bluuebunny/crossref_metadata_2025 huggingface dataset:
Three-dimensionally ordered photonic crystal heterostructures with a double photonic stop band
Authors: Nair Rajesh V. , Vijaya R.
Published: September 2007

The recently reported inward growing self-assembling method is used to fabricate photonic crystal heterostructures in less than 6h using polymeric colloidal suspensions. Structural characterization shows good ordering of the two types of photonic crystals constituting the heterostructure. The reflection/transmission spectra measured from the (111) plane of the heterostructure clearly demonstrate the signature of the double photonic stop band. The reduction in the reflectance values obtained for the heterostructure is explained in terms of the interface roughness. The double photonic stop band of the heterostructures exactly matches the stop bands of the individual photonic crystals.
First-principles calculations of the effects of Cu and Ag additions on the electromigration of Sn-based solder
Authors: Yu Chun , Lu Hao
Published: September 2007

First-principles calculations were performed to investigate the mechanisms of Cu and Ag improving the electromigration resistance of Sn-based solder. The calculated diffusion activation energies in both Sn31Cu and Sn31Ag were higher than that in Sn32. The barrier energy of the first nearest neighbor (FNN) Sn was higher than that of Cu and Ag. The results indicated that the electromigration process of Sn alloyed with Cu or Ag would be delayed. Once electromigration occurred, Cu or Ag would be the dominant diffusing species. The calculated results of electronic structures verified that the doped systems were more stable. Particularly, the FNN Sn atoms were greatly stabilized.
Negatively charged donors in parabolic quantum-well wires under magnetic fields
Authors: Zhai Li-Xue , Liu Jian-Jun
Published: September 2007

The ground state of a negatively charged donor (D−) in a parabolic GaAs quantum-well wire in the presence of a magnetic field is investigated using the finite difference method within the quasi-one-dimensional effective potential model. The magnetic effects on the binding energies of the ground state of a D− center are calculated for various parabolic potentials. The distance between the electrons and the donor ion and the distance between the two electrons are also calculated, respectively, as a function of the strength of the parabolic potential and the magnetic field. We find that the interplay of the spatial confinement and the magnetic confinement of electrons in quantum-well wires leads to complicated behavior of the binding energies of the D− center and that the increase of the electron-donor ion attraction dominates the increase of the electron-electron repulsion as the spatial and magnetic confinement increases for the ground state of a D− center in a parabolic quantum-well wire.
Critical behaviors of the conductivity and dielectric constant of Ti3SiC2∕Al2O3 hybrids
Authors: Wu Rui-Fen , Pan Wei , Shi Sui-Lin , Han Ruo-Bing
Published: September 2007

Ti 3 Si C 2 ∕ Al 2 O 3 hybrids were prepared by a spark plasma sintering process. The effective dc conductivity of the hybrids was measured at room temperature, which agrees with the percolation theory and follows the power law around the percolation threshold. The ac conductivity and dielectric constants of the hybrids were also characterized and follow the power law when the concentration of the conductive phase is close to the percolation threshold; meanwhile, the dielectric constant could increase over three orders of magnitude compared with Al2O3.
Domain switching in lead magnesium niobate-lead titanate polycrystalline sheets at single grain level
Authors: Su Wei-Sheng , Chen Yang-Fang , Shih Wan Y. , Luo Hongyu , Shih Wei-Heng
Published: September 2007

The authors provide direct evidence of non-180° domain switching in the piezoelectric response of substrate-free 40μm thick polycrystalline [Pb(Mg1∕3Nb2∕3)O3]0.63(PbTiO3)0.37 (PMN-37PT) sheets under dc electric fields through piezoresponse force microscopy (PFM) at the single grain level. The sheet’s polarization preferred pointing in the planar direction which was switched to the normal direction at electric field ranging between 1.3 and 1.9kV∕cm. An independent d31 measurement of PMN-37PT sheets deduced from the axial tip displacement measurements of a 4mm long PMN-PT/copper cantilever showed enhanced d31 values that peaked at –2700pm∕V in the same range of electric field, consistent with the PFM observation.
Local structure characterization in quasicrystal-forming Zr80Pt20 binary amorphous alloy
Authors: Saida Junji , Sanada Takashi , Sato Shigeo , Imafuku Muneyuki , Inoue Akihisa
Published: September 2007

The local structure of melt-spun Zr80Pt20 alloy was investigated in the amorphous and icosahedral quasicrystal (QC)-formed states by x-ray diffraction and extended x-ray absorption fine structure measurements. While the local environment around the Zr atom in the amorphous state is considerably different from that in the QC-formed state, it remains during the quasicrystallization around the Pt atom. It is suggested that the stable icosahedral local structure is mainly formed in the center of the Pt atom in the amorphous state.
(Anti)symmetric multivariate trigonometric functions and corresponding Fourier transforms
Authors: Klimyk A. , Patera J.
Published: September 2007

Four families of special functions, depending on n variables, are studied. We call them symmetric and antisymmetric multivariate sine and cosine functions. They are given as determinants or antideterminants of matrices, whose matrix elements are sine or cosine functions of one variable each. These functions are eigenfunctions of the Laplace operator, satisfying specific conditions at the boundary of a certain domain F of the n-dimensional Euclidean space. Discrete and continuous orthogonality on F of the functions within each family allows one to introduce symmetrized and antisymmetrized multivariate Fourier-like transforms involving the symmetric and antisymmetric multivariate sine and cosine functions.
Current-induced magnetic vortex core switching in a Permalloy nanodisk
Authors: Liu Y. , Gliga S. , Hertel R. , Schneider C. M.
Published: September 2007

The authors report on the switching of a magnetic vortex core in a submicron Permalloy disk, induced by a short current pulse applied in the film plane. Micromagnetic simulations including the adiabatic and nonadiabatic spin-torque terms are used to investigate the current-driven magnetization dynamics. They predict that a core reversal can be triggered by current bursts a tenth of a nanosecond long. The vortex core reversal process is found to be the same as when an external field pulse is applied. The control of a vortex core’s orientation using current pulses introduces the technologically relevant possibility to address individual nanomagnets within dense arrays.
Vacuum electron acceleration and bunch compression by a flat-top laser beam
Authors: Wang W. , Wang P. X. , Ho Y. K. , Kong Q. , Gu Y. , Wang S. J.
Published: September 2007

The field intensity distribution and phase velocity characteristics of a flat-top laser beam are analyzed and discussed. The dynamics of electron acceleration in this kind of beam are investigated using three-dimensional test particle simulations. Compared with the standard (i.e., TEM00 mode) Gaussian beam, a flat-top laser beam has a stronger longitudinal electric field and a larger diffraction angle. These characteristics make it easier for electrons to be trapped and accelerated by the beam. With a flat-top shape, the laser beam is also applicable to the acceleration of low energy electron and bunch compression.
Phase interrogation of localized surface plasmon resonance biosensors based on electro-optic modulation
Authors: Wang Tzyy-Jiann , Hsieh Chih-Wei
Published: September 2007

A resolution-tunable localized surface plasmon resonance (LSPR) biosensor employing electro-optically modulated phase interrogation is presented. This biosensor modulates the analyte-dependent LSPR phase characteristic through electro-optic effect by varying the wave vector of lightwave for exciting surface plasmon. The induced LSPR phase change is measured by the collinear heterodyne technique and its relation with the applied voltage is utilized to determine the analyte concentration. Experimental results show that the regression slope of the phase-voltage relation decreases with the analyte concentration and the detection sensitivity can be increased by widening the waveguide width and using thinner gold film beneath gold nanoparticles. Detection resolution of this LSPR biosensor can be enhanced by increasing the applied voltage to enlarge the induced phase change. The presented LSPR biosensor employing phase interrogation has the features of resolution tunability, fast modulation speed, high modulation stability, and noise reduction.
Piezoelectricity of zinc-blende and wurtzite structure binary compounds
Authors: Xin Jun , Zheng Yanqing , Shi Erwei
Published: September 2007

First-principles calculations were performed on binary compounds of zinc-blende and wurtzite structures to disclose the relationships between the piezoelectric performance and the microscopic structure. The authors defined the structure parameters P and θ to represent the degree of asymmetry in structure. They were found to be linear to piezoelectric constants e14 and e33 for zinc-blende and wurtzite structure binary compounds, respectively.
Excellent passivation of highly doped p-type Si surfaces by the negative-charge-dielectric Al2O3
Authors: Hoex B. , Schmidt J. , Bock R. , Altermatt P. P. , van de Sanden M. C. M. , Kessels W. M. M.
Published: September 2007

From lifetime measurements, including a direct experimental comparison with thermal SiO2, a-Si:H, and as-deposited a-SiNx:H, it is demonstrated that Al2O3 provides an excellent level of surface passivation on highly B-doped c-Si with doping concentrations around 1019cm−3. The Al2O3 films, synthesized by plasma-assisted atomic layer deposition and with a high fixed negative charge density, limit the emitter saturation current density of B-diffused p+-emitters to ∼10 and ∼30fA∕cm2 on >100 and 54Ω∕sq sheet resistance p+-emitters, respectively. These results demonstrate that highly doped p-type Si surfaces can be passivated as effectively as highly doped n-type surfaces.
Highly efficient simplified organic light emitting diodes
Authors: Meyer J. , Hamwi S. , Bülow T. , Johannes H.-H. , Riedl T. , Kowalsky W.
Published: September 2007

The authors report on highly efficient organic light emitting diodes (OLEDs) consisting of only two organic layers. The key to the simplification is the direct injection of holes into the wide band gap hole transport material 4,4′,4″-tris(N-carbazolyl)-triphenyl amine (highest occupied molecular orbital is 5.9eV) through an indium tin oxide/tungsten oxide (WO3) anode. Kelvin probe analysis has revealed an extremely high work function of 6.4eV for WO3. The efficiencies of the simplified OLEDs exceed 40lm∕W and 45cd∕A at a brightness of 100cd∕m2, unsurpassed by other comparably simple OLED devices. Therefore, our OLED architecture demonstrates highly efficient, yet easy to fabricate devices.
Direct mass determination of hydrogen uptake using a quartz crystal microbalance
Authors: Kulchytskyy Ihor , Kocanda Martin G. , Xu Tao
Published: September 2007

The authors demonstrate the application of a quartz crystal microbalance for direct mass determination of hydrogen uptake in storage materials in the pressure range of 0–40bars. The frequency shift of a quartz crystal coated with hydrogen absorbing materials is affected by the hydrogen mass uptake on the crystal, the pressure and the viscosity of the gases, and the crystal surface roughness, of which the roughness contribution has no analytical expression. Through a control experiment on the same crystal in helium, the roughness contribution in hydrogen can be derived and the frequency shift due to the hydrogen mass uptake can be obtained.
Via-hole-based vertical GaN light emitting diodes
Authors: Jung Hyun-Min , Nam Gi-Yeon , Choi Byung-Kyun , Lee Tae-Hee , Kim Hyun-Suk , Jeon Soo-Kun , Park Eun-Hyun , Kim Chang-Tae
Published: September 2007

A vertical GaN-light emitting diode (LED) has been fabricated on a sapphire substrate with periodic via holes formed by a laser drilling technique. n-contact metal which was deposited on the backside of sapphire substrate was directly connected with an Ohmic metal of n-GaN layer through the via holes. The via-hole-based vertical GaN-LED demonstrated an optical power improvement of up to 12.5% with lower forward operating voltage compared with a conventional GaN-LED. In addition, this vertical LED showed just 0.8% and 1.5% variations of optical power and operation voltage at the 500h reliability test.
Effect of measured distance and angle tuning on transmission properties of split-ring resonators
Authors: Li Chuang , Fan Huiqing , Li Nanjing
Published: September 2007

Transmission properties of a layer of split-ring resonators (SRRs) are investigated experimentally in free space with the propagation direction of the electromagnetic field perpendicular to the SRR-patterned substrate. It is shown that the response frequency of SRRs is independent of the measured distance. In addition, the qualitative change from electric resonance of SRRs to magnetic resonance with the variation of angle between electric field and the symmetric axis of SRR is presented. The results suggest a simple way of obtaining magnetic resonance of SRRs, even left-handed behavior.
Socialisation in a Space of Law: Student Performativity at ‘Coffee House’ in a University Law Faculty
Authors: Turner Sarah , Manderson Desmond
Published: September 2007

Working with ideas of performance and performativity, the geographies of law, and the sociology of the legal profession, this paper reports on a study of the microgeography of a social space in a major Canadian law school, and, more specifically, questions what it means to be a law student there. ‘Coffee House’ at McGill University Faculty of Law is a weekly social event sponsored for half the academic year by prominent Canadian law firms who supply free alcohol and food to the students attending in an effort to ‘brand’ their firm. These events contribute in different ways to the socialisation and identity of the law students present. We argue that a performativity of what it is to be a McGill law student heading towards corporate success begins to be structured through the repetition of a range of performances undertaken in this space.
Infrastructural Fractals: Revisiting the Micro—Macro Distinction in Social Theory
Authors: Jensen Casper B
Published: September 2007

The relationship between the supposedly small—the micro—and the supposedly large—the macro—has been a long-standing concern in social theory. However, although many attempts have been made to link these two seemingly disjoint dimensions, in the present paper I argue against such an endeavour. Instead, I outline a fractal approach to the study of space, society, and infrastructure. A fractal orientation requires a number of related conceptual reorientations. It has implications for thinking about scale and perspective, and (sociotechnical) relations, and for considering the role of the social theorist in analyzing such relations. I find empirical illustration in the case of the development of electronic patient records in Danish health care. The role of the social theorist is explored through a comparison of the political and normative stance enabled, respectively, by a critical social theory and a fractal social theory.
The Performative Landscape of Going-To-Work: On the Edge of a Jewish Ultraorthodox Neighborhood
Authors: Blumen Orna
Published: September 2007

Following recent insights into performativity and space, I explore the widespread routine of going-to-work as a capitalist ritual. Going-to-work produces a powerful yet ordinary, unspectacular landscape, whose performativity is fourfold: the compatibility of the material form and human use of it; the movements of people and the clothes they wear; the variety of individual practices of going-to-work; and the timing and spacing of this collective ritual. Generally, going-to-work is performative, because it transforms people into employees, defining productivity in terms of paid work. Hence, the prime quality of this landscape is to enhance economically productive bodies. In the second part of this paper, I examine this productive—nonproductive distinction in a unique setting on the edge of an Israeli neighborhood of ultraorthodox Jews, whose definition of men's work—unpaid religious studies—contrasts with that of the majority of the modern population. The distinctive ultraorthodox appearance, originally designed to mark a particular Jewish identity, signifies their nonproductivity as a spatial performance of Otherness. This provides an opportunity to probe going-to-work in this specific place as an arena where the ultraorthodox identity as Other intersects with their capitalist identity as Other. Short street interviews with modern and ultra-orthodox Jews show that they recognize work as the main theme of this landscape. They are also aware that work is socially defined and can be criticized on both capitalist and ultraorthodox—religious grounds, and they illustrate how the controversy over the definition of work lies within the struggle over Jewish identity. I conclude by illuminating the performative role of space in displaying identity and social ideas.
On the trend, detrending, and variability of nonlinear and nonstationary time series
Authors: Wu Zhaohua , Huang Norden E. , Long Steven R. , Peng Chung-Kang
Published: September 2007

Determining trend and implementing detrending operations are important steps in data analysis. Yet there is no precise definition of “trend” nor any logical algorithm for extracting it. As a result, various ad hoc extrinsic methods have been used to determine trend and to facilitate a detrending operation. In this article, a simple and logical definition of trend is given for any nonlinear and nonstationary time series as an intrinsically determined monotonic function within a certain temporal span (most often that of the data span), or a function in which there can be at most one extremum within that temporal span. Being intrinsic, the method to derive the trend has to be adaptive. This definition of trend also presumes the existence of a natural time scale. All these requirements suggest the Empirical Mode Decomposition (EMD) method as the logical choice of algorithm for extracting various trends from a data set. Once the trend is determined, the corresponding detrending operation can be implemented. With this definition of trend, the variability of the data on various time scales also can be derived naturally. Climate data are used to illustrate the determination of the intrinsic trend and natural variability.
Energetics of water permeation through fullerene membrane
Authors: Isobe Hiroyuki , Homma Tatsuya , Nakamura Eiichi
Published: September 2007

Lipid bilayer membranes are important as fundamental structures in biology and possess characteristic water-permeability, stability, and mechanical properties. Water permeation through a lipid bilayer membrane occurs readily, and more readily at higher temperature, which is largely due to an enthalpy cost of the liquid-to-gas phase transition of water. A fullerene bilayer membrane formed by dissolution of a water-soluble fullerene, Ph
5
C
60
K, has now been shown to possess properties entirely different from those of the lipid membranes. The fullerene membrane is several orders of magnitude less permeable to water than a lipid membrane, and the permeability decreases at higher temperature. Water permeation is burdened by a very large entropy loss and may be favored slightly by an enthalpy gain, which is contrary to the energetics observed for the lipid membrane. We ascribe this energetics to favorable interactions of water molecules to the surface of the fullerene molecules as they pass through the clefts of the rigid fullerene bilayer. The findings provide possibilities of membrane design in science and technology.
Tipin is required for stalled replication forks to resume DNA replication after removal of aphidicolin in
Xenopus
egg extracts
Authors: Errico Alessia , Costanzo Vincenzo , Hunt Tim
Published: September 2007

Tipin and its interacting partner Tim1 (Timeless) form a complex at replication forks that plays an important role in the DNA damage checkpoint response. Here we identify
Xenopus laevis
Tipin as a substrate for cyclin E/cyclin-dependent kinases 2 that is phosphorylated in interphase and undergoes further phosphorylation upon entry into mitosis. During unperturbed DNA replication, the Tipin/Tim1 complex is bound to chromatin, and we were able to detect interactions between Tipin and the MCM helicase. Depletion of Tipin from
Xenopus
extracts did not significantly impair normal replication but substantially blocked the ability of stalled replication forks to recover after removal of a block imposed by aphidicolin. Tipin-depleted extracts also showed defects in the activation of Chk1 in response to aphidicolin, probably because of a failure to load the checkpoint mediator protein Claspin onto chromatin.
Envelope variation as a primary determinant of lentiviral vaccine efficacy
Authors: Craigo Jodi K. , Zhang Baoshan , Barnes Shannon , Tagmyer Tara L. , Cook Sheila J. , Issel Charles J. , Montelaro Ronald C.
Published: September 2007

Lentiviral envelope antigenic variation and associated immune evasion are believed to present major obstacles to effective vaccine development. Although this perception is widely assumed by the scientific community, there is, to date, no rigorous experimental data assessing the effect of increasing levels of lentiviral Env variation on vaccine efficacy. It is our working hypothesis that Env is, in fact, a primary determinant of vaccine effectiveness. We previously reported that a successful experimental attenuated equine infectious anemia virus vaccine, derived by mutation of the viral S2 accessory gene, provided 100% protection from disease after virulent virus challenge. Here, we sought to comprehensively test our hypothesis by challenging vaccinated animals with proviral strains of defined, increasing Env variation, using variant envelope SU genes that arose naturally during experimental infection of ponies with equine infectious anemia virus. The reference attenuated vaccine combined with these variant Env challenge strains facilitated evaluation of the protection conferred by ancestral immunogens, because the Env of the attenuated vaccine is a direct ancestor to the variant proviral strain Envs. The results demonstrated that ancestral Env proteins did not impart broad levels of protection against challenge. Furthermore, the results displayed a significant inverse linear correlation of Env divergence and protection from disease. This study demonstrates potential obstacles to the use of single isolate ancestral Env immunogens. Finally, these findings reveal that relatively minor Env variation can pose a substantial challenge to lentiviral vaccine immunity, even when attenuated vaccines are used that, to date, achieve the highest levels of vaccine protection.
Current status of scrapie.
Authors: Saegerman C. , Vanopdenbosch E. , Berkvens D.
Published: September 2007

Despite being controlled in many developed countries, scrapie remains endemic in many parts of the world. Economic losses result from mortality and culling of small ruminants and from market restrictions. Moreover, it is difficult to develop all-inclusive guidelines that could establish a scrapie-free status for a country. Unfortunately, the global picture remains incomplete because in many countries confusion still remains regarding the clinical picture of scrapie and information is not available owing to the absence of adequate epidemiosurveillance networks. Currently, the predominant theory is that PrPSc is the infectious agent where host genetic factors play a central role. The precise transmission routes of scrapie and their relative contributions to the overall transmission intensity remain poorly documented and the physiopathology is not fully understood. However, it is evident that the purchase of female sheep from scrapie flocks, sharing pastures with scrapie flocks, sharing breeding rams and genetic host susceptibility are the main risk factors for the spread of the disease. A better understanding of the epidemiology of scrapie would greatly aid the development and evaluation of control and eradication strategies that were mainly based on selective depopulation of infected animals and genetically susceptible and/or related animals and also on the biosecurity and the use of selective genetic breeding programmes in healthy flocks. Some numbers of a new transmissible spongiform encephalopathy (TSE) form in small ruminants (atypical scrapie) have meanwhile been identified by TSE rapid testing using an assay, which also recognizes comparatively less proteinase K-resistant PrPSc. Uncertainties remain regarding the pathogenesis of this new TSE form, as well as regarding its potential transmissibility within the affected species and to other species. Thus far, no bovine spongiform encephalopathy (BSE) cases have been confirmed in sheep under natural conditions (a report of vertical transmission after experimental infection merits attention), but two historical cases of BSE in goats born in the 1990s have been identified. Currently BSE must also be considered in the differential diagnosis of scrapie. The development of prevention and control programmes should be assisted by new scientific findings.
Sources and epidemiology of
Streptococcus uberis
, with special emphasis on mastitis in dairy cattle.
Authors: Zadoks R. N.
Published: September 2007

Streptococcus uberis
is an important cause of mastitis in dairy cattle around the world. The organism has also been associated with mastitis in goats, sheep, camels and buffaloes, and with a variety of other conditions in ruminants and non-ruminant species.
S. uberis
has been reported in humans but the accuracy of its identification is debated. Many extra-mammary sources harbour
S. uberis
, including body sites, the gastro-intestinal tract, soil, water, forage and insects. Faecal shedding by cows may be needed to maintain
S. uberis
in the environment. Because of its occurrence in the environment and because of its epidemiology,
S. uberis
is considered an environmental organism. In addition,
S. uberis
can spread as contagious pathogen. Evidence for environmental and contagious modes of transmission derived from management data and molecular typing studies is reviewed. Potential mechanisms of host-adaptation are discussed, and results from field studies on treatment are interpreted in the context of a proposed conceptual framework, which encompasses environmental and contagious manifestations of
S. uberis
mastitis. Vaccine development strategies and current control measures are summarized. The relative importance of transmission mechanisms and control measures differs between herds and geographic areas. Standard mastitis prevention measures may reduce the prevalence of contagious
S. uberis
mastitis, resulting in a shift to predominantly environmental
S. uberis
mastitis. Overemphasis on environmental mastitis may result in a re-emergence of contagious mastitis.
Diagnosis of
Babesia equi
infection: an update on the methods available.
Authors: Kumar S. , Kumar R.
Published: September 2007

Equine babesiosis, a tick-transmitted haemoprotozoan disease caused by
Babesia equi
, is globally distributed and poses a serious threat in international movement of horses. The earlier conventional sero-tests available were not sufficient for sensitive and specific diagnosis of the latently infected equids. Hence, in the last decade, new improved diagnostic methods were designed for accurate and rapid diagnosis. Demonstration of parasites in the blood collected from a carrier animal by blood smear examination or by
in vitro
cultivation technique is an absolute and reliable method of confirmation. These techniques are not very sensitive and, recently, geographically conserved genes in
B. equi
genome (
ema
-1 and
ema
-2) were exploited using PCR (and nested PCR) and DNA probes. These techniques proved to be an efficient tool in specific diagnosis, but are limited to well-equipped laboratories. Many different serodiagnostic tests have been described, such as complement fixation test (CFT), indirect fluorescent antibody test (IFAT) and enzyme-linked immunosorbent assay (ELISA). A remarkable improvement in ELISA has been made and problems associated with native antigen were overcome by production of recombinant antigen. Competitive inhibition ELISA (CI-ELISA; a specific monoclonal-antibody-based assay) has proved to be highly sensitive and specific and has recently been prescribed by Office International des Epizooties (OIE) as a test for international trade. Latex agglutination test (LAT) and immunochromatographic test (ICT) are the new standardized tests based on specific recombinant antigen and much quicker than the other available diagnostic tests: further validation may, however, be required.
Risks of transmitting mycoplasmas by semen and embryo transfer techniques in cattle, sheep, goats and pigs.
Authors: Wrathall A. E. , Ayling R. D. , Simmons H. A.
Published: September 2007

This object of this review is to consider whether mycoplasmas, particularly those that are important pathogens in cattle, sheep, goats and pigs, are likely to be transmitted by semen and embryo transfer techniques, and if so, what can be done to prevent such transmission. The first part gives a brief overview of semen and embryo transfer techniques, focusing on general risks of disease transmission and on routine disease control strategies. Subsequent parts provide information about mycoplasmas, including their classification, pathogenesis, diagnosis and control. Details are then given of the specific mycoplasmas of cattle, sheep, goats and pigs, and the seriously pathogenic species are distinguished from the opportunist pathogens and harmless commensals. It is emphasized, however, that within species the virulence of different strains can vary widely. An important feature of the mycoplasmas is that they often reside in the reproductive tracts of their hosts and therefore tend to pose a higher risk of being transmitted by semen and embryos than do many other micro-organisms. They also tend to adhere to cells and tissues, including semen and embryos, and can be difficult to remove. Some mycoplasmas can also invade and reside within non-phagocytic cells. Their resistance to routine disease control procedures such as semen and embryo washing, and to the inclusion of antibiotics in semen diluents and in embryo media, adds further challenges. It remains true, nevertheless, that semen and embryo transfer techniques offer great advantages over the movement of live animals for transferring genetic material, and will minimize the risks of disease transmission between different farms or countries. The review concludes by recommending control strategies, uniquely rigorous ones in this case, to avoid the transfer of mycoplasmas via semen and embryos.
Combined genetic, genomic and transcriptomic methods in the analysis of animal traits.
Authors: Kadarmideen H. N. , Reverter A.
Published: September 2007

This paper reviews advances and current status in genetic, genomic and transcriptomic investigations of quantitative traits in livestock species and proposes possible strategies for integrating the vast amounts of information (outputs/datasets) arising from all three investigations into a systems genetics approach. This systems genetics approach is characterized by investigations of the genetic basis of -omic variations and gene regulatory/co-regulatory networks. This review is structured as follows. Genetics/genomics, transcriptomics, combined transcriptomics-genomics and, finally, systems genetics/biology. In the genetics or genomics part, we discuss current status and advances in quantitative trait loci (QTLs) mapping to fine-map multiple causative/candidate genes. We discuss the potential of single nucleotide polymorphism (SNP) genotyping arrays (e.g. Affymetrix GeneChip arrays) to identify SNP-trait associations and fine-map QTLs to less than 0.1 cM. We provide references and resources for SNP analytical methods and tools. In the transcriptomics part, we formulate common biological questions relevant to livestock microarray gene expression profiling (MGEP) experiments to detect differentially expressed (DE) genes. In the combined transcriptomics-genomics (known as genetical genomics), we discuss detection and mapping of expression QTL (eQTL) that harbour regulatory genes for normal trait QTLs or candidate genes detected under 'genetics' and 'genomics' approaches. Illustrations from our own recent genetical genomic investigations in mouse and pigs are provided. One of the current challenges in genetical genomics is to have a coherent approach to design an experiment with due considerations for sample size and controlling false discovery rates (FDRs), while maintaining statistical power to detect eQTLs. Here we provide some concepts for the design of genetical genomics experiments with factors affecting FDR and power. This is followed by a systems biology/genetics section where we focus on combining research outputs from four different sources, namely: genetics or genomics (e.g. SNP, QTL and eQTLs), transcriptomics (e.g. DE genes, gene networks, and heritability of gene transcripts) and phenomics (e.g. phenotypes and pedigree). As a proof of principle, we provide results from systems biology/genetics approach anchored to a gene network for myogenin (MYOG), a muscle-specific transcription factor essential for the development of skeletal muscle. Using bovine expression datasets and in silico approaches, we built a gene network for MYOG that represents 35 significant connections between genes in this network. In conclusion, this paper provides strategies and tools to integrate data from genetics and -omics experiments in animals and highlighted the value of such 'systems genetics' strategy in understanding the genetics of complex traits.
Herbicide-resistant crops as weeds in North America.
Authors: Beckie H. J. , Owen M. D. K.
Published: September 2007

Growers have rapidly adopted transgenic herbicide-resistant (HR) crops, such as canola (
Brassica napus
L.), soyabean [
Glycine max
(L.) Merr.], maize (
Zea mays
L.) and cotton (
Gossypium hirsutum
L.), across North America (USA and Canada) since their commercial introduction in the 1990s. With their widespread cultivation, increasing attention is focused on management of HR volunteers in crops that follow in rotation. In this review, we describe the impact and management of HR crop volunteers in different agroecosystems in North America. The relative risks of planting HR crops and subsequent potential for volunteerism of these crops are assessed. HR volunteers are common weeds and the relative weediness depends on species, genotype, seed shatter prior to harvest and disbursement of seed at harvest, management practices, and environment. Chemical control options may be more limited if the crop volunteers are HR. There are generally no marked changes in volunteer weed problems associated with these crops, except in no-tillage systems when glyphosate (GLY) is used alone to control volunteers. The increasing use of GLY in North American cropping systems, spurred by increasing area and frequency in rotation of GLY - HR crops, may require increased alternative herbicide use or other novel tactics to control GLY-HR crop volunteers.
Role of immunostimulants in disease resistance of fish.
Authors: Sahoo P. K.
Published: September 2007

There is an increasing demand to prevent and control a broad spectrum of fish diseases occurring in aquaculture systems without recourse to antibiotics and chemotherapeutics. Application of immunostimulants alone or together with vaccination has emerged as one of the more promising approaches to prevent or control fish diseases. Many such substances viz. glucans, levamisole, lactoferrin, chitosan, chitin, vitamins C and E, prolactin, growth hormone, triiodothyronine, Freund's complete adjuvant, lipopolysaccharides, animal or plant extracts, double-stranded RNA, CpG motifs and other biological substances have been reported to produce increased protection against major bacterial, few viral and parasitic pathogens. These immunostimulants mainly promote the function of phagocytes and increase their microbicidal power. They also enhance production of acute phase proteins that trigger the innate defence mechanism of the host. However, a controversy exists over the use of these substances, as in a few cases they have failed to render enhanced protection or increase in immunity. Long-term exposure, over- and under-dosing problems, timing and method of application of these substances are discussed here. This review article mainly considers the recent developments in this area to control fish diseases describing the newer molecular approaches going on to evaluate these substances, discusses the practicaldifficulties on their applications and emphasizes further research needs in this important area.
Mechanisms of S-RNase-based self-incompatibility.
Authors: Sims T. L.
Published: September 2007

Gametophytic self-incompatibility (GSI), a genetic mechanism that acts to prevent self-fertilization in many angiosperms, is based on the ability of the pistil to selectively inhibit growth of self pollen while allowing the growth of non-self pollen. In the most widespread variant of GSI (studied most thoroughly in the Solanaceae, Rosaceae and Plantaginaceae), a style-expressed ribonuclease (the S-RNase) is imported into both self and non-self pollen tubes. In pollen tubes recognized as self, the S-RNase degrades RNA, slowing protein synthesis and growth of the pollen tube, whereas in non-self pollen tubes the action of the S-RNase is inhibited and growth continues normally. Recognition of self versus non-self in pollen appears to be mediated through the action of the recently identified SLF/SFB protein. Protein interaction studies suggest that SLF/SFB acts via a modified SCFSLF E3 ubiquitin ligase complex. Several questions remain, however, about the precise mechanism by which the S-RNase remains inactive in non-self pollen tubes. Experiments tracking the fate of protein components of self-incompatibility in pollinated styles suggest that in compatible pollinations, the S-RNase remains sequestered in a membrane-bounded vacuolar compartment, while it is released in incompatible pollen tubes. Other experiments suggest that ubiquitination, and possibly degradation, of S-RNases occurs preferentially in incompatible pollen compared with compatible pollen. Finally, the analysis of SFB mutants in the Rosaceae, along with investigations into the breakdown of GSI in tetraploid plants, suggest that details of the GSI response may differ in the Rosaceae compared with the Solanaceae and Plantaginaceae.
Defining early steps in mRNA transport: mutant mRNA in myotonic dystrophy type I is blocked at entry into SC-35 domains
Authors: Smith Kelly P. , Byron Meg , Johnson Carol , Xing Yigong , Lawrence Jeanne B.
Published: September 2007

In myotonic dystrophy type 1 (DM1), triplet repeat expansion in the 3′ untranslated region of dystrophia myotonica protein kinase (DMPK) causes the nuclear retention of mutant messenger RNA (mRNA). Although the DMPK gene locus positions precisely at the outer edge of a factor-rich SC-35 domain, the normal mRNA consistently accumulates within the domain, and this RNA is depleted upon transcriptional inhibition. In DM1, mutant transcripts detach from the gene but accumulate in granules that abut but do not enter SC-35 domains, suggesting that RNA entry into the domain is blocked. Despite their exclusion from these compartments, mutant transcripts are spliced. MBNL1 (muscleblind-like protein 1) is an alternative splicing factor that becomes highly concentrated with mutant RNA foci. Small interfering RNA–mediated knockdown of MBNL1 promotes the accumulation or entry of newly synthesized mutant transcripts in the SC-35 domain. Collectively, these data suggest that an initial step in the intranuclear path of some mRNAs is passage from the gene into an SC-35 domain and implicate these structures in postsplicing steps before export.
Splicing-independent recruitment of spliceosomal small nuclear RNPs to nascent RNA polymerase II transcripts
Authors: Patel Snehal Bhikhu , Novikova Natalya , Bellini Michel
Published: September 2007

In amphibian oocytes, most lateral loops of the lampbrush chromosomes correspond to active transcriptional sites for RNA polymerase II. We show that newly assembled small nuclear ribonucleoprotein (RNP [snRNP]) particles, which are formed upon cytoplasmic injection of fluorescently labeled spliceosomal small nuclear RNAs (snRNAs), target the nascent transcripts of the chromosomal loops. With this new targeting assay, we demonstrate that nonfunctional forms of U1 and U2 snRNAs still associate with the active transcriptional units. In particular, we find that their association with nascent RNP fibrils is independent of their base pairing with pre–messenger RNAs. Additionally, stem loop I of the U1 snRNA is identified as a discrete domain that is both necessary and sufficient for association with nascent transcripts. Finally, in oocytes deficient in splicing, the recruitment of U1, U4, and U5 snRNPs to transcriptional units is not affected. Collectively, these data indicate that the recruitment of snRNPs to nascent transcripts and the assembly of the spliceosome are uncoupled events.
High basal STAT4 balanced by STAT1 induction to control type 1 interferon effects in natural killer cells
Authors: Miyagi Takuya , Gil M. Pilar , Wang Xin , Louten Jennifer , Chu Wen-Ming , Biron Christine A.
Published: September 2007

The best-characterized type 1 interferon (IFN) signaling pathway depends on signal transducer and activator of transcription 1 (STAT1) and STAT2. The cytokines can, however, conditionally activate all STATs. Regulation of their access to particular signaling pathways is poorly understood. STAT4 is important for IFN-γ induction, and NK cells are major producers of this cytokine. We report that NK cells have high basal STAT4 levels and sensitivity to type 1 IFN–mediated STAT4 activation for IFN-γ production. Increases in STAT1, driven during viral infection by either type 1 IFN or IFN-γ, are associated with decreased STAT4 access. Both STAT1 and STAT2 are important for antiviral defense, but STAT1 has a unique role in protecting against sustained NK cell IFN-γ production and resulting disease. The regulation occurs with an NK cell type 1 IFN receptor switch from a STAT4 to a STAT1 association. Thus, a fundamental characteristic of NK cells is high STAT4 bound to the type 1 IFN receptor. The conditions of infection result in STAT1 induction with displacement of STAT4. These studies elucidate the critical role of STAT4 levels in predisposing selection of specific signaling pathways, define the biological importance of regulation within particular cell lineages, and provide mechanistic insights for how this is accomplished in vivo.
The Mechanism of Fast-Gate Opening in ClC-0
Authors: Engh Anita M. , Faraldo-Gómez José D. , Maduke Merritt
Published: September 2007

ClC-0 is a chloride channel whose gating is sensitive to both voltage and chloride. Based on analysis of gating kinetics using single-channel recordings, a five-state model was proposed to describe the dependence of ClC-0 fast-gate opening on voltage and external chloride (Chen, T.-Y., and C. Miller. 1996. J. Gen. Physiol. 108:237–250). We aimed to use this five-state model as a starting point for understanding the structural changes that occur during gating. Using macroscopic patch recordings, we were able to reproduce the effects of voltage and chloride that were reported by Chen and Miller and to fit our opening rate constant data to the five-state model. Upon further analysis of both our data and those of Chen and Miller, we learned that in contrast to their conclusions, (a) the features in the data are not adequate to rule out a simpler four-state model, and (b) the chloride-binding step is voltage dependent. In order to be able to evaluate the effects of mutants on gating (described in the companion paper, see Engh et al. on p. 351 of this issue), we developed a method for determining the error on gating model parameters, and evaluated the sources of this error. To begin to mesh the kinetic model(s) with the known CLC structures, a model of ClC-0 was generated computationally based on the X-ray crystal structure of the prokaryotic homolog ClC-ec1. Analysis of pore electrostatics in this homology model suggests that at least two of the conclusions derived from the gating kinetics analysis are consistent with the known CLC structures: (1) chloride binding is necessary for channel opening, and (2) chloride binding to any of the three known chloride-binding sites must be voltage dependent.
The Role of a Conserved Lysine in Chloride- and Voltage-dependent ClC-0 Fast Gating
Authors: Engh Anita M. , Faraldo-Gómez José D. , Maduke Merritt
Published: September 2007

ClC-0 is a chloride channel whose gating is sensitive to voltage, chloride, and pH. In a previous publication, we showed that the K149C mutation causes a +70-mV shift in the voltage dependence of ClC-0 fast gating. In this paper we analyze the effects of a series of mutations at K149 on the voltage and chloride dependence of gating. By fitting our data to the previously proposed four-state model for ClC-0 fast gating, we show which steps in fast-gate opening are likely to be affected by these mutations. Computational analysis of mutant ClC-0 homology models show electrostatic contributions to chloride binding that may partially account for the effects of K149 on gating. The analysis of gating kinetics in combination with the available structural information suggests some of the structural changes likely to underpin fast-gate opening.
Triadin Binding to the C-Terminal Luminal Loop of the Ryanodine Receptor is Important for Skeletal Muscle Excitation–Contraction Coupling
Authors: Goonasekera Sanjeewa A. , Beard Nicole A. , Groom Linda , Kimura Takashi , Lyfenko Alla D. , Rosenfeld Andrew , Marty Isabelle , Dulhunty Angela F. , Dirksen Robert T.
Published: September 2007

Ca2+ release from intracellular stores is controlled by complex interactions between multiple proteins. Triadin is a transmembrane glycoprotein of the junctional sarcoplasmic reticulum of striated muscle that interacts with both calsequestrin and the type 1 ryanodine receptor (RyR1) to communicate changes in luminal Ca2+ to the release machinery. However, the potential impact of the triadin association with RyR1 in skeletal muscle excitation–contraction coupling remains elusive. Here we show that triadin binding to RyR1 is critically important for rapid Ca2+ release during excitation–contraction coupling. To assess the functional impact of the triadin-RyR1 interaction, we expressed RyR1 mutants in which one or more of three negatively charged residues (D4878, D4907, and E4908) in the terminal RyR1 intraluminal loop were mutated to alanines in RyR1-null (dyspedic) myotubes. Coimmunoprecipitation revealed that triadin, but not junctin, binding to RyR1 was abolished in the triple (D4878A/D4907A/E4908A) mutant and one of the double (D4907A/E4908A) mutants, partially reduced in the D4878A/D4907A double mutant, but not affected by either individual (D4878A, D4907A, E4908A) mutations or the D4878A/E4908A double mutation. Functional studies revealed that the rate of voltage- and ligand-gated SR Ca2+ release were reduced in proportion to the degree of interruption in triadin binding. Ryanodine binding, single channel recording, and calcium release experiments conducted on WT and triple mutant channels in the absence of triadin demonstrated that the luminal loop mutations do not directly alter RyR1 function. These findings demonstrate that junctin and triadin bind to different sites on RyR1 and that triadin plays an important role in ensuring rapid Ca2+ release during excitation–contraction coupling in skeletal muscle.