bluuebunny/crossref_metadata_2025 huggingface dataset:
Fundamental band edge absorption in nominally undoped and doped 4H-SiC
Authors: Grivickas P. , Grivickas V. , Linnros J. , Galeckas A.
Published: June 2007

Fundamental band edge absorption is investigated in nominally undoped (n<1014cm−3) and heavily doped (n∼8×1018cm−3) 4H-SiC by a spectroscopy technique based on spatially and time-resolved free-carrier absorption. The spectra are extracted over a wide absorption range (0.02–500cm−1) at temperatures from 75to450K. The experimental results are supported by an indirect transition theory with a unique set of dominating momentum-conserving phonons, showing good correlation with earlier findings of differential absorption measurements at 2K. Exciton binding energy of 30±10meV is derived from fitting the data at 75K. The detected polarization anisotropy of absorption with respect to c axis is shown to be consistent with the selection rules for the corresponding phonon branches. An analytical model related to constant degree of involved phonons describes well the obtained energy gap variation with temperature. Finally, doping induced band gap narrowing is characterized above the impurity-Mott transition and compared with theoretical calculations in the random phase approximation. The shape of the fundamental absorption edge at high carrier concentrations is discussed in terms of excitonic enhancement above the Mott transition, as recently detected in Si.
Characteristic tensile strength and Weibull shape parameter of carbon nanotubes
Authors: Klein Claude A.
Published: June 2007

Recently, it has been argued [N. M. Pugno and R. S. Ruoff, J. Appl. Phys. 99, 024301 (2006)] that available carbon-nanotube (CNT) tensile strength data do not obey the “classical” Weibull statistical model. In this paper we formulate Weibull’s theory in a manner suitable for assessing CNT fracture-strength data and demonstrate that, on taking into account the area S subjected to uniform tensile stresses, the data are consistent with Weibull’s model. Based on available data, a characteristic strength σC (S=1μm2) equal to 17.6±2.5GPa in conjunction with a shape parameter m equal to 2.77±0.34 provides a good description of the CNT fracture strength. In terms of effective strengths, and on assuming that the relevant area-scaling laws apply, carbon nanotubes and diamond nanofilms exhibit similar features for stressed areas ranging from 1to104μm2.
Characterization of textural surfaces using wave atoms
Authors: Ma Jianwei
Published: June 2007

Surface texture is one of the most important factors affecting the functional performance of components in many disciplines including metrology, tribology, fluid mechanics, optics, and manufacturing. Applications of wavelets and curvelets on functional surfaces have become an increasing interest. Unfortunately, they are not optimal to analyze the textural surfaces because they ignore the geometric properties of textures. In this letter, a wave atom transform combined with total variation minimization is proposed to characterize surfaces with oriented textural scratches. In comparison to curvelets, wave atoms not only capture the coherence of the pattern along the oscillations but also the pattern across the oscillations. The ability of the developed geometric multiscale method is demonstrated on engineering surfaces.
Improved dye-sensitized solar cells with a ZnO-nanoflower photoanode
Authors: Jiang C. Y. , Sun X. W. , Lo G. Q. , Kwong D. L. , Wang J. X.
Published: June 2007

In this letter, the authors report a dye-sensitized solar cell (DSSC) using a ZnO-nanoflower film photoanode, which was grown by a hydrothermal method at 95°C. The dye used was cis-bis(isothiocyanato)bis(2,2′-bipyridyl-4,4′-dicarboxylato)-ruthenium(II) bis-tetrabutylam-monium (N-719). At AM1.5G irradiation with 100mW∕cm2 light intensity, the DSSC based on ZnO-nanoflower film showed an energy conversion efficiency of 1.9%, which is much higher compared to that (1.0%) of the control device constructed using a photoanode of upstanding ZnO-nanorod array fabricated by hydrothermal method as well. The better performance of ZnO-nanoflower DSSC was due to a better dye loading and light harvesting of the ZnO-nanoflower film. The results demonstrate potential application of ZnO-nanoflower array for efficient dye-sensitized solar cells.
Effect of interface scattering on phonon thermal conductivity percolation in random nanowire composites
Authors: Tian Weixue , Yang Ronggui
Published: June 2007

The effect of phonon-interface scattering on the percolation of the phonon thermal conductivity in random nanowire composites is investigated by solving the phonon Boltzmann transport equation using the Monte Carlo simulation. The forming of a geometric percolating network does not lead to dramatic increase of the thermal conductivity in nanowire composites because of the dominance of the phonon-interface scattering. The thermal conductivity of nanocomposites is much less sensitive to the thermal conductivity contrast ratios of the constituent materials than that of bulk composites, especially when the volumetric concentration of the high thermal conductivity constituent is below the percolation threshold.
Enhanced photoluminescence of ZnO∕Er2O3 core-shell structure nanorods synthesized by pulsed laser deposition
Authors: Li S. Z. , Gan C. L. , Cai H. , Yuan C. L. , Guo J. , Lee P. S. , Ma J.
Published: June 2007

A narrow size distribution of ZnO nanorod array has been synthesized on silicon substrate by pulsed laser deposition (PLD) in argon ambient. ZnO∕Er2O3 core-shell nanostructures were then formed through PLD of a thin Er2O3 layer onto the fabricated ZnO nanorod surface. Transmission electron microscopy analysis shows that both the ZnO core and Er2O3 shell are polycrystalline. Photoluminescence measurement was carried out to characterize the optical properties of the core-shell nanostructures. The band diagram of the core-shell structure shows that a type-II nanostructure may have formed, which explains the ultraviolet emission enhancement of the core-shell structure over pure ZnO nanorods.
Epitaxial electrodeposition of freestanding large area single crystal substrates
Authors: Shin Jae Wook , Standley Adam , Chason Eric
Published: June 2007

The authors report on a method for producing freestanding single crystal metal films over large areas using electrodeposition and selective etching. The method can be turned into an inexpensive continuous process for making long ribbons or a large area of single crystal films. Results from a 5×5mm2 Ni single crystal film using electron backscattering pattern pole figures and x-ray diffraction demonstrate that the quality of material produced is equivalent to the initial substrate without annealing or polishing.
Nuclear magnetic resonance force microscopy with a microwire rf source
Authors: Poggio M. , Degen C. L. , Rettner C. T. , Mamin H. J. , Rugar D.
Published: June 2007

The authors use a 1.0μm wide patterned Cu wire with an integrated nanomagnetic tip to measure the statistical nuclear polarization of F19 in CaF2 by magnetic resonance force microscopy. With less than 350μW of dissipated power, the authors achieve rf magnetic fields over 4mT at 115MHz for a sample positioned within 100nm of the “microwire” rf source. A 200nm diameter FeCo tip integrated onto the wire produces field gradients greater than 105T∕m at the same position. The large rf fields from the broadband microwire enable long rotating-frame spin lifetimes of up to 15s at 4K.
Photoluminescence spectroscopy of bioconjugated CdSe∕ZnS quantum dots
Authors: Dybiec M. , Chornokur G. , Ostapenko S. , Wolcott A. , Zhang J. Z. , Zajac A. , Phelan C. , Sellers T. , Gerion D.
Published: June 2007

The authors performed scanning photoluminescence (PL) spectroscopy on CdSe∕ZnS core/shell quantum dots (QDs) bioconjugated to Interleukin 10 (IL10) antibody. The influence of IL10 on the QD photoluminescence spectra was explored on samples dried on solid substrates at various temperatures. A “blue” up to 15nm spectral shift of the PL maximum was observed on the bioconjugated QDs. The spectral shift is strongly increased after samples annealing above room temperature. A mechanism of the observed effect is attributed to changes in the QD electronic energy levels caused by local electric or stress field or chemical reactions which occurred on the QD surface.
Ultrabroadband near-infrared emission from a colorless bismuth-doped glass
Authors: Arai Yusuke , Suzuki Takenobu , Ohishi Yasutake , Morimoto Shigeki , Khonthon Sasithorn
Published: June 2007

The characteristics of bismuth-doped glasses were investigated as colorless ultrabroadband near-infrared gain media. The colorless Bi-doped soda-lime-silicate glass was prepared under controlled redox conditions, and it realized the broadest near-infrared emission of about 600nm in full width at half maximum, centered at 1000nm, under 720nm excitation. The emission band extended toward shorter wavelengths compared with the shortest wavelength for the Bi-doped glass ever reported. The colorless Bi-doped glass developed in this work has a good potential for the broadband gain media for amplifiers and tunable lasers.
Resistance to cereal rusts at the plant cell wall—what can we learn from other host-pathogen systems?
Authors: Collins N. C. , Niks R. E. , Schulze-Lefert P.
Published: June 2007

The ability of plant cells to resist invasion by pathogenic fungi at the cell periphery (pre-invasion resistance) differs from other types of resistance that are generally triggered after parasite entry and during differentiation of specialised intracellular feeding structures. Genetic sources of pre-invasion resistance such as mlo for barley powdery mildew and Lr34 for resistance to wheat leaf rust have proven to be broad-spectrum in effect and durable in the field. Continued breeding for this type of resistance (often quantitative in effect) is therefore considered an important strategy to protect cereal crops long-term against potentially devastating fungal diseases such as rusts. Considerable progress has been made in characterising genes and processes underlying pre-invasion resistance using mutant analysis, molecular genetics, gene cloning, and the model plant Arabidopsis, as well as comparative functional analysis of genes in Arabidopsis and cereals. This review summarises the current knowledge in this field, and discusses several aspects of pre-invasion resistance potentially pertinent to use in breeding; namely, biological cost of the resistance and effectiveness of individual resistance genes against multiple pathogen types. We show that mutations in Mlo, Ror1, and Ror2 genes known to affect powdery mildew pre-invasion resistance have no detectable effect on partial resistance to barley leaf rust as measured by latency period.
Challenges for sustainable cereal rust control in South Africa
Authors: Pretorius Z. A. , Pakendorf K. W. , Marais G. F. , Prins R. , Komen J. S.
Published: June 2007

The cultivation of small grain cereals was introduced to South Africa by Dutch settlers in the 17th Century. According to historical records the first documented epidemic of wheat stem rust occurred in the south-western parts of the current Western Cape in 1726. Recurring stem and leaf rust epidemics were associated with expanding wheat production and became particularly severe in the winter-rainfall regions of the Western and Eastern Cape, as well as in the summer-rainfall regions of the Free State. The wheat stripe rust pathogen was first detected in South Africa in 1996. Due to susceptibility of cultivars at the time of this exotic introduction, stripe rust has caused significant losses in commercial wheat production over the past 10 years. Pathotype surveys of Puccinia graminis and P. triticina were initiated in the 1920s, but were discontinued until research on wheat stem rust was resumed in the 1960s. Recent evidence has shown that P. graminis f. sp. tritici continues to evolve. In addition, the annual number of wheat stem rust collections is increasing, emphasising the sustained threat of this damaging pathogen. A stem rust pathotype first detected in 2000, with newly acquired virulence for Sr8b and Sr38, currently constitutes more than 80% of all collections. Leaf and stem rust diseases also occur on barley, oat, triticale, and rye and are important production constraints in several regions. Some studies have described variability in these pathogens but long-term records of pathogenicity changes in barley and oat rust are not available. Cereal rust diseases have clearly played an important role in South African agriculture and many production regions remain favourable for rust development. Current expertise in cereal rusts covers most technologies necessary to study the respective host–pathogen systems. However, a general lack of capacity and fragmentation of research groups prevent a unified approach and remain a challenge for sustainable cereal rust control in South Africa. A national strategy for cereal rust control, with particular emphasis on pathogen and host resources, and breeding for resistance, is urgently needed.
Breeding triple rust resistant wheat cultivars for Australia using conventional and marker-assisted selection technologies
Authors: Bariana H. S. , Brown G. N. , Bansal U. K. , Miah H. , Standen G. E. , Lu M.
Published: June 2007

Stem rust susceptibility of European wheats under Australian conditions posed a significant threat to wheat production for the early British settlers in Australia. The famous Australian wheat breeder, William Farrer, tackled the problem of stem rust susceptibility through breeding fast-maturing wheat cultivars. South-eastern Australia suffered a severe stem rust epidemic in 1973, which gave rise to a national approach to breeding for rust resistance. The National Wheat Rust Control Program was set up in 1975, modelled on the University of Sydney’s own rust resistance breeding program, at the University of Sydney Plant Breeding Institute, Castle Hill (now Cobbitty). Back-crossing of a range of sources of resistance provided genetically diverse germplasm for evaluation in various breeding programs. Current efforts are directed to building gene combinations through marker-assisted selection. Major genes for resistance to stem rust and leaf rust are being used in the back-crossing program of the ACRCP to create genetic diversity among Australian germplasm. Stripe rust and to a lesser extent leaf rust resistance in the Australian germplasm is largely based on combinations of adult plant resistance genes and our knowledge of their genomic locations has increased. Additional genes, other than Yr18/Lr34 and Yr29/Lr46, appeared to control adult plant resistance to both leaf rust and stripe rust. Two adult-plant stem rust resistance genes have also been identified. The development of selection technologies to achieve genotype-based selection of resistance gene combinations in the absence of bioassays has evolved in the last 5 years. Robust molecular markers are now available for several commercially important rust resistance genes. Marker-assisted selection for rust resistance is performed routinely in many wheat-breeding programs. Modified pedigree and limited back-cross methods have been used for breeding rust-resistant wheat cultivars in the University of Sydney wheat-breeding program. The single back-cross methodology has proved more successful in producing cultivars with combinations of adult plant resistance genes.
Pathotypic evolution in Puccinia striiformis in India during 1995 - 2004
Authors: Prashar M. , Bhardwaj S. C. , Jain S. K. , Datta D.
Published: June 2007

Yellow rust pathogen (Puccinia striiformis) distribution was monitored in different wheat-production zones (north-western plains zone, north hills zone, and south hills zone) of India during the last decade (1994–2004). Studies indicated the predominance of 3 pathotypes: 46S102 (46E149), 47S103 (47E148), and 46S119 (46E149+Yr9) in the north-western plains zone. These pathotypes were detected for the first time in 1995–96 and are evolving frequently. Another pathotype (78S84), although present in low frequency, was first detected from northern India and is virulent on Yr9 and Yr27, posing a major threat to cv. PBW343, which carries these genes. The high altitudes of the northern hills where very primitive wheat cultivars are grown showed less variability for the yellow rust pathogen. Continued breeding efforts and replacement of cultivars have resulted in low specialisation in the yellow rust pathogen in the south hills zone and pathotype 38S102 predominated in this area during the last decade.
High genetic diversity in Chilean populations of wheat yellow rust (Puccinia striiformis f. sp. tritici West.) assessed by RAPD and AFLP
Authors: Becerra V. , Paredes M. , Madariaga R. , Bariana H. S. , Mellado M. , Rojo C.
Published: June 2007

Wheat yellow rust (Puccinia striiformis f. sp. tritici West. PST) is one of the main fungal diseases that causes major yield losses in the central and southern wheat production area of Chile. Chilean plant breeding programs have been using specific resistance genes to control this disease and resistance was frequently lost due to the appearance of new pathotypes of this pathogen. This resulted in a frequent change of wheat cultivars in the country. The objective of this work was to determine the genetic polymorphism among PST samples collected in wheat fields throughout the country, using randomly amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP). Twenty-nine PST populations from 5 locations were analysed with 64 RAPD primers and 6 combinations of AFLP primers. The coefficients of similarity (53% for RAPD and 14% for AFLP) indicated that the populations of yellow rust in Chile are highly diverse, in contrast with similar studies performed in other countries. This observation is supported by the virulence spectrum of PST population. This stressed the need to pyramid 2 or more major genes in commercial cultivars. Alternatively, the deployment of adult plant resistance gene combinations should be conducted. AFLP technique was more robust for analysis of the genetic diversity of PST compared with RAPD, because of its reproducibility and high level of polymorphism. The analysis of genetic similarity data among yellow rust populations grouped most of the PST population according to their geographic origin.
From Farrer to the Australian Cereal Rust Control Program
Authors: McIntosh R. A.
Published: June 2007

Australia has a proud history in the development of rust-resistant wheat, a history that has evolved with the development of knowledge of host–pathogen genetics and the continuing transition of plant breeding from an art to science. William Farrer, who migrated to Australia to relieve his problem of tuberculosis, witnessed rust problems on farmers’ fields and addressed the problem as a private individual. Before the rediscovery of Mendel’s principles of inheritance he, like contemporaries in other countries, appreciated that variability was present and was inherited such that different traits could be recombined. He appreciated that there were 2 separate rusts and that both, particularly the less frequent stem rust, had to be present for effective selection in breeding programs. The University of Sydney has the oldest Faculty of Agriculture in the country and one of its first graduates initiated, in 1921, studies on cereal rust pathogen variability, host resistance, and resistance breeding. That program continues to the present time with the recurring themes of pathogen variability, host resistance, and the best ways of achieving lasting resistance. Until the 1970s, most of the knowledge of rust variability at the national level was applied to the University’s breeding program, targeted to prime hard-quality wheat for northern NSW. Following the 1973 rust epidemic in southern Australia, a National Wheat Rust Control Program was initiated, and it has evolved through several steps to the present Australian Cereal Rust Control Program with international dimensions. This paper reviews some of the history, development, applications, and achievements of 88 years of cereal rust research.
Molecular phylogenetics of the Muscidae (Diptera:Calyptratae): new ideas in a congruence context
Authors: Schnell e Schuehli Guilherme , Barros de Carvalho Claudio José , Wiegmann Brian M.
Published: June 2007

Hypotheses about the evolution of Muscidae have long been the subject of continuous re-evaluation and reinterpretation. Current understandings of the relationships among these flies are based mainly on a single set of characters and are therefore questionable. Our understanding of muscid phylogeny thus needs greater support and further corroboration from additional suites of characters. In the current study, we analysed phylogenetic relationships among 24 species of muscid flies (18 genera and six subfamilies) using 2989 characters derived from sequences of mitochondrial (COI and COII) and nuclear genes (CAD and EF-1α). Data from each gene partition were analysed both in combined and separate phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference. Support was found for the monophyly of the Muscidae in all analyses and for a sister-group relationship between Coenosiini and Phaoniinae. The latter group was placed in a clade with sampled species of Reinwardtiini and Cyrtoneurininae. The genera Ophyra and Hydrotaea were placed in the Muscinae and a sister-group relationship for Musca and Stomoxys was supported. Sampled species of Polietina form a monophyletic lineage, while Morellia was found to be paraphyletic. Combined analysis of gene partitions improved support and resolution for resulting topologies despite significant incongruence between data partitions found through application of the Incongruence Length Difference test.
Six proteins regulate the activation of
Myf5
expression in embryonic mouse limbs
Authors: Giordani Julien , Bajard Lola , Demignon Josiane , Daubas Philippe , Buckingham Margaret , Maire Pascal
Published: June 2007

Myf5, a member of the myogenic regulatory factor family, plays a major role in determining myogenic cell fate at the onset of skeletal muscle formation in the embryo. Spatiotemporal control of its expression during development requires multiple enhancer elements spread over >100 kb at the
Myf5
locus. Transcription in embryonic limbs is regulated by a 145-bp element located at −57.5 kb from the
Myf5
gene. In the present study we show that
Myf5
expression is severely impaired in the limb buds of
Six1
−/−
and
Six1
−/−
Six4
−/+
mouse mutants despite the presence of myogenic progenitor cells. The 145-bp regulatory element contains a sequence that binds Six1 and Six4 in electromobility shift assays
in vitro
and in chromatin immunoprecipitation assays with embryonic extracts. We further show that Six1 is able to transactivate a reporter gene under the control of this sequence.
In vivo
functionality of the Six binding site is demonstrated by transgenic analysis. Mutation of this site impairs reporter gene expression in the limbs and in mature somites where the 145-bp regulatory element is also active. Six1/4 therefore regulate
Myf5
transcription, together with Pax3, which was previously shown to be required for the activity of the 145-bp element. Six homeoproteins, which also directly regulate the myogenic differentiation gene
Myogenin
and lie genetically upstream of
Pax3
, thus control hypaxial myogenesis at multiple levels.
Intergenic variants of
HBS1L-MYB
are responsible for a major quantitative trait locus on chromosome 6q23 influencing fetal hemoglobin levels in adults
Authors: Thein Swee Lay , Menzel Stephan , Peng Xu , Best Steve , Jiang Jie , Close James , Silver Nicholas , Gerovasilli Ageliki , Ping Chen , Yamaguchi Masao , Wahlberg Karin , Ulug Pinar , Spector Tim D. , Garner Chad , Matsuda Fumihiko , Farrall Martin , Lathrop Mark
Published: June 2007

Individual variation in fetal hemoglobin (HbF, α
2
γ
2
) response underlies the remarkable diversity in phenotypic severity of sickle cell disease and β thalassemia. HbF levels and HbF-associated quantitative traits (e.g., F cell levels) are highly heritable. We have previously mapped a major quantitative trait locus (QTL) controlling F cell levels in an extended Asian-Indian kindred with β thalassemia to a 1.5-Mb interval on chromosome 6q23, but the causative gene(s) are not known. The QTL encompasses several genes including
HBS1L
, a member of the GTP-binding protein family that is expressed in erythroid progenitor cells. In this high-resolution association study, we have identified multiple genetic variants within and 5′ to
HBS1L
at 6q23 that are strongly associated with F cell levels in families of Northern European ancestry (
P
= 10
−75
). The region accounts for 17.6% of the F cell variance in northern Europeans. Although mRNA levels of
HBS1L
and
MYB
in erythroid precursors grown
in vitro
are positively correlated, only
HBS1L
expression correlates with high F cell alleles. The results support a key role for the
HBS1L
-related genetic variants in HbF control and illustrate the biological complexity of the mechanism of 6q QTL as a modifier of fetal hemoglobin levels in the β hemoglobinopathies.
Global patterns in bacterial diversity
Authors: Lozupone Catherine A. , Knight Rob
Published: June 2007

Microbes are difficult to culture. Consequently, the primary source of information about a fundamental evolutionary topic, life's diversity, is the environmental distribution of gene sequences. We report the most comprehensive analysis of the environmental distribution of bacteria to date, based on 21,752 16S rRNA sequences compiled from 111 studies of diverse physical environments. We clustered the samples based on similarities in the phylogenetic lineages that they contain and found that, surprisingly, the major environmental determinant of microbial community composition is salinity rather than extremes of temperature, pH, or other physical and chemical factors represented in our samples. We find that sediments are more phylogenetically diverse than any other environment type. Surprisingly, soil, which has high species-level diversity, has below-average phylogenetic diversity. This work provides a framework for understanding the impact of environmental factors on bacterial evolution and for the direction of future sequencing efforts to discover new lineages.
A previously unknown reovirus of bat origin is associated with an acute respiratory disease in humans
Authors: Chua Kaw Bing , Crameri Gary , Hyatt Alex , Yu Meng , Tompang Mohd Rosli , Rosli Juliana , McEachern Jennifer , Crameri Sandra , Kumarasamy Verasingam , Eaton Bryan T. , Wang Lin-Fa
Published: June 2007

Respiratory infections constitute the most widespread human infectious disease, and a substantial proportion of them are caused by unknown etiological agents. Reoviruses (respiratory enteric orphan viruses) were first isolated from humans in the early 1950s and so named because they were not associated with any known disease. Here, we report a previously unknown reovirus (named “Melaka virus”) isolated from a 39-year-old male patient in Melaka, Malaysia, who was suffering from high fever and acute respiratory disease at the time of virus isolation. Two of his family members developed similar symptoms ≈1 week later and had serological evidence of infection with the same virus. Epidemiological tracing revealed that the family was exposed to a bat in the house ≈1 week before the onset of the father's clinical symptoms. Genome sequence analysis indicated a close genetic relationship between Melaka virus and Pulau virus, a reovirus isolated in 1999 from fruit bats in Tioman Island, Malaysia. Screening of sera collected from human volunteers on the island revealed that 14 of 109 (13%) were positive for both Pulau and Melaka viruses. This is the first report of an orthoreovirus in association with acute human respiratory diseases. Melaka virus is serologically not related to the different types of mammalian reoviruses that were known to infect humans asymptomatically. These data indicate that bat-borne reoviruses can be transmitted to and cause clinical diseases in humans.
Targeted dendrotomy reveals active and passive contributions of the dendritic tree to synaptic integration and neuronal output
Authors: Bekkers John M. , Häusser Michael
Published: June 2007

Neurons typically function as transduction devices, converting patterns of synaptic inputs, received on the dendrites, into trains of output action potentials in the axon. This transduction process is surprisingly complex and has been proposed to involve a two-way dialogue between axosomatic and dendritic compartments that can generate mutually interacting regenerative responses. To manipulate this process, we have developed a new approach for rapid and reversible occlusion or amputation of the primary dendrites of individual neurons in brain slices. By applying these techniques to cerebellar Purkinje and layer 5 cortical pyramidal neurons, we show directly that both the active and passive properties of dendrites differentially affect firing in the axon depending on the strength of stimulation. For weak excitation, dendrites act as a passive electrical load, raising spike threshold and dampening axonal excitability. For strong excitation, dendrites contribute regenerative inward currents, which trigger burst firing and enhance neuronal excitability. These findings provide direct support for the idea that dendritic morphology and conductances act in concert to regulate the excitability of the neuron.
Pathological role of osteoclast costimulation in arthritis-induced bone loss
Authors: Ochi Sae , Shinohara Masahiro , Sato Kojiro , Gober Hans-Jürgen , Koga Takako , Kodama Tatsuhiko , Takai Toshiyuki , Miyasaka Nobuyuki , Takayanagi Hiroshi
Published: June 2007

Abnormal T cell immune responses induce aberrant expression of inflammatory cytokines such as TNF-α, leading to osteoclastmediated bone erosion and osteoporosis in autoimmune arthritis. However, the mechanism underlying enhanced osteoclastogenesis in arthritis is not completely understood. Here we show that TNF-α contributes to inflammatory bone loss by enhancing the osteoclastogenic potential of osteoclast precursor cells through inducing paired Ig-like receptor-A (PIR-A), a costimulatory receptor for receptor activator of NF-κB (RANK). In fact, bone erosion and osteoporosis, but not inflammation, caused by aberrant TNF-α expression were ameliorated in mice deficient in Fc receptor common γ subunit or β2-microglobulin, in which the expression of PIR-As and PIR-A ligands is impaired, respectively. These results establish the pathological role of costimulatory receptors for RANK in bone loss in arthritis and may provide a molecular basis for the future therapy of inflammatory diseases.
Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy
Authors: Schanda Paul , Forge Vincent , Brutscher Bernhard
Published: June 2007

Atom-resolved real-time studies of kinetic processes in proteins have been hampered in the past by the lack of experimental techniques that yield sufficient temporal and atomic resolution. Here we present band-selective optimized flip-angle short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous observation of reaction kinetics for a large number of nuclear sites along the polypeptide chain of a protein with an unprecedented time resolution of a few seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational transition of α-lactalbumin from a molten globular to the native state for a large number of amide sites along the polypeptide chain. The kinetic behavior observed for the disappearance of the molten globule and the appearance of the native state is monoexponential and uniform along the polypeptide chain. This observation confirms previous findings that a single transition state ensemble controls folding of α-lactalbumin from the molten globule to the native state. In a second application, the spontaneous unfolding of native ubiquitin under nondenaturing conditions is characterized by amide hydrogen exchange rate constants measured at high pH by using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual manner with distinct unfolding regimes.
Hippocampal long-term depression mediates acute stress-induced spatial memory retrieval impairment
Authors: Wong Tak Pan , Howland John G. , Robillard Julie M. , Ge Yuan , Yu Wayne , Titterness Andrea K. , Brebner Karen , Liu Lidong , Weinberg Joanne , Christie Brian R. , Phillips Anthony G. , Wang Yu Tian
Published: June 2007

Acute stress impairs memory retrieval and facilitates the induction of long-term depression (LTD) in the hippocampal CA1 region of the adult rodent brain. However, whether such alterations in synaptic plasticity cause the behavioral effects of stress is not known. Here, we report that two selective inhibitors of the induction or expression of stress-enabled,
N
-methyl-
d
-aspartate receptor-dependent hippocampal LTD also block spatial memory retrieval impairments caused by acute stress. Additionally, we demonstrate that facilitating the induction of hippocampal LTD
in vivo
by blockade of glutamate transport mimics the behavioral effects of acute stress by impairing spatial memory retrieval. Thus, the present study demonstrates that hippocampal LTD is both necessary and sufficient to cause acute stress-induced impairment of spatial memory retrieval and provides a new perspective from which to consider the nature of cognitive deficits in disorders whose symptoms are aggravated by stress.
Ductile crystalline–amorphous nanolaminates
Authors: Wang Yinmin , Li Ju , Hamza Alex V. , Barbee Troy W.
Published: June 2007

It is known that the room-temperature plastic deformation of bulk metallic glasses is compromised by strain softening and shear localization, resulting in near-zero tensile ductility. The incorporation of metallic glasses into engineering materials, therefore, is often accompanied by complete brittleness or an apparent loss of useful tensile ductility. Here we report the observation of an exceptional tensile ductility in crystalline copper/copper–zirconium glass nanolaminates. These nanocrystalline–amorphous nanolaminates exhibit a high flow stress of 1.09 ± 0.02 GPa, a nearly elastic-perfectly plastic behavior without necking, and a tensile elongation to failure of 13.8 ± 1.7%, which is six to eight times higher than that typically observed in conventional crystalline–crystalline nanolaminates (<2%) and most other nanocrystalline materials. Transmission electron microscopy and atomistic simulations demonstrate that shear banding instability no longer afflicts the 5- to 10-nm-thick nanolaminate glassy layers during tensile deformation, which also act as high-capacity sinks for dislocations, enabling absorption of free volume and free energy transported by the dislocations; the amorphous–crystal interfaces exhibit unique inelastic shear (slip) transfer characteristics, fundamentally different from those of grain boundaries. Nanoscale metallic glass layers therefore may offer great benefits in engineering the plasticity of crystalline materials and opening new avenues for improving their strength and ductility.
Asymmetric redistribution of GABA receptors during GABA gradient sensing by nerve growth cones analyzed by single quantum dot imaging
Authors: Bouzigues Cédric , Morel Mathieu , Triller Antoine , Dahan Maxime
Published: June 2007

During development of the nervous system, the tip of a growing axon, the growth cone (GC), must respond accurately to stimuli that direct its growth. This axonal navigation depends on extracellular concentration gradients of numerous guidance cues, including GABA. GCs can detect even weak directional signals, yet the mechanisms underlying this sensitivity remain unclear. Past studies in other eukaryotic chemotactic systems have pointed to the role of the spatial reorganization of the transduction pathway in their sensitive response. Here we have developed a single-molecule assay to observe individual GABAAreceptors (GABAARs) in the plasma membrane of nerve GCs subjected to directional stimuli. We report that in the presence of an external GABA gradient GABAARs redistribute asymmetrically across the GC toward the gradient source. Single-particle tracking of GABAARs shows that the redistribution results from transient interactions between the receptors and the microtubules. Moreover, the relocalization is accompanied by an enhancement in the asymmetry of intracellular calcium concentration. Altogether, our results reveal a microtubule-dependent polarized reorganization of chemoreceptors at the cell surface and suggest that this polarization serves as an amplification step in GABA gradient sensing by nerve GCs.
Zebrafish model for human long QT syndrome
Authors: Arnaout Rima , Ferrer Tania , Huisken Jan , Spitzer Kenneth , Stainier Didier Y. R. , Tristani-Firouzi Martin , Chi Neil C.
Published: June 2007

Long QT syndrome (LQTS) is a disorder of ventricular repolarization that predisposes affected individuals to lethal cardiac arrhythmias. To date, an appropriate animal model of inherited LQTS does not exist. The zebrafish is a powerful vertebrate model used to dissect molecular pathways of cardiovascular development and disease. Because fundamental electrical properties of the zebrafish heart are remarkably similar to those of the human heart, the zebrafish may be an appropriate model for studying human inherited arrhythmias. Here we describe the molecular, cellular, and electrophysiological basis of a zebrafish mutant characterized by ventricular asystole. Genetic mapping and direct sequencing identify the affected gene as
kcnh2
, which encodes the channel responsible for the rapidly activating delayed rectifier K
+
current (
I
Kr
). We show that complete loss of functional
I
Kr
in embryonic hearts leads to ventricular cell membrane depolarization, inability to generate action potentials (APs), and disrupted calcium release. A small hyperpolarizing current restores spontaneous APs, implying wild-type function of other ionic currents critical for AP generation. Heterozygous fish manifest overt cellular and electrocardiographic evidence for delayed ventricular repolarization. Our findings provide insight into the pathogenesis of homozygous
kcnh2
mutations and expand the use of zebrafish mutants as a model system to study human arrhythmias.
Colloids with high-definition surface structures
Authors: Chen Hsien-Yeh , Rouillard Jean-Marie , Gulari Erdogan , Lahann Joerg
Published: June 2007

Compared with the well equipped arsenal of surface modification methods for flat surfaces, techniques that are applicable to curved, colloidal surfaces are still in their infancy. This technological gap exists because spin-coating techniques used in traditional photolithographic processes are not applicable to the curved surfaces of spherical objects. By replacing spin-coated photoresist with a vapor-deposited, photodefinable polymer coating, we have now fabricated microstructured colloids with a wide range of surface patterns, including asymmetric and chiral surface structures, that so far were typically reserved for flat substrates. This high-throughput method can yield surface-structured colloidal particles at a rate of ≈10
7
to 10
8
particles per operator per day. Equipped with spatially defined binding pockets, microstructured colloids can engage in programmable interactions, which can lead to directed self-assembly. The ability to create a wide range of colloids with both simple and complex surface patterns may contribute to the genesis of previously unknown colloidal structures and may have important technological implications in a range of different applications, including photonic and phononic materials or chemical sensors.
Essential roles of inhibin beta A in mouse epididymal coiling
Authors: Tomaszewski Jessica , Joseph Avenel , Archambeault Denise , Yao Humphrey Hung-Chang
Published: June 2007

Testis-derived testosterone has been recognized as the key factor for morphogenesis of the Wolffian duct, the precursor of several male reproductive tract structures. Evidence supports that testosterone is required for the maintenance of the Wolffian duct via its action on the mesenchyme. However, it remains uncertain how testosterone alone is able to facilitate formation of regionally specific structures such as the epididymis, vas deferens, and seminal vesicle from a straight Wolffian duct. In this study, we identified inhibin beta A (orInhba) as a regional paracrine factor in mouse mesonephroi that controls coiling of the epithelium in the anterior Wolffian duct, the future epididymis.Inhbawas expressed specifically in the mesenchyme of the anterior Wolffian duct at embryonic day 12.5 before the production of androgens. In the absence ofInhba, the epididymis failed to develop the characteristic coiling in the epithelium, which showed a dramatic decrease in proliferation. This loss of epididymal coiling did not result from testosterone deficiency, because testosterone production and parameters for testosterone action such as testis descent and anogenital distance remained normal. We further found that initialInhbaexpression did not require testosterone asInhbawas also expressed in the anterior Wolffian duct of female embryos where no testosterone was produced. However,Inhbaexpression at later stages depended on testosterone. These results demonstrated thatInhba,amesenchyme-specific gene, acts collectively with testosterone to facilitate epididymal coiling by stimulating epithelial proliferation.
Metal-free superoxide dismutase forms soluble oligomers under physiological conditions: A possible general mechanism for familial ALS
Authors: Banci Lucia , Bertini Ivano , Durazo Armando , Girotto Stefania , Gralla Edith Butler , Martinelli Manuele , Valentine Joan Selverstone , Vieru Miguela , Whitelegge Julian P.
Published: June 2007

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder selectively affecting motor neurons; 90% of the total cases are sporadic, but 2% are associated with mutations in the gene coding for the antioxidant enzyme copper–zinc superoxide dismutase (SOD1). The causes of motor neuron death in ALS are poorly understood in general, but for SOD1-linked familial ALS, aberrant oligomerization of SOD1 mutant proteins has been strongly implicated. In this work, we show that wild-type human SOD1, when lacking both its metal ions, forms large, stable, soluble protein oligomers with an average molecular mass of ≈650 kDa under physiological conditions, i.e., 37°C, pH 7.0, and 100 μM protein concentration. It further is shown here that intermolecular disulfide bonds are formed during oligomerization and that Cys-6 and Cys-111 are implicated in this bonding. The formation of the soluble oligomers was monitored by their ability to enhance the fluorescence of thioflavin T, a benzothiazole dye that increases in fluorescence intensity upon binding to amyloid fibers, and by disruption of this binding upon addition of the chaotropic agent guanidine hydrochloride. Our results suggest a general, unifying picture of SOD1 aggregation that could operate when wild-type or mutant SOD1 proteins lack their metal ions. Although we cannot exclude other mechanisms in SOD1-linked familial ALS, the one proposed here has the strength of explaining how a large and diverse set of SOD1 mutant proteins all could lead to disease through the same mechanism.
Enhanced plant tolerance to iron starvation by functional substitution of chloroplast ferredoxin with a bacterial flavodoxin
Authors: Tognetti Vanesa B. , Zurbriggen Matias D. , Morandi Eligio N. , Fillat María F. , Valle Estela M. , Hajirezaei Mohammad-Reza , Carrillo Néstor
Published: June 2007

Iron limitation affects one-third of the cultivable land on Earth and represents a major concern for agriculture. It causes decline of many photosynthetic components, including the Fe-S protein ferredoxin (Fd), involved in essential oxidoreductive pathways of chloroplasts. In cyanobacteria and some algae, Fd down-regulation under Fe deficit is compensated by induction of an isofunctional electron carrier, flavodoxin (Fld), a flavin mononucleotide-containing protein not found in plants. Transgenic tobacco lines expressing a cyanobacterial Fld in chloroplasts were able to grow in Fe-deficient media that severely compromised survival of WT plants. Fld expression did not improve Fe uptake or mobilization, and stressed transformants elicited a normal deficit response, including induction of ferric-chelate reductase and metal transporters. However, the presence of Fld did prevent decrease of several photosynthetic proteins (but not Fd) and partially protected photosynthesis from inactivation. It also preserved the activation state of enzymes depending on the Fd-thioredoxin pathway, which correlated with higher levels of intermediates of carbohydrate metabolism and the Calvin cycle, as well as increased contents of sucrose, glutamate, and other amino acids. These metabolic routes depend, directly or indirectly, on the provision of reduced Fd. The results indicate that Fld could compensate Fd decline during episodes of Fe deficiency by productively interacting with Fd-dependent pathways of the host, providing fresh genetic resources for the design of plants able to survive in Fe-poor lands.
Oligonucleotide transformation of yeast reveals mismatch repair complexes to be differentially active on DNA replication strands
Authors: Kow Yoke W. , Bao Gaobin , Reeves Jason W. , Jinks-Robertson Sue , Crouse Gray F.
Published: June 2007

Transformation of both prokaryotes and eukaryotes with single-stranded oligonucleotides can transfer sequence information from the oligonucleotide to the chromosome. We have studied this process using oligonucleotides that correct a −1 frameshift mutation in the
LYS2
gene of
Saccharomyces cerevisiae
. We demonstrate that transformation by oligonucleotides occurs preferentially on the lagging strand of replication and is strongly inhibited by the mismatch-repair system. These results are consistent with a mechanism in which oligonucleotides anneal to single-stranded regions of DNA at a replication fork and serve as primers for DNA synthesis. Because the mispairs the primers create are efficiently removed by the mismatch-repair system, single-stranded oligonucleotides can be used to probe mismatch-repair function in a chromosomal context. Removal of mispairs created by annealing of the single-stranded oligonucleotides to the chromosomal DNA is as expected, with 7-nt loops being recognized solely by MutSβ and 1-nt loops being recognized by both MutSα and MutSβ. We also find evidence for Mlh1-independent repair of 7-nt, but not 1-nt, loops. Unexpectedly, we find a strand asymmetry of mismatch-repair function; transformation is blocked more efficiently by MutSα on the lagging strand of replication, whereas MutSβ does not show a significant strand bias. These results suggest an inherent strand-related difference in how the yeast MutSα and MutSβ complexes access and/or repair mismatches that arise in the context of DNA replication.