bluuebunny/crossref_metadata_2025 huggingface dataset:
Community service for youth: The value of psychological engagement over number of hours spent
Authors: McGuire Jenifer K. , Gamble Wendy C.
Published: August 2005

This study examined the relative contribution of psychological engagement with a service activity and number of hours spent in that activity as predictors of change over time in community belonging and social responsibility. Sixty‐eight primarily rural adolescents participated as teen leaders in a sexuality education program, and completed assessments of social responsibility and community belonging before and after program participation. Psychological engagement with the service activity and number of hours spent were used to predict changes in social responsibility and community belonging, while controlling for gender, prior program participation, and sexual behaviour history. Psychological engagement, but not number of hours spent, accounted for significant unique variability of change in community belonging and social responsibility.
Some protein interaction data do not exhibit power law statistics
Authors: Tanaka Reiko , Yi Tau-Mu , Doyle John
Published: August 2005

It has been claimed that protein–protein interaction (PPI) networks are scale‐free, and that identifying high‐degree “hub” proteins reveals important features of PPI networks. In this paper, we evaluate the claims that PPI node degree sequences follow a power law, a necessary condition for networks to be scale‐free. We provide two PPI network examples which clearly do not have power laws when analyzed correctly, and thus at least these PPI networks are not scale‐free. We also show that these PPI networks do appear to have power laws according to methods that have become standard in the existing literature. We explain the source of this error using numerically generated data from analytic formulas, where there are no sampling or noise ambiguities.
Subcellular distribution of chromogranins A and B in bovine adrenal chromaffin cells
Authors: Huh Yang Hoon , Bahk Sook Jin , Ghee Jung Yeon , Yoo Seung Hyun
Published: August 2005

The major secretory granule proteins chromogranins A (CGA) and B (CGB) have recently been shown to play critical roles in inositol 1,4,5‐trisphosphate‐dependent intracellular Ca2+ mobilizations. We determined here the subcellular distribution of CGA and CGB based on 3D‐images of chromaffin cells, and found that ∼95% of cellular CGA was present in secretory granules while ∼5% was in the endoplasmic reticulum (ER), whereas ∼57% of cellular CGB was in secretory granules while ∼24% and ∼19% were in the ER and nucleus, respectively. These results suggest that chromogranins are at the center of intracellular Ca2+ homeostasis in secretory cells.
Fatty acid synthesis is a target for antibacterial activity of unsaturated fatty acids
Authors: Zheng Chang Ji , Yoo Jung-Sung , Lee Tae-Gyu , Cho Hee-Young , Kim Young-Ho , Kim Won-Gon
Published: August 2005

Long‐chain unsaturated fatty acids, such as linoleic acid, show antibacterial activity and are the key ingredients of antimicrobial food additives and some antibacterial herbs. However, the precise mechanism for this antimicrobial activity remains unclear. We found that linoleic acid inhibited bacterial enoyl‐acyl carrier protein reductase (FabI), an essential component of bacterial fatty acid synthesis, which has served as a promising target for antibacterial drugs. Additional unsaturated fatty acids including palmitoleic acid, oleic acid, linolenic acid, and arachidonic acid also exhibited the inhibition of FabI. However, neither the saturated form (stearic acid) nor the methyl ester of linoleic acid inhibited FabI. These FabI‐inhibitory activities of various fatty acids and their derivatives very well correlated with the inhibition of fatty acid biosynthesis using [14C] acetate incorporation assay, and importantly, also correlated with antibacterial activity. Furthermore, the supplementation with exogenous fatty acids reversed the antibacterial effect of linoleic acid, which showing that it target fatty acid synthesis. Our data demonstrate for the first time that the antibacterial action of unsaturated fatty acids is mediated by the inhibition of fatty acid synthesis.
The effect of nanocrystal surface structure on the luminescence properties: Photoemission study of HF-etched InP nanocrystals
Authors: Adam S. , Talapin D. V. , Borchert H. , Lobo A. , McGinley C. , de Castro A. R. B. , Haase M. , Weller H. , Möller T.
Published: August 2005

InP nanocrystals with narrow size distribution and mean particle diameter tunable from ∼2 up to ∼7nm were synthesized via the dehalosilylation reaction between InCl3 and tris(trimethylsilyl)phosphine. Specific capping of the nanocrystal surface with a shell of organic ligands protects the nanocrystals from oxidation and provides solubility of the particles in various organic solvents. InP nanocrystals with enhanced photoluminescence (PL) efficiency were obtained from the initial nanocrystals by photoassisted etching of the nanocrystal surface with HF. The resulting PL quantum efficiency of InP nanocrystals dispersed in n-butanol is about three orders of magnitude higher when compared to the nonetched InP samples and approaches ∼40% at room temperature. High-resolution photoelectron spectroscopy with the use of synchrotron radiation was applied to reveal the changes of the nanocrystal surface responsible for the dramatic improvement of the PL efficiency. The analysis of high-resolution P 2p core-level spectra confirmed significant changes of the nanocrystal surface structure induced by the postpreparative treatments and allowed us to propose the description of the etching mechanism. In the nonetched InP nanocrystals, some surface P atoms generate energy states located inside the band gap which provide nonradiative recombination pathways. Photoassisted treatment of InP nanocrystals with HF results in selective removal of these phosphorous atoms from the nanocrystal surface. The reconstructed surface of the etched InP nanocrystals is terminated mainly with In atoms and is efficiently passivated with tri-n-octylphosphine oxide ligands.
A novel conical intersection topography and its consequences: The 1, 2A2 conical intersection seam of the vinoxy radical
Authors: Young R. Andrew , Yarkony David R.
Published: August 2005

A region of the 1, 2A2 seam of accidental conical intersections in the vinoxy radical exhibits a novel topography which has important consequences for both upper-state to lower-state and lower-state to upper-state nonadiabatic transitions. The impact of this topography on these nonadiabatic transitions is described. We also considered the possibility that this conical intersection seam provides a dynamical bottleneck to the photodissociation of vinoxy to H+ketene by facilitating nonadiabatic recrossing. Our analysis of the conical topographies and the proximity of the conical intersections to the transition state for dissociation to H+ketene does not support nonadiabatic recrossing as an effective dynamical bottleneck blocking the H+ketene channel.
The properties of ion-water clusters. I. The protonated 21-water cluster
Authors: Iyengar Srinivasan S. , Petersen Matt K. , Day Tyler J. F. , Burnham Christian J. , Teige Virginia E. , Voth Gregory A.
Published: August 2005

The ab initio atom-centered density-matrix propagation approach and the multistate empirical valence bond method have been employed to study the structure, dynamics, and rovibrational spectrum of a hydrated proton in the “magic” 21 water cluster. In addition to the conclusion that the hydrated proton tends to reside on the surface of the cluster, with the lone pair on the protonated oxygen pointing “outwards,” it is also found that dynamical effects play an important role in determining the vibrational properties of such clusters. This result is used to analyze and complement recent experimental and theoretical studies.
Calorimetric and dielectric studies of ferroelectric sodium nitrite confined in a nanoscale porous glass matrix
Authors: Kutnjak Zdravko , Vodopivec Boris , Blinc Robert , Fokin Alexander V. , Kumzerov Yuri A. , Vakhrushev Sergey B.
Published: August 2005

Heat-capacity measurements of the sodium nitrite confined in a nanoscale porous glass matrix show that the intermediate incommensurate phase, present in the bulk, has disappeared and that the first-order ferroelectric transition becomes suppressed and gradual. The ferroelectric transition temperature is shifted considerably to lower temperatures. Two noncritical dielectric modes were observed; however, the observed giant growth of the dielectric constant on heating through the transition temperature TC is shown to be mainly due to the electrode polarization effect.
Overtone spectroscopy of C–H ethyl stretches of 1-butyne
Authors: Portnov Alexander , Bespechansky Evgeny , Rosenwaks Salman , Bar Ilana
Published: August 2005

Room-temperature photoacoustic (PA) spectra and jet-cooled action spectra of the first to third overtone regions of the ethyl C–H stretches in vapor phase 1-butyne, CH3CH2CC–H, were measured. Both the PA and action spectra exhibit a complex multiple peak structure being better resolved and more pronounced in the latter, due to inhomogeneous structure reduction. The observed manifolds were analyzed in terms of a simplified joint local-/normal-mode (LM/NM) model accounting for two types of C–H stretches (methyl and methylene) and for Fermi resonances between stretches and deformations. The retrieved parameters, used for calculation of the eigenstates, come from the best-fit parameters based on the diagonalization of the vibrational Hamiltonian in the LM/NM basis. The parameters were obtained by comparing the eigenvalues and the sum of the squares of the expansion coefficients of the eigenvectors of the C–H stretches of methyl and methylene to the action spectra peak positions and intensities, respectively. This approximate model vibrational Hamiltonian is proposed to explain most observed spectral features, corresponding to C–H stretch bands and to combinations of C–H stretches and deformations, indicating the importance of the Fermi resonance. The model was also applied to calculate the dynamics of the C–H stretching modes resulting from coupling with the deformations, implying rapid initial state decay on subpicosecond time scale. Decays of several picoseconds were found for complete transfer of probability from the initially prepared state of methylene and methyl to the counterpart LM states.
Compact strain-sensitive flexible photonic crystals for sensors
Authors: Pursiainen Otto L. J. , Baumberg Jeremy J. , Ryan Kevin , Bauer Josef , Winkler Holger , Viel Benjamin , Ruhl Tilmann
Published: August 2005

A promising fabrication route to produce absorbing flexible photonic crystals is presented, which exploits self-assembly during the shear processing of multi-shelled polymer spheres. When absorbing material is incorporated in the interstitial space surrounding high-refractive-index spheres, a dramatic enhancement in the transmission edge on the short-wavelength side of the band gap is observed. This effect originates from the shifting optical field spatial distribution as the incident wavelength is tuned around the band gap, and results in a contrast up to 100 times better than similar but nonabsorbing photonic crystals. An order-of-magnitude improvement in strain sensitivity is shown, suggesting the use of these thin films in photonic sensors.
The effect of bubbles on the wall drag in a turbulent channel flow
Authors: Lu Jiacai , Fernández Arturo , Tryggvason Gretar
Published: August 2005

The effect of a few relatively large bubbles injected near the walls on the wall drag in the “minimum turbulent channel” is examined by direct numerical simulations. A front-tracking/finite-volume method is used to fully resolve all flow scales including the bubbles and the flow around them. The Reynolds number, using the friction velocity and the channel half-height, is 135 and the bubbles are 54 wall units in diameter. The results show that deformable bubbles can lead to significant reduction of the wall drag by suppression of streamwise vorticity. Less deformable bubbles, on the other hand, are slowed down by the viscous sublayer and lead to a large increase in drag.
Optimal rotary control of the cylinder wake using proper orthogonal decomposition reduced-order model
Authors: Bergmann Michel , Cordier Laurent , Brancher Jean-Pierre
Published: August 2005

In this paper we investigate the optimal control approach for the active control and drag optimization of incompressible viscous flow past circular cylinders. The control function is the time angular velocity of the rotating cylinder. The wake flow is solved in the laminar regime (Re=200) with a finite-element method. Due to the CPU and memory costs related to the optimal control theory, a proper orthogonal decomposition (POD) reduced-order model (ROM) is used as the state equation. The key enablers to an accurate and robust POD ROM are the introduction of a time-dependent eddy-viscosity estimated for each POD mode as the solution of an auxiliary optimization problem and the use of a snapshot ensemble for POD based on chirp-forced transients. Since the POD basis represents only velocities, we minimize a drag-related cost functional characteristic of the wake unsteadiness. The optimization problem is solved using Lagrange multipliers to enforce the constraints. 25% of relative drag reduction is found when the Navier-Stokes equations are controlled using a harmonic control function deduced from the optimal solution determined with the POD ROM. Earlier numerical studies concerning mean drag reduction are confirmed: it is shown, in particular, that without a sufficient penalization of the control input, our approach is energetically inefficient. The main result is that cost-reduction factors of 100 and 760 are obtained for the CPU time and the memory, respectively. Finally, limits of the performance of our approach are discussed.
On the spatial linear growth of gravity-capillary water waves sheared by a laminar air flow
Authors: Tsai Y. S. , Grass A. J. , Simons R. R.
Published: August 2005

The initial growth of mechanically generated small amplitude water waves below a laminar air stream was examined numerically and experimentally in order to explore the primary growth mechanism, that is, the interfacial instability of coupled laminar air and water flows. Measurements of the laminar velocity profile in the air over the water surface were found to be consistent with Lock’s [Q. J. Mech. Appl. Math. 4, 42 (1951)] theory. This profile was then used to calculate the spatial growth rates by solving the Orr-Sommerfeld equations. The simulation shows that the growth of the boundary layer affects the exponential growth of water waves along the fetch. The sensitivity of the growth rate is observed to vary by a factor of 2 for changes in the laminar velocity profile as small as 2% at the water surface. This indicates that the interfacial instability is strongly influenced by the wind-induced surface current. A laminar airflow was produced in the wind tunnel over mechanically generated monochromatic gravity-capillary water waves with the ka value in the order of 10−3. The novel experiment was designed to measure the minute changes in the wave slope and phase velocity simultaneously using a highly sensitive reflected twin laser beam technique. Agreement between linear theory and experiments for the spatial development of wave height and phase velocity suggests that the linear instability mechanism determines the initial stages of development of small-scale water waves.
Libraries of cluster-assembled titania films for chemical sensing
Authors: Mazza T. , Barborini E. , Kholmanov I. N. , Piseri P. , Bongiorno G. , Vinati S. , Milani P. , Ducati C. , Cattaneo D. , Li Bassi A. , Bottani C. E. , Taurino A. M. , Siciliano P.
Published: August 2005

We report the fabrication of libraries of nanostructured TiO2 films with a gradient in nanoparticle crystalline phase and dimensions. By supersonic cluster beam deposition it is possible to produce rutile nanoparticles with a diameter smaller than 10nm and to spread them into a co-deposited amorphous titania matrix. Upon thermal annealing rutile nanocrystals act as growth seeds of a film with a spatially controlled rutile/anatase ratio. Films with controlled crystalline phase variation have been deposited on micropatterned substrate to produce arrays of chemoresistive sensors of volatile organic compounds. Devices with different nanocrystalline structures and performances are obtained by a simple one-step thermal treatment after deposition.
Photonic bands in two-dimensionally patterned multimode GaN waveguides for light extraction
Authors: David A. , Meier C. , Sharma R. , Diana F. S. , DenBaars S. P. , Hu E. , Nakamura S. , Weisbuch C. , Benisty H.
Published: August 2005

We observe experimentally by photoluminescence the band structure and specific emission properties of an in-plane, light-diffracting photonic crystal formed onto a multimode gallium nitride waveguide. Clear-cut two-dimensional photonic crystal effects are reported. Comparison with modeling results in identification of the band structure, provides insight into the light diffraction mechanism and points out design issues for enhancement of the extraction efficiency.
Packing-induced electronic structure changes in bundled single-wall carbon nanotubes
Authors: Castrucci P. , Scarselli M. , De Crescenzi M. , Diociaiuti M. , Chistolini P. , El Khakani M. A. , Rosei F.
Published: August 2005

The electronic structure of free-standing parallel and braided bundles of single-wall carbon nanotubes (∼1.2nm diameter) was probed by transmission electron microscopy and electron energy loss spectroscopy. The observed dramatic changes in the carbon K(1s) near-edge structures are attributed to the tubes’ structural packing in bundles which consequently alters their electronic structure. The π*- and the σ*-states are shown to be strongly affected by the way the tubes are packed in the bundles (i.e., parallel, braided, turned, or twisted).
Open-circuit voltage quantum efficiency technique for defect spectroscopy in semiconductors
Authors: Mäckel Helmut , Cuevas Andrés
Published: August 2005

The temperature-dependent quantum efficiency of the open-circuit voltage is introduced for defect characterization in semiconductors. This technique measures the spectral response of the open-circuit voltage of a diode at different temperatures. The diffusion length is extracted from the spectral photovoltage and converted into carrier lifetime. This results in temperature-dependent lifetime curves that can be analyzed with the Shockley–Read–Hall model. The method allows defect analysis to be performed as soon as a junction is formed in the device and is also applicable to solar cells and Schottky diodes. The determination of the lifetime via the spectral response avoids trapping effects that commonly hamper other lifetime spectroscopy techniques. Examples of the application of the technique are given, showing good agreement with the temperature-dependent quantum efficiency of the short-circuit current. The results are consistent with temperature-dependent lifetime spectroscopy reported in the literature.
Interaction between superconductor and ferromagnetic domains in iron sheath: Peak effect in MgB2∕Fe wires
Authors: Horvat J. , Yeoh W. K. , Miller L. M.
Published: August 2005

Interaction between the superconductor and ferromagnet in MgB2∕Fe wires results in either a plateau or a peak effect in the field dependence of transport critical current, Ic(H). This is in addition to magnetic shielding of external field. Current theoretical models cannot account for the observed peak effect in Ic(H). This letter shows that the theoretical explanation of the peak effect should be sought in terms of interaction between superconductor and magnetic domain structure, obtained after the remagnetization of the iron sheath by the self-field of the current. There is a minimum value of critical current, below which the remagnetization of the iron sheath and peak effect in Ic(H) are not observed.
Hindering effect of the core-cladding interface on the progression of the second-order nonlinearity layer in thermally poled optical fibers
Authors: An Honglin , Fleming Simon
Published: August 2005

The spatial distribution of the second-order nonlinearity layer induced in thermally poled Ge-doped optical fibers has been investigated with second-harmonic microscopy. It was found that the core-cladding interface acts as an insurmountable barrier to the nonlinear layer at lower poling voltages. At higher poling voltages (>2.5kV), the nonlinear layer can partially overcome this barrier and reach the fiber core, in which it is isolated from the rest of the nonlinear layer in the cladding.
Scanning near field infrared radiometry for thermal imaging of infrared emitters with subwavelength resolution
Authors: Sade Sharon , Nagli Lev , Katzir Abraham
Published: August 2005

We have developed a scanning near field microscopy system based on tapered silver halide fibers which had tips of diameters smaller than a wavelength. The system was calibrated for temperature measurement and then determined the dependence of the minimum resolvable temperature difference and that of the spatial resolution on the tip diameter. This system was used for measurement of the temperature distribution of miniature infrared (IR) emitters. As an example we used a tapered fiber of tip diameter 5μm to carry out infrared emission measurements on a miniature IR emitter of dimensions 30μm×30μm in the spectral range 8.5–13.5μm. These measurements made it possible to obtain the thermal image of the element with a subwavelength resolution. Such a system would be useful for measuring the temperature distribution on a scene simulator projector or on an integrated circuit.
Tunable entanglement generation for mobile-electron spin qubits
Authors: Signal A. I. , Zülicke U.
Published: August 2005

Recent studies have shown that linear electron optics can be used to generate entangled two-particle states from nonentangled ones if additional measurements of charge or parity are performed. We have investigated such nondeterministic entanglement production in electronic versions of the Mach-Zehnder interferometer, where spin-dependent interference occurs due to the presence of electric-field tunable Rashba spin splitting. Adjustment of the spin-precession length turns out to switch the entangler on and off, as well as control the detailed form of entangled output states.
Room temperature ferromagnetism in laser ablated Ni-doped In2O3 thin films
Authors: Hong Nguyen Hoa , Sakai Joe , Huong Ngo Thu , Brizé Virginie
Published: August 2005

Ni-doped In2O3 thin films were fabricated by laser ablation on sapphire and MgO substrates under various conditions. All Ni:In2O3 films are well-crystallized, single phase, and show clear evidences of room temperature ferromagnetism (FM). Ni atoms were well substituted for In atoms, and distributed very uniformly over the whole thickness of the films. However, the films grown at 550 °C have the Ni concentration exactly the same as in the synthesized target, and as the results, they have the best crystallinity and the largest magnetic moment (maximum about 0.7μB∕Ni). The observed FM in this type of wide-band gap semiconductors has proved that by applying appropriate growth conditions, doping few percent of Ni into In2O3 could indeed result in a potential magnetic material.
Experimental determination of electronic stopping for ions in silicon dioxide
Authors: Zhang Y. , Weber W. J. , McCready D. E. , Grove D. A. , Jensen J. , Possnert G.
Published: August 2005

The electronic energy loss for He4, Li7, Be9, C12, O16, F19, and Si28 ions in self-supporting silicon dioxide foils has been measured over a continuous range of energies. The measured He stopping powers are in good agreement with the SRIM-2003 (Stopping and Range of Ions in Matter) prediction. In the case of Li and C ions, the measured stopping powers exhibit some deviation from the SRIM-2003 predictions only around the Bragg peak; however, for Be, O, F, and Si ions, the measure stopping powers exhibit up to 10% deviation from the SRIM-2003 predictions over the entire energy range. The results indicate that the modified Bohr formula is suitable for scaling the stopping number for C and heavier ions in the classical interaction regime.
Smoothing of Si0.7Ge0.3 virtual substrates by gas-cluster-ion beam
Authors: Chen H. , Chen F. , Wang X. M. , Yu X. K. , Liu J. R. , Ma K. B. , Chu W. K. , Cheng H. H. , Yu I. S. , Ho Y. T. , Horng K. Y.
Published: August 2005

The planarization of the SiGe virtual substrate surface is crucial for the fabrication of high-performance strained-Si metal-oxide-semiconductor field-effect transistors. In this letter, we report on the smoothing of the inherently crosshatched rough surfaces of SiGe deposited by molecular beam epitaxy on Si substrates by gas cluster ion beams. Atomic force microscopy measurements show that the average surface roughness (Ra) of the SiGe layer could be reduced considerably from 3.2 to 0.7 nm without any crosshatched pattern. Rutherford backscattering in combination with channeling was used to study the damage produced by cluster bombardment. No visible surface damage was observed for the normal-incidence smoothed SiGe with postsmoothing glancing angle cluster ion beam etching.
Tuning the hole injection barrier height at organic/metal interfaces with (sub-) monolayers of electron acceptor molecules
Authors: Koch Norbert , Duhm Steffen , Rabe Jürgen P. , Rentenberger Stephan , Johnson Robert L. , Klankermayer Jürgen , Schreiber Frank
Published: August 2005

We demonstrate that the insertion of an electron acceptor molecular (sub-) monolayer at organic/metal interfaces enables systematic tuning of the hole injection barrier height (Δh). Ultraviolet photoemission spectroscopy results show that Δh for α-sexithiophene thin films deposited on Ag(111) can be reduced from 1.3to1.0eV by introducing a chemisorbed monolayer of 11,11,12,12-tetracyano-9,10-anthraquinodimethane (TCAQ) on the metal surface. Fine-tuning of Δh within the interval of 0.3eV is achieved by using TCAQ coverages in the submonolayer range.
Construction of gene interaction and regulatory networks in bovine skeletal muscle from expression data
Authors: Reverter A. , Barris W. , Moreno-Sánchez N. , McWilliam S. , Wang Y. H. , Harper G. S. , Lehnert S. A. , Dalrymple B. P.
Published: August 2005

We propose a data-driven reverse engineering approach to isolate the components of a gene interaction and regulatory network. We apply this method to the construction of a network for bovine skeletal muscle. Key nodes in the network include muscle-specific genes and transcription factors. muscle-specific genes are identified from data mining the USA National Cancer Institute, Cancer Genome Anatomy Project database, while transcription factors are predicted by accurate function annotation. A total of 5 microarray studies spanning 78 hybridisations and 23 different experimental conditions provided raw expression data. A recently-reported analytical method based on multivariate mixed-model equations is used to compute gene co-expression measures across 624 genes. The resulting network included 102 genes (of which 40 were muscle-specific genes and 7 were transcription factors) that clustered in 7 distinct modules with clear biological interpretation.
Advances in methodology for random regression analyses
Authors: Meyer K.
Published: August 2005

Random regression analyses have become standard methodology for the analysis of traits with repeated records that are thought of as representing points on a trajectory. Modelling curves as a regression on functions of a continuous covariable, such as time, for each individual, random regression models are readily implemented in standard, linear mixed model analyses. Early applications have made extensive use of regressions on orthogonal polynomials. Recently, spline functions have been considered as an alternative. The use of a particular type of spline function, the so-called B-splines, as basis functions for random regression analyses is outlined, emphasising the local influence of individual observations and low degree of polynomials employed. While such analyses are likely to involve more regression coefficients than polynomial models, it is demonstrated that reduced rank estimation via the leading principal components is feasible and likely to yield more parsimonious models and more stable estimates than full rank analyses. The combined application of B-spline basis function and reduced rank estimation is illustrated for a small set of data for beef cattle.
Breeding robust pigs
Authors: Knap P. W.
Published: August 2005

Past developments in livestock breeding have led to considerable genetic change in production traits, but the follow-up of nutrition and management is often incomplete. The pig production sector is moving to hotter climates, and to more intensive and limiting conditions. This increases demands for animal robustness. Robustness can be implemented as a breeding objective trait just like production traits. Breeding for robustness is feasible, but requires substantial investment in data and technology. As for all low-heritability traits with complicated data recording, DNA markers provide a useful tool to support selection; this requires good association studies and ongoing multiple marker development. Breeding for increased robustness must be implemented in balance with breeding for increased production. It is therefore useful to define robustness in terms of performance-relevant issues. A convenient approach is through the environmental sensitivity of the expression of genetic production potential. Environmental sensitivity illustrates loss of flexibility to deal with intensive or limiting conditions, due to unbalanced resource allocation. It can be quantified for individual animals in terms of reaction norm parameters, which can be used as estimated breeding values to support selection. The challenges of implementing such a system will be (i) the set-up of proper data collection in a wide range of environmental settings; (ii) the development of proper data processing tools; (iii) the design of suitable breeding objectives and selection criteria, including MAS; and (iv) the successful integration of the first 3 objectives.
Molecular and bioinformatic strategies for gene discovery for meat traits: a reverse genetics approach
Authors: Hagen I. J. , Zadissa A. , McEwan J. C. , Veenvliet B. A. , Hickey S. M. , Cullen N. G. , Morris C. A. , Wilson T.
Published: August 2005

The identification of genes that influence meat quality and meat yield has relevance for several livestock species. Candidate genes include those involved in the biochemical pathways controlling muscle differentiation, growth and development. Mutations in one such gene, myostatin, have previously been reported to have dramatic effects on muscle phenotype in cattle. Here we report a screening strategy for the discovery of novel mutations in 10 genes involved in muscle development using single-stand conformation polymorphism gels and DNA sequencing. Several novel mutations, both non-synonymous and synonymous were discovered, and some of these may alter gene function. In addition, we also conducted a meta-analysis of published quantitative trait loci from cattle, sheep, pigs and mice, identifying those muscle development genes most likely to contribute to variation in muscle traits within species. From this strategy we found several genes that map into regions that are part of the extended muscle development pathway.
Bovine mammary epithelial cells, initiators of innate immune responses to mastitis
Authors: Gray C. , Strandberg Y. , Donaldson L. , Tellam R. L.
Published: August 2005

Innate immunity plays a vital role in the protection of the bovine mammary gland against mastitis. Until recently, the migration of effector cells such as neutrophils and monocytes into the mammary gland was thought to provide the only defence against invading pathogens. However, mammary epithelial cells may also play an important role in the immune response, contributing to the innate defence of the mammary tissue through secretion of antimicrobial peptides and attraction of circulating immune effector cells. This paper reviews the innate immune pathways in mammary epithelial cells and examines their role in the initiation of an innate immune response to Gram-positive and Gram-negative bacteria.
Application and impact of new genetic technologies on beef cattle breeding: a 'real world' perspective
Authors: Pollak E. J.
Published: August 2005

Molecular genetics is a maturing discipline with innovations that are finding application in animal breeding. Currently, DNA tests are available for parent identification or verification, and markers tests also exist for quantitative trait loci affecting important traits in beef cattle. The beef industry is, however, a particularly challenging industry in which to design breeding programs that fully capitalise on the potential of this technology. Hence, adoption within this industry to date has been below expectation. This paper examines several applications that are being investigated and will include discussion on issues constraining the transfer of DNA technology. An example of using DNA parentage testing for expanding the reach of selection programs into the commercial sector of the beef industry is explored in some depth, as it represents a potential high impact application. Use of molecular information in selection programs and in genetic evaluations is also discussed.
Insulin-like growth factor-I measured in juvenile pigs is genetically correlated with economically important performance traits
Authors: Bunter K. L. , Hermesch S. , Luxford B. G. , Graser H-U. , Crump R. E.
Published: August 2005

Insulin-like growth factor-I (IGF-I) is a naturally occurring polypeptide produced in the liver, muscle and fat tissues. It is known to be associated with growth and development during the postnatal growth period. Evidence for strong genetic correlations between juvenile IGF-I and performance traits would suggest this physiological measure would be useful as an early selection criterion. This paper reports estimates of genetic parameters from 9 trials where IGF-I was measured in juvenile pigs. All trials involved populations undergoing active selection for improved performance (e.g. efficient lean meat growth). Juvenile IGF-I was moderately heritable (average h2: 0.31) and influenced by common litter effects (average c2: 0.15). Genetic correlations (rg) between juvenile IGF-I and backfat (BF), feed intake (FI) or feed conversion ratio (FCR) traits were generally large and positive: rg averaged 0.57, 0.41 and 0.65, respectively. Phenotypic correlations (rp) between juvenile IGF-I and BF, FI or FCR were much lower (rp averaged 0.21, 0.09, and 0.15, respectively) as residual correlations between IGF-I and these performance traits were low, consistent with being measured at very different times. Correlations (genetic or phenotypic) between juvenile IGF-I and growth traits (e.g. lifetime daily gain or test daily gain) were relatively low, with average values within ± 0.09 of zero. Results from the trials reported here, and several physiological studies, indicate that information on juvenile IGF-I concentration can be used as an early physiological indicator of performance traits traditionally measured later in life. There is a clear role for juvenile IGF-I to facilitate pre-selection and more accurate selection of livestock for hard to measure traits, such as FCR, in pig breeding programs.
Expression of imprinted genes surrounding the callipyge mutation in ovine skeletal muscle
Authors: Vuocolo T. , Cockett N. E. , Tellam R. L.
Published: August 2005

The callipyge mutation in sheep results in postnatal hypertrophy and leanness of skeletal muscles in the pelvic limbs and loins. Associated changes also occur in the expression of a number of imprinted genes flanking the site of the mutation, which lies at the telomeric end of ovine chromosome 18. The transcripts from several of these genes are either spliced or undergo substantial RNA processing, sometimes in a very complex manner. The current investigation examined the effects of the callipyge mutation on the relative expression of some of these splice variants in samples taken: at birth, when the muscle hypertrophy phenotype is not expressed; and at 12 weeks of age, when the phenotype is fully apparent. It was concluded that changes in the postnatal developmental expression pattern of Dlk-1 are closely associated with the expression of the phenotype and that the callipyge mutation may promote a fetal-like gene expression program for some genes during postnatal life.
Gene expression profiling of ovine skin and wool follicle development using a combined ovine - bovine skin cDNA microarray
Authors: Norris B. J. , Bower N. I. , Smith W. J. M. , Cam G. R. , Reverter A.
Published: August 2005

Low fibre diameter and high fleece weight are important determinants of the economic value of the Merino fleece. The combination of these traits is found in Merino sheep with high follicle densities resulting from a high secondary to primary follicle ratio. Morphological stages in the development of primary and secondary follicles of fetal sheep skin have been well described. We have used gene expression profiling of fetal skin to identify genes that may be important in controlling these follicle developmental processes. A combined ovine (2.3 K) and bovine (6.14 K) cDNA microarray of 2 fetal and 1 adult stage skin tissues was constructed to compare gene expression levels between fetal day 82, day 105, day 120 and adult sheep skin developmental stages. The transcript profile resulted in 238 differentially expressed array elements relative to the adult expression, which represented 132 unique genes. These clustered into 50 up- and 82 down-regulated genes and distinct gene ontologies including structural constituents, phosphate transport, signal transduction and organogenesis. Northern blot analysis of 2 selected genes, S100A7LI and TAGLN, validated the microarray results. This list of genes contains candidates of interest for further investigation into the molecular control of wool follicle development.
Using mixture models to detect differentially expressed genes
Authors: McLachlan G. J. , Bean R. W. , Jones L. Ben-Tovim , Zhu J. X.
Published: August 2005

An important and common problem in microarray experiments is the detection of genes that are differentially expressed in a given number of classes. As this problem concerns the selection of significant genes from a large pool of candidate genes, it needs to be carried out within the framework of multiple hypothesis testing. In this paper, we focus on the use of mixture models to handle the multiplicity issue. With this approach, a measure of the local false discovery rate is provided for each gene, and it can be implemented so that the implied global false discovery rate is bounded as with the Benjamini-Hochberg methodology based on tail areas. The latter procedure is too conservative, unless it is modified according to the prior probability that a gene is not differentially expressed. An attractive feature of the mixture model approach is that it provides a framework for the estimation of this probability and its subsequent use in forming a decision rule. The rule can also be formed to take the false negative rate into account.
Comparative genomic analysis of non-coding sequences and the application of RNA interference tools for bovine functional genomics
Authors: Lew A. E. , Jackson L. A. , Bellgard M. I.
Published: August 2005

Non-coding (nc) RNAs are important regulators of developmental genes, and essential for the modification of cellular DNA and chromatin through a process known as RNA interference (RNAi). The mediators of RNAi can be in the form of short double stranded (ds) RNAs, micro (mi) RNAs or small interfering (si) RNAs. miRNAs are involved in a translation repression pathway that inhibits protein translation in mRNA targets. Comparative genomic screens have revealed conserved regulatory non-coding sequences, which assist to predict the function of endogenous miRNAs. Only a few comparative studies include bovine genomic sequence, and RNAi has yet to be applied in bovine genome functional screens. siRNAs target homologous mRNAs for degradation, and thereby, silence specific genes. The use of synthetic siRNAs facilitates the elucidation of gene pathways by specific gene knockdown. A survey of the literature identifies a small number of reports using RNAi to examine immune pathways in bovine cell lines; however, they do not target genes involved in specific production traits. Applications of RNAi to elucidate bovine immune pathways for relevant bacterial and parasite diseases are yet to be reported. The inhibition of viral replication using RNAi has been demonstrated with bovine RNA viruses such as pestivirus and foot and mouth disease virus signifying the potential of RNAi as an antiviral therapeutic. RNAi approaches combined with genome data for protozoan parasites, insects and nematodes, will expedite the identification of novel targets for the treatment and prevention of economically important parasitic infections. This review will examine the approaches used in mammalian RNAi research, the current status of its applications to livestock systems and will discuss potential applications in beef cattle programs.
Transcriptional profiling of muscle tissue in growing Japanese Black cattle to identify genes involved with the development of intramuscular fat
Authors: Wang Y. H. , Reverter A. , Mannen H. , Taniguchi M. , Harper G. S. , Oyama K. , Byrne K. A. , Oka A. , Tsuji S. , Lehnert S. A.
Published: August 2005

Japanese Black cattle are characterised by a unique ability to deposit intramuscular fat with lower melting temperature. In this study, 3 consecutive biopsies from Longissimus muscle tissue were taken and RNA isolated from 3 Japanese Black (Tajima strain) and 3 Holstein animals at age 11–20 months. The gene expression changes in these samples were analysed using a bovine fat/muscle cDNA microarray. A mixed-ANOVA model was fitted to the intensity signals. A total of 335 (4.8%) array elements were identified as differentially expressed genes in this breed × time comparison study. Genes preferentially expressed in Japanese Black are associated with mono-unsaturated fatty acid synthesis, fat deposition, adipogenesis development and muscle regulation, while examples of genes preferentially expressed in Holstein come from functional classes involved in connective tissue and skeletal muscle development. The gene expression differences detected between the Longissimus muscle of the 2 breeds give important clues to the molecular basis for the unique features of the Japanese Black breed, such as the onset and rate of adipose tissue development, metabolic differences, and signalling pathways involved in converting carbohydrate to lipid during lipogenesis. These findings will impact on industry management strategies designed to manipulate intramuscular adipose development at different development stages to gain maximum return for beef products.
CRC 'Regional Combinations' project — effects of genetics and growth paths on beef production and meat quality: experimental design, methods and measurements.
Authors: McKiernan W. A. , Wilkins J. F. , Barwick S. A. , Tudor G. D. , McIntyre B. L. , Graham J. F. , Deland M. P. B. , Davies L.
Published: August 2005

As a component of the second term of the Cooperative Research Centre (CRC) for Cattle and Beef Quality, a project to further test and validate the effects of varying nutritional growth paths pre-finishing and slaughter on cattle of varying genetic potential for meat yield and eating quality was designed and implemented. This project, ‘Regional Combinations’, was a multi-site experiment, using Bos taurus cattle generated at 4 locations across southern Australia. The design of imposing different growth paths between weaning and finishing on cattle with specific genetic potential is common across sites. Treatment and interaction effects on beef production and meat quality were examined within and across sites. This paper describes the experimental designs, generation of experimental cattle at the various sites and the measurements, collection and storage of the data for multi-site analyses.
Westran — highly inbred pigs for xenotransplantation research
Authors: Moran C.
Published: August 2005

This paper reviews the history, breeding and biological characterisation of a highly inbred line of pigs, the Westran, developed by Westmead Hospital and the Veterinary Faculty of the University of Sydney, as an experimental large animal model for transplantation research. The review ranges from the historical origins of Westran pigs, from a pair of animals released on Kangaroo Island in 1803, to the context and relevance of the line in xenotransplantation (i.e. the transplantation of organs, tissues and cells across species boundaries).
Integrated and comparative maps in livestock genomics
Authors: Nicholas F. W.
Published: August 2005

The creation of a single integrated map incorporating all available mapping information for an unsequenced species provides the best possible resource for meta analyses of quantitative trait loci, for a backbone on which to assemble sequence and for comparative mapping. Using a strategy encapsulated in the Location DataBase, integrated maps for cattle, sheep and pigs have been produced from all publicly-available mapping information for these livestock species. A very useful tool for comparative mapping is the Oxford grid. Of particular interest are grids comparing an integrated map from an unsequenced species with the annotated sequence map from a sequenced species. By an additional iteration of the Location DataBase approach or a variant of the Oxford-grid software, it is possible to create a virtual genome of the unsequenced species, which is a map comprising predicted locations for all loci identified in the sequenced species.
The use of linkage disequilibrium to map quantitative trait loci
Authors: Goddard M. E. , Meuwissen T. H. E.
Published: August 2005

This paper reviews the causes of linkage disequilibrium and its use in mapping quantitative trait loci. The many causes of linkage disequilibrium can be understood as due to similarity in the coalescence tree of different loci. Consideration of the way this comes about allows us to divide linkage disequilibrium into 2 types: linkage disequilibrium between any 2 loci, even if they are unlinked, caused by variation in the relatedness of pairs of animals; and linkage disequilibrium due to the inheritance of chromosome segments that are identical by descent from a common ancestor. The extent of linkage disequilibrium due to the latter cause can be logically measured by the chromosome segment homozygosity which is the probability that chromosome segments taken at random from the population are identical by descent. This latter cause of linkage disequilibrium allows us to map quantitative trait loci to chromosome regions. The former cause of linkage disequilibrium can cause artefactual quantitative trait loci at any position in the genome. These artefacts can be avoided by fitting the relatedness of animals in the statistical model used to map quantitative trait loci. In the future it may be convenient to estimate this degree of relatedness between individuals from markers covering the whole genome. The statistical model for mapping quantitative trait loci also requires us to estimate the probability that 2 animals share quantitative trait loci alleles at a particular position because they have inherited a chromosome segment containing the quantitative trait loci identical by descent. Current methods to do this all involve approximations. Methods based on concepts of coalescence and chromosome segment homozygosity are useful, but improvements are needed for practical analysis of large datasets. Once these probabilities are estimated they can be used in flexible linear models that conveniently combine linkage and linkage disequilibrium information.