were investigated in laboratory experiments. The ability of field pea to germinate was affected by cultivar and the environment under which seed development occurred on the parent plant. Averaged over locations, germination of the cv. Dundale (82%) was lower than of Dunwa (93%) or Helena (95%). Germination of seeds ranged from 85% for those grown at Merredin to 91% at Scaddan and 94% at Mullewa. The effect of growing location on germination was most pronounced in cv. Dundale from Merredin where the largest number of hard seeds was observed. Initial seed water content was positively (r2 = 0.55*) correlated with germination across cultivars and sites. Small and large seeds within a seed lot with the same initial seed water content had a similar germination percentage. During imbibition, water entered the seed through the strophiole and this would be an appropriate place to look for a mechanism that affects imbibition. Careful selection of cultivar and favourable growing site should improve germination for the sprout producer.
Summer dormancy in Festuca arundinacea Schreb.; the influence of season of sowing and a simulated mid-summer storm on two contrasting cultivars
Authors: Norton M. R. , Volaire F. , Lelièvre F.
Published: November 2006

Due to the shortage of information on summer dormancy in tall fescue (Festuca arundinacea, syn. Lolium arundinaceum), we tested the response of 2 cultivars of differing dormancy expression and growth stage to a range of summer moisture conditions, including full irrigation, drought, and a simulated mid-summer storm and analysed whether traits associated with summer dormancy conferred better survival under severe field drought. Autumn-sown reproductive and younger, spring-sown plants of 2 cultivars, claimed to exhibit contrasting summer dormancy, were established and then tested in summer 2002 under either long drought, drought + simulated mid-summer storm, or full irrigation. The autumn-sown reproductive plants of cv. Flecha exhibited traits that can be associated with partial summer dormancy since under summer irrigation they reduced aerial growth significantly and exhibited earlier herbage senescence. Moreover, cv. Flecha used 35% less soil water over the first summer. However, the water status of leaf bases of young vegetative tillers of both cultivars was similar under irrigation and also throughout most of the drought (leaf potential and water content maintained over –4 MPa and at approx. 1 g H2O/g DM, respectively). The summer-active cv. Demeter did not stop leaf elongation even in drought and produced twice as much biomass as Flecha under irrigation. Cultivar Demeter responded to the simulated storm with a decline in dehydrin expression in leaf bases, whereas no decline occurred in Flecha, presumably because it remained partially dormant. The younger, spring-sown swards of both cultivars had similar biomass production under summer irrigation but whereas Demeter regrew in response to the simulated storm, cv. Flecha did not, indicating that dormancy, although only partially expressed, was reinforced by summer drought. In all trials, cv. Flecha out-yielded Demeter in autumn regrowth. In particular, the severe drought in 2003 caused a 25% loss of the basal cover in cv. Demeter, whereas Flecha fully maintained its sward allowing it to produce a higher post-drought autumn yield. This work links summer dormancy with higher persistence over long, dry summers.
Equilibria between pyranoses and furanoses. III. Deoxyaldoses. The stability of furanoses
Authors: Angyal SJ , Pickles VA
Published: November 2006

The proportion of the pyranose and furanose forms in
aqueous solutions of deoxyaldoses has been determined
by p.m.r. spectroscopy. Removal of a hydroxyl group
from C2 or C3 of an aldose causes an increase in the furanose content, particularly if the group was cis to another group. The strongest
unfavourable interaction in the furanose ring appears
to be the one between the side-chain and a neighbouring cis hydroxyl group.
Acridone studies. XII. Relative rates of reaction of sodium methoxide with 1,2,3,4-Tetramethoxy-10-methylacridone
Authors: Prager RH , Hodgeman DKC
Published: November 2006

The relative and absolute
rates of exchange of the four methoxyl groups in
1,2,3,4-tetramethoxy-10methylacridone (melicopicine)
have been measured at 50�. The reaction at C1 is more
than 15 times faster than at C3. These rates of reaction are compared with
those of 1,4-dimethoxy-l0-methyl-2,3-methylenedioxyacridone (melicopidine), and suggestions made to account for the
differences.
A critical role for TNF receptor-associated factor 1 and Bim down-regulation in CD8 memory T cell survival
Authors: Sabbagh Laurent , Srokowski Cathy C. , Pulle Gayle , Snell Laura M. , Sedgmen Bradley J. , Liu Yuanqing , Tsitsikov Erdyni N. , Watts Tania H.
Published: November 2006

The mechanisms that allow the maintenance of immunological memory remain incompletely defined. Here we report that tumor necrosis factor receptor (TNFR)-associated factor (TRAF) 1, a protein recruited in response to several costimulatory TNFR family members, is required for maximal CD8 T cell responses to influenza virus in mice. Decreased recovery of CD8 T cells
in vivo
occurred under conditions where cell division was unimpaired.
In vitro
, TRAF1-deficient, antigen-activated T cells accumulated higher levels of the proapoptotic BH3-only family member Bim, particularly the most toxic isoform, Bim
S
. In the presence of excess IL-15, memory phenotype T cells with similar surface phenotype and comparable levels of Bcl-2 family members could be generated from WT or TRAF1-deficient T cell receptor transgenic OT-I T cells. However, when the memory CD8 T cells were allowed to compete for survival signals in the absence of antigen
in vivo
, the TRAF1-deficient T cells showed decreased recovery compared with TRAF1-sufficient T cells. This defect in T cell recovery
in vivo
was alleviated by introduction of siRNA to down-modulate Bim in TRAF1-deficient memory T cells. These studies identify the TRAF1 signaling axis and Bim down-regulation as critical for CD8 memory T cell survival
in vivo
.
Blocking the apolipoprotein E/amyloid-β interaction as a potential therapeutic approach for Alzheimer's disease
Authors: Sadowski Martin J. , Pankiewicz Joanna , Scholtzova Henrieta , Mehta Pankaj D. , Prelli Frances , Quartermain David , Wisniewski Thomas
Published: November 2006

The amyloid-β (Aβ) cascade hypothesis of Alzheimer's disease (AD) maintains that accumulation of Aβ peptide constitutes a critical event in the early disease pathogenesis. The direct binding between Aβ and apolipoprotein E (apoE) is an important factor implicated in both Aβ clearance and its deposition in the brain's parenchyma and the walls of meningoencephalic vessels as cerebral amyloid angiopathy. With the aim of testing the effect of blocking the apoE/Aβ interaction
in vivo
as a potential novel therapeutic target for AD pharmacotherapy, we have developed Aβ12-28P, which is a blood-brain-barrier-permeable nontoxic, and nonfibrillogenic synthetic peptide homologous to the apoE binding site on the full-length Aβ. Aβ12-28P binds with high affinity to apoE, preventing its binding to Aβ, but has no direct effect on Aβ aggregation. Aβ12-28P shows a strong pharmacological effect
in vivo
. Its systemic administration resulted in a significant reduction of Aβ plaques and cerebral amyloid angiopathy burden and a reduction of the total brain level of Aβ in two AD transgenic mice models. The treatment did not affect the levels of soluble Aβ fraction or Aβ oligomers, indicating that inhibition of the apoE/Aβ interaction
in vivo
has a net effect of increasing Aβ clearance over deposition and at the same time does not create conditions favoring formation of toxic oligomers. Furthermore, behavioral studies demonstrated that treatment with Aβ12-28P prevents a memory deficit in transgenic animals. These findings provide evidence of another therapeutic approach for AD.
Divergent activities of an engineered antibody in murine and human systems have implications for therapeutic antibodies
Authors: Vaccaro Carlos , Bawdon Roger , Wanjie Sylvia , Ober Raimund J. , Ward E. Sally
Published: November 2006

The MHC class I-related receptor, neonatal Fc receptor (FcRn), plays a central role in regulating the transport andin vivopersistence of immunoglobulin G (IgG). IgG–FcRn interactions can be targeted for engineering to modulate thein vivolongevity and transport of an antibody, and this has implications for the successful application of therapeutic IgGs. Although mice are widely used to preclinically test antibodies, human and mouse FcRn have significant differences in binding specificity. Here we show that an engineered human IgG1 has disparate properties in murine and human systems. The mutant shows improved transport relative to wild-type human IgG1 in assays of human FcRn function but has shortin vivopersistence and competitively inhibits FcRn activity in mice. These studies indicate potential limitations of using mice as preclinical models for the analysis of engineered antibodies. Alternative assays are proposed that serve as indicators of the properties of IgGs in humans.
Oncoprotein Akt/PKB induces trophic effects in murine models of Parkinson's disease
Authors: Ries Vincent , Henchcliffe Claire , Kareva Tatyana , Rzhetskaya Margarita , Bland Ross , During Matthew J. , Kholodilov Nikolai , Burke Robert E.
Published: November 2006

Despite promising preclinical studies, neurotrophic factors have not yet achieved an established role in the treatment of human neurodegenerative diseases. One impediment has been the difficulty in providing these macromolecules in sufficient quantity and duration at affected sites. An alternative approach is to directly activate, by viral vector transduction, intracellular signaling pathways that mediate neurotrophic effects. We have evaluated this approach in dopamine neurons of the substantia nigra, neurons affected in Parkinson's disease, by adeno-associated virus 1 transduction with a gene encoding a myristoylated, constitutively active form of the oncoprotein Akt/PKB. Adeno-associated virus Myr-Akt has pronounced trophic effects on dopamine neurons of adult and aged mice, including increases in neuron size, phenotypic markers, and sprouting. Transduction confers almost complete protection against apoptotic cell death in a highly destructive neurotoxin model. Activation of intracellular neurotrophic signaling pathways by vector transfer is a feasible approach to neuroprotection and restorative treatment of neurodegenerative disease.
Photoinduced electron flow in a self-assembling supramolecular extension cable
Authors: Ferrer Belén , Rogez Guillaume , Credi Alberto , Ballardini Roberto , Gandolfi Maria Teresa , Balzani Vincenzo , Liu Yi , Tseng Hsian-Rong , Stoddart J. Fraser
Published: November 2006

We report the design, bottom-up construction, characterization, and operation of a supramolecular system capable of mimicking the function played by a macroscopic electrical extension cable. The system is made up of a light-powered electron source, an electron drain, and a cable as the molecular components programmed to self-assemble by means of two distinct plug/socket junctions. Such connections are reversible and can be operated independently by orthogonal chemical inputs. In the source–connector–drain supermolecule, photoinduced electron transfer from source to drain occurs, and it can be switched off by dual-mode chemically controlled disassembling of the molecular components.
Poly(ADP-ribose) (PAR) polymer is a death signal
Authors: Andrabi Shaida A. , Kim No Soo , Yu Seong-Woon , Wang Hongmin , Koh David W. , Sasaki Masayuki , Klaus Judith A. , Otsuka Takashi , Zhang Zhizheng , Koehler Raymond C. , Hurn Patricia D. , Poirier Guy G. , Dawson Valina L. , Dawson Ted M.
Published: November 2006

Excessive activation of the nuclear enzyme, poly(ADP-ribose) polymerase-1 (PARP-1) plays a prominent role in various of models of cellular injury. Here, we identify poly(ADP-ribose) (PAR) polymer, a product of PARP-1 activity, as a previously uncharacterized cell death signal. PAR polymer is directly toxic to neurons, and degradation of PAR polymer by poly(ADP-ribose) glycohydrolase (PARG) or phosphodiesterase 1 prevents PAR polymer-induced cell death. PARP-1-dependent, NMDA excitotoxicity of cortical neurons is reduced by neutralizing antibodies to PAR and by overexpression of PARG. Neuronal cultures with reduced levels of PARG are more sensitive to NMDA excitotoxicity than WT cultures. Transgenic mice overexpressing PARG have significantly reduced infarct volumes after focal ischemia. Conversely, mice with reduced levels of PARG have significantly increased infarct volumes after focal ischemia compared with WT littermate controls. These results reveal PAR polymer as a signaling molecule that induces cell death and suggests that interference with PAR polymer signaling may offer innovative therapeutic approaches for the treatment of cellular injury.
Charge transfer through DNA nanoscaled assembly programmable with DNA building blocks
Authors: Osakada Yasuko , Kawai Kiyohiko , Fujitsuka Mamoru , Majima Tetsuro
Published: November 2006

DNA nanostructures based on programmable DNA molecular recognition have been developed, but the nanoelectronics of using DNA is still challenging. A more rapid charge-transfer (CT) process through the DNA nanoassembly is required for further development of programmable DNA nanoelectronics. In this article, we present direct absorption measurements of the long-range CT over a 140-Å DNA assembly based on a GC repetitive sequence constructed by simply mixing DNA building blocks. We show that a CT through DNA nanoscale assembly is possible and programmable with the designed DNA sequence.
Speech perception problems of the hearing impaired reflect inability to use temporal fine structure
Authors: Lorenzi Christian , Gilbert Gaëtan , Carn Héloïse , Garnier Stéphane , Moore Brian C. J.
Published: November 2006

People with sensorineural hearing loss have difficulty understanding speech, especially when background sounds are present. A reduction in the ability to resolve the frequency components of complex sounds is one factor contributing to this difficulty. Here, we show that a reduced ability to process the temporal fine structure of sounds plays an important role. Speech sounds were processed by filtering them into 16 adjacent frequency bands. The signal in each band was processed by using the Hilbert transform so as to preserve either the envelope (E, the relatively slow variations in amplitude over time) or the temporal fine structure (TFS, the rapid oscillations with rate close to the center frequency of the band). The band signals were then recombined and the stimuli were presented to subjects for identification. After training, normal-hearing subjects scored perfectly with unprocessed speech, and were ≈90% correct with E and TFS speech. Both young and elderly subjects with moderate flat hearing loss performed almost as well as normal with unprocessed and E speech but performed very poorly with TFS speech, indicating a greatly reduced ability to use TFS. For the younger hearing-impaired group, TFS scores were highly correlated with the ability to take advantage of temporal dips in a background noise when identifying unprocessed speech. The results suggest that the ability to use TFS may be critical for “listening in the background dips.” TFS stimuli may be useful in evaluating impaired hearing and in guiding the design of hearing aids and cochlear implants.
A second isoform of the ferredoxin:NADP oxidoreductase generated by an in-frame initiation of translation
Authors: Thomas Jean-Claude , Ughy Bettina , Lagoutte Bernard , Ajlani Ghada
Published: November 2006

Ferredoxin:NADP oxidoreductases (FNRs) constitute a family of flavoenzymes that catalyze the exchange of reducing equivalents between one-electron carriers and the two-electron-carrying NADP(H). The main role of FNRs in cyanobacteria and leaf plastids is to provide the NADPH for photoautotrophic metabolism. In root plastids, a distinct FNR isoform is found that has been postulated to function in the opposite direction, providing electrons for nitrogen assimilation at the expense of NADPH generated by heterotrophic metabolism. A multiple gene family encodes FNR isoenzymes in plants, whereas there is only one FNR gene (
petH
) in cyanobacteria. Nevertheless, we detected two FNR isoforms in the cyanobacterium
Synechocystis
sp. strain PCC6803. One of them (FNR
S
≈34 kDa) is similar in size to the plastid FNR and specifically accumulates under heterotrophic conditions, whereas the other one (FNR
L
≈46 kDa) contains an extra N-terminal domain that allows its association with the phycobilisome. Site-directed mutants allowed us to conclude that the smaller isoform, FNR
S
, is produced from an internal ribosome entry site within the
petH
ORF. Thus we have uncovered a mechanism by which two isoforms are produced from a single gene, which is, to our knowledge, novel in photosynthetic bacteria. Our results strongly suggest that FNR
L
is an NADP
+
reductase, whereas FNR
S
is an NADPH oxidase.
Stepwise binding and bending of DNA by
Escherichia coli
integration host factor
Authors: Sugimura Sawako , Crothers Donald M.
Published: November 2006

Integration host factor (IHF) is a prokaryotic protein required for the integration of λ phage DNA into its host genome. An x-ray crystal structure of the complex shows that IHF binds to the minor groove of DNA and bends the double helix by 160° [Rice PA, Yang S, Mizuuchi K, Nash HA (1996)
Cell
87:1295–1306]. We sought to dissect the complex formation process into its component binding and bending reaction steps, using stopped-flow fluorimetry to observe changes in resonance energy transfer between DNA-bound dyes, which in turn reflect distance changes upon bending. Different DNA substrates that are likely to increase or decrease the DNA bending rate were studied, including one with a nick in a critical kink position, and a substrate with longer DNA ends to increase hydrodynamic friction during bending. Kinetic experiments were carried out under pseudofirst-order conditions, in which the protein concentration is in substantial excess over DNA. At lower concentrations, the reaction rate rises linearly with protein concentration, implying rate limitation by the bimolecular reaction step. At high concentrations the rate reaches a plateau value, which strongly depends on temperature and the nature of the DNA substrate. We ascribe this reaction limit to the DNA bending rate and propose that complex formation is sequential at high concentration: IHF binds rapidly to DNA, followed by slower DNA bending. Our observations on the bending step kinetics are in agreement with results using the temperature-jump kinetic method.
Opposing forces of aerosol cooling and El Niño drive coral bleaching on Caribbean reefs
Authors: Gill Jennifer A. , Watkinson Andrew R. , McWilliams John P. , Côté Isabelle M.
Published: November 2006

Bleaching of corals as a result of elevated sea surface temperatures (SST) is rapidly becoming a primary source of stress for reefs globally; the scale and extent of this threat will depend on how the drivers of SST interact to influence bleaching patterns. We demonstrate how the opposing forces of the El Niño–Southern Oscillation (ENSO) and levels of atmospheric aerosols drive regional-scale patterns of coral bleaching across the Caribbean. When aerosol levels are low, bleaching is largely determined by El Niño strength, but high aerosol levels mitigate the effects of a severe El Niño. High aerosol levels, resulting principally from recent volcanic activity, have thus protected Caribbean reefs from more frequent widespread bleaching events but cannot be relied on to provide similar protection in the future.
Polymeric triple-shape materials
Authors: Bellin I. , Kelch S. , Langer R. , Lendlein A.
Published: November 2006

Shape-memory polymers represent a promising class of materials that can move from one shape to another in response to a stimulus such as heat. Thus far, these systems are dual-shape materials. Here, we report a triple-shape polymer able to change from a first shape (A) to a second shape (B) and from there to a third shape (C). Shapes B and C are recalled by subsequent temperature increases. Whereas shapes A and B are fixed by physical cross-links, shape C is defined by covalent cross-links established during network formation. The triple-shape effect is a general concept that requires the application of a two-step programming process to suitable polymers and can be realized for various polymer networks whose molecular structure allows formation of at least two separated domains providing pronounced physical cross-links. These domains can act as the switches, which are used in the two-step programming process for temporarily fixing shapes A and B. It is demonstrated that different combinations of shapes A and B for a polymer network in a given shape C can be obtained by adjusting specific parameters of the programming process. Dual-shape materials have already found various applications. However, as later discussed and illustrated by two examples, the ability to induce two shape changes that are not limited to be unidirectional rather than one could potentially offer unique opportunities, such as in medical devices or fasteners.
Using cryo-EM to measure the dipole potential of a lipid membrane
Authors: Wang Liguo , Bose Pulkit S. , Sigworth Fred J.
Published: November 2006

The dipole potential of a lipid bilayer membrane accounts for its much larger permeability to anions than cations and affects the conformation and function of membrane proteins. The absolute value of the dipole potential has been very difficult to measure, although its value has been estimated to range from 200 to 1,000 mV from ion translocation rates, the surface potential of lipid monolayers, and molecular dynamics calculations. Here, a point charge probe method was used to investigate the dipole potentials of both ester and ether lipid membranes. The interactions between electrons and lipid molecules were recorded by phase-contrast imaging using cryo-EM. The magnitude and the profile of the dipole potential along the bilayer normal were obtained by subtracting the contribution of the atomic potential from the cryo-EM image intensity. The peak dipole potential was estimated to be 510 and 260 mV for diphytanoylphosphatidylcholine and diphytanylphosphatidylcholine, respectively.
High-resolution
in situ
x-ray study of the hydrophobic gap at the water–octadecyl-trichlorosilane interface
Authors: Mezger Markus , Reichert Harald , Schöder Sebastian , Okasinski John , Schröder Heiko , Dosch Helmut , Palms Dennis , Ralston John , Honkimäki Veijo
Published: November 2006

The knowledge of the microscopic structure of water at interfaces is essential for the understanding of interfacial phenomena in numerous natural and technological environments. To study deeply buried liquid water–solid interfaces, high-energy x-ray reflectivity measurements have been performed. Silicon wafers, functionalized by a self-assembled monolayer of octadecyl-trichlorosilane, provide strongly hydrophobic substrates. We show interfacial density profiles with angstrom resolution near the solid–liquid interface of water in contact with an octadecyl-trichlorosilane layer. The experimental data provide clear evidence for the existence of a hydrophobic gap on the molecular scale with an integrated density deficit ρ
d
= 1.1 Å g cm
−3
at the solid–water interface. In addition, measurements on the influence of gases (Ar, Xe, Kr, N
2
, O
2
, CO, and CO
2
) and HCl, dissolved in the water, have been performed. No effect on the hydrophobic water gap was found.
Costs and benefits of processivity in enzymatic degradation of recalcitrant polysaccharides
Authors: Horn Svein J. , Sikorski Pawel , Cederkvist Jannicke B. , Vaaje-Kolstad Gustav , Sørlie Morten , Synstad Bjørnar , Vriend Gert , Vårum Kjell M. , Eijsink Vincent G. H.
Published: November 2006

Many enzymes that hydrolyze insoluble crystalline polysaccharides such as cellulose and chitin guide detached single-polymer chains through long and deep active-site clefts, leading to processive (stepwise) degradation of the polysaccharide. We have studied the links between enzyme efficiency and processivity by analyzing the effects of mutating aromatic residues in the substrate-binding groove of a processive chitobiohydrolase, chitinase B from
Serratia marcescens
. Mutation of two tryptophan residues (Trp-97 and Trp-220) close to the catalytic center (subsites +1 and +2) led to reduced processivity and a reduced ability to degrade crystalline chitin, suggesting that these two properties are linked. Most remarkably, the loss of processivity in the W97A mutant was accompanied by a 29-fold increase in the degradation rate for single-polymer chains as present in the soluble chitin-derivative chitosan. The properties of the W220A mutant showed a similar trend, although mutational effects were less dramatic. Processivity is thought to contribute to the degradation of crystalline polysaccharides because detached single-polymer chains are kept from reassociating with the solid material. The present results show that this processivity comes at a large cost in terms of enzyme speed. Thus, in some cases, it might be better to focus strategies for enzymatic depolymerization of polysaccharide biomass on improving substrate accessibility for nonprocessive enzymes rather than on improving the properties of processive enzymes.
Gfi-1 plays an important role in IL-2-mediated Th2 cell expansion
Authors: Zhu Jinfang , Jankovic Dragana , Grinberg Alex , Guo Liying , Paul William E.
Published: November 2006

Enforced expression of growth factor independent 1 (Gfi-1), a transcription repressor induced by T cell activation and IL-4/Stat6 signaling, strikingly enhances Th2 cell expansion. Using conditionallyGfi1-deficient mice prepared for this study, we show thatin vitroorin vivodeletion of this factor dramatically reduces Th2, but not Th1, cell expansion in response to IL-2. Both increased cell apoptosis and reduced cell proliferation resulted fromGfi1deletion. IL-2-Stat5 signaling was partially reduced inGfi1-deficient Th2 cells, but overexpression of Stat5 failed to restore normal Th2 expansion in these cells, suggesting that Gfi-1 also functioned downstream of, or in parallel with, Stat5 signaling. Reduced Th2 cell expansion in the absence of Gfi-1 was confirmed by the diminished frequency of IL-4-producing cells when these mice were infected withSchistosoma mansoni.
Influence of dominant HIV-1 epitopes on HLA-A3/peptide complex formation
Authors: Racape Judith , Connan Francine , Hoebeke Johan , Choppin Jeannine , Guillet Jean-Gérard
Published: November 2006

The binding of peptides to MHC class I molecules induces MHC/peptide complexes that have specific conformational features. Little is known about the molecular and structural bases required for an optimal MHC/peptide association able to induce a dominant T cell response. We sought to characterize the interaction between purified HLA-A3 molecules and four well known CD8 epitopes from HIV-1 proteins. To define the characteristics of HLA–peptide complex formation and to identify potential structural changes, we used biochemical assays that detect well formed complexes. We tested the amplitude, stability, and kinetic parameters of the interaction between HLA-A3, peptides, and anti-HLA mAbs. Our results show that the four epitopes Nef73–82, Pol325–333, Env37–46, and Gag20–28 bind strongly to HLA-A3 molecules and form very stable complexes that are detected with differential patterns of mAb reactivity. The most striking result is the nonrecognition of the HLA-A3/Gag20–28 complex by the A11.1M mAb specific to HLA-A3/-A11 alleles. To explain this observation, from the data published on HLA-A11 crystallographic structure, we propose molecular models of the HLA-A3 molecule complexed with Nef73–82, Pol325–333, and Gag20–28 epitopes. In the HLA-A3/Gag20–28 complex, we suggest that Arg at position P1 of the peptide may push the α2 helix residue Trp-167 of HLA-A3 and affect mAb recognition. Such observations may have great implications for T cell antigen receptor recognition and the immunogenicity of HLA/peptide complexes.
Tipin and Timeless form a mutually protective complex required for genotoxic stress resistance and checkpoint function
Authors: Chou Danny M. , Elledge Stephen J.
Published: November 2006

Tipin is a mammalian protein that interacts with Timeless, which plays a role in DNA damage checkpoint responses. Here, we show that Tipin is a nuclear protein that associates with the replicative helicase and protects cells against genotoxic agents. Tipin is required for efficient cell cycle arrest in response to DNA damage, and depletion of Tipin renders cells sensitive to ionizing radiation as well as replication stress. Loss of Tipin results in spontaneous γ-H2AX foci, a marker for DNA double-strand breaks. We find that Tipin and Timeless form a complex that maintains the level of both proteins in cells and that the loss of either one will lead to the loss of the interacting partner. This observation explains the similar checkpoint phenotypes observed in both Tipin- and Timeless-depleted cells.
Induction of a virus-specific effector–memory CD4+ T cell response by attenuated SIV infection
Authors: Gauduin Marie-Claire , Yu Yi , Barabasz Amy , Carville Angela , Piatak Mike , Lifson Jeffrey D. , Desrosiers Ronald C. , Johnson R. Paul
Published: November 2006

We investigated simian immunodeficiency virus (SIV)-specific CD4+ T cell responses in rhesus macaques chronically infected with attenuated or pathogenic SIV strains. Analysis of SIVΔnef-infected animals revealed a relatively high frequency of SIV-specific CD4+ T cells representing 4–10% of all CD4+ T lymphocytes directed against multiple SIV proteins. Gag-specific CD4+ T cells in wild-type SIV-infected animals were 5–10-fold lower in frequency and inversely correlated with the level of plasma viremia. SIV-specific CD4+ cells from SIVΔnef animals were predominantly CD27−CD28−CD45RAlowCCR7−CCR5−, consistent with an effector–memory subset, and included a fully differentiated CD45RA+CCR7− subpopulation. In contrast, SIV-specific CD4+ T cells from SIV-infected animals were mostly CD27+CD28+CD45RA−CCR7+CCR5+, consistent with an early central memory phenotype. The CD45RA+CCR7−CD4+ subset from SIVΔnef animals was highly enriched for effector CD4+ T cells, as indicated by the perforin expression and up-regulation of the lysosomal membrane protein CD107a after SIV Gag stimulation. SIV-specific CD4+ T cells in attenuated SIV-infected animals were increased in frequency in bronchioalveolar lavage and decreased in lymph nodes, consistent with an effector–memory T cell population. The ability of SIVΔnef to induce a high frequency virus-specific CD4+ T cell response with direct effector function may play a key role in protective immunity produced by vaccination with attenuated SIV strains.
Physiological and genetic characteristics of black‐boned sheep (Ovis aries)
Authors: Deng W. D. , Yang S. L. , Huo Y. Q. , Gou X. , Shi X. W. , Mao H. M.
Published: November 2006

Here we report for the first time the discovery of sheep that have black bones and black muscles. The spectral pattern of pigment extracted from tissues of these black‐boned sheep is similar to that of black‐boned Chinese silky fowl. Additionally, black‐boned sheep have significantly higher plasma colour, tyrosinase activity and kidney function than normal sheep. Synonymous nucleotide substitutions in the tyrosinase (TYR) and melanocortin 1 receptor (MC1R) genes were detected in black‐boned sheep when compared with the corresponding sequences in normal sheep. In addition, a missense mutation (215T>C) in exon 2 of tyrosinase‐related protein 1 (TYRP1) was detected in black‐boned sheep, and this resulted in a putative valine‐to‐alanine substitution at codon 68 (Val68Ala).
Characterization of the porcine FABP5 gene and its association with the FAT1 QTL in an Iberian by Landrace cross
Authors: Estellé J. , Pérez‐Enciso M. , Mercadé A. , Varona L. , Alves E. , Sánchez A. , Folch J. M.
Published: November 2006

We have characterized and mapped the porcine fatty acid binding protein 5, epidermal (FABP5) gene. According to linkage and RH mapping, this gene is located close to the FABP4 (fatty acid binding protein 4, adipocyte) gene on swine chromosome 4. We resequenced 4.7 kb of the FABP5 gene in the parental population of an Iberian × Landrace cross (IBMAP), identifying seven SNPs arranged in two distinct FABP5 haplotypes. QTL and association analyses in the IBMAP population showed that this gene is strongly associated with fat deposition. QTL and haplotype analysis revealed that both FABP4 and FABP5 (clustered in mammals) are major candidate genes for the FAT1 QTL; the most likely position for the FAT1 QTL is between these two genes. Finally, our results suggest the presence of more than one QTL affecting fatness traits on porcine chromosome 4.
Substitution of phenylephrine for pseudoephedrine as a nasal decongeststant. An illogical way to control methamphetamine abuse
Authors: Eccles Ronald
Published: November 2006

The aim of this review was to investigate the rationale for replacing the nasal decongestant pseudoephedrine (PDE) with phenylephrine (PE) as a means of controlling the illicit production of methamphetamine. A literature search was conducted in electronic databases and use of textbooks. Restrictions have been placed on the sale of PDE in the USA in an attempt to control the illicit production of methamphetamine. This has caused a switch from PDE to PE in many common cold and cough medicines. PE is a poor substitute for PDE as an orally administered decongestant as it is extensively metabolized in the gut and its efficacy as a decongestant is unproven. Both PDE and PE have a good safety record, but the efficacy of PDE as a nasal decongestant is supported by clinical trials. Studies in the USA indicate that restricting the sale of PDE to the public as a medicine has had little impact on the morbidity and number of arrests associated with methamphetamine abuse. Restricting the sale of PDE in order to control the illicit production of methamphetamine will deprive the public of a safe and effective nasal decongestant and force the pharmaceutical industry to replace PDE with PE, which may be an ineffective decongestant. Restrictions on sales of PDE to the public may not reduce the problems associated with methamphetamine abuse.
Adaptive differences in plant physiology and ecosystem paradoxes: insights from metabolic scaling theory
Authors: ENQUIST BRIAN J. , KERKHOFF ANDREW J. , HUXMAN TRAVIS E. , ECONOMO EVAN P.
Published: November 2006

The link between variation in species‐specific plant traits, larger scale patterns of productivity, and other ecosystem processes is an important focus for global change research. Understanding such linkages requires synthesis of evolutionary, biogeograpahic, and biogeochemical approaches to ecological research. Recent observations reveal several apparently paradoxical patterns across ecosystems. When compared with warmer low latitudes, ecosystems from cold northerly latitudes are described by (1) a greater temperature normalized instantaneous flux of CO2 and energy; and (2) similar annual values of gross primary production (GPP), and possibly net primary production. Recently, several authors attributed constancy in GPP to historical and abiotic factors.

Here, we show that metabolic scaling theory can be used to provide an alternative ‘biotically driven’ hypothesis. The model provides a baseline for understanding how potentially adaptive variation in plant size and traits associated with metabolism and biomass production in differing biomes can influence whole‐ecosystem processes. The implication is that one cannot extrapolate leaf/lab/forest level functional responses to the globe without considering evolutionary and geographic variation in traits associated with metabolism. We test one key implication of this model – that directional and adaptive changes in metabolic and stoichiometric traits of autotrophs may mediate patterns of plant growth across broad temperature gradients.

In support of our model, on average, mass‐corrected whole‐plant growth rates are not related to differences in growing season temperature or latitude. Further, we show how these changes in autotrophic physiology and nutrient content across gradients may have important implications for understanding: (i) the origin of paradoxical ecosystem behavior; (ii) the potential efficiency of whole‐ecosystem carbon dynamics as measured by the quotient of system capacities for respiration, R, and assimilation, A; and (iii) the origin of several ‘ecosystem constants’– attributes of ecological systems that apparently do not vary with temperature (and thus with latitude). Together, these results highlight the potential critical importance of community ecology and functional evolutionary/physiological ecology for understanding the role of the biosphere within the integrated earth system.