bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanostructural origin of the ac conductance in dielectric granular metals: The case study of Co20(ZrO2)80
Authors: Konstantinović Z. , García del Muro M. , Batlle X. , Labarta A. , Varela M.
Published: August 2007

The authors show which is the nanostructure required in granular Co20(ZrO2)80 thin films to produce an ac response such as the one that is universally observed in a very wide variety of dielectric materials. A bimodal size distribution of Co particles yields randomly competing conductance channels which allow both the thermally assisted tunneling through small particles and capacitive conductance among larger particles that are further apart. A model consisting on a simple cubic random resistance-capacitor network describes quantitatively the experimental results as functions of temperature and frequency, and enables the determination of the microscopic parameters controlling the ac response of the samples.
Microstructures of coherent phase decomposition near morphotropic phase boundary in lead zirconate titanate
Authors: Rao Wei-Feng , Wang Yu U.
Published: July 2007

Microstructures of coherent phase decomposition near morphotropic phase boundary in lead zirconate titanate are investigated by using computer modeling and simulation. The model is based on the recently proposed incoherent equilibrium phase diagram [G. A. Rossetti, Jr. et al., Appl. Phys. Lett. 88, 072912 (2006)] and takes into account the coherency strain energy and electrostatic energy. It reveals characteristic multidomain microstructures, where nanoscale lamellar domains of tetragonal and rhombohedral phases coexist with well-defined crystallographic orientation relationships and produce coherent diffraction effects. The simulated microstructures provide important information for interpretation of diffraction data and identification of phases near morphotropic phase boundary.
Electrical properties of HfTiON gate-dielectric metal-oxide-semiconductor capacitors with different Si-surface nitridations
Authors: Ji F. , Xu J. P. , Lai P. T. , Li C. X. , Guan J. G.
Published: July 2007

Electrical properties of HfTiON gate-dielectric metal-oxide-semiconductor (MOS) capacitors with different Si-surface nitridations in N2O, NO, and NH3 prior to high-k film deposition are investigated and compared. It is found that the NO-nitrided sample exhibits low interface-state density and gate leakage current, and high reliability. This is attributed to formation of a SiON interlayer with suitable proportions of N and O. The MOS capacitor with Hf0.4Ti0.6OxNy∕SiON gate dielectric stack (capacitance equivalent thickness of 1.52nm and k value of 18.9) prepared by NO surface nitridation has an interface-state density of 1.22×1011cm−2eV−1 and gate leakage current density of 6×10−4Acm−2 (Vg=1V). Moreover, only a small degradation of electrical properties after a stressing at 10MV∕cm for 3000s is observed for the NO-nitrided sample.
Orientation of core-shell nanoparticles in an electric field
Authors: Park Jonghyun , Lu Wei
Published: August 2007

Coated nanoparticles, which have a core-shell structure, have many applications. This letter investigates the induced torque and orientation of such nanoparticles in an electric field. The authors show that the shell of a nanoparticle has an important effect on its orientation, even when the shell is thin and takes only a small portion of the total volume. For lossy dielectric particles, the permittivity, conductivity, field frequency, and core-shell structure together determine the magnitude and direction of the induced torque, suggesting a significant degree of experimental control over nanoparticle rotation and alignment.
Strain on wrinkled bilayer thin film
Authors: Huang Wu-Ping , Cheng Henry H. , Fedorchenko Alexander I. , Wang An-Bang
Published: July 2007

The authors report strain measurement on bilayer wrinkling silicon-germanium (SiGe) thin film. In combination of atomic force microscopy and ultraviolet micro-Raman measurement, the relationship between the spatial profile and strain distribution is established. Theoretical analysis on the mechanism of strain relaxation shows that, in contrast to self-rolling nanotube, both bending and shearing force play an important role in determining the morphology. The behavior demonstrated in the SiGe system should also exist in a wide range of material systems under various strain situations. This study advances the understanding of nanostructure engineered by strain and has significant implications on the performance of nanodevices.
Switching of tunnel magnetoresistance by domain wall motion in (Ga,Mn)As-based magnetic tunnel junctions
Authors: Fukuda M. , Yamanouchi M. , Matsukura F. , Ohno H.
Published: July 2007

Switching of tunnel magnetoresistance in magnetic tunnel junctions (MTJs) has been achieved by magnetic domain wall motion in one of the electrodes. The fabricated devices have two (Ga,Mn)As-based MTJs with a common bottom (Ga,Mn)As electrode, in which the domain wall motion takes place both by magnetic field and by current. This configuration allows not only the observation of switching but also time-resolved detection of the position of the domain wall by the tunnel magnetoresistance.
Sink-effect of nanocavities: Thermodynamic and kinetic approach
Authors: Ouyang G. , Li X. L. , Yang G. W.
Published: July 2007

Sink-effect of nanocavities in a host crystal to metallic impurity atoms is proposed on the basis of the established thermodynamic and kinetic approach at the nanometer scale. The trapping impurity mechanisms of nanocavities are attributed to the thermodynamic contact epitaxy of impurity atoms on the inner surface of nanocavities and the kinetic diffusion flux of impurity atoms pointing to nanocavities. These theoretical results exhibit that the nanocavity in a host crystal as a functional unit could be used to fabricate nanodevices.
Record of the lowest frequency shot noise measurement below 10Hz
Authors: Cho B. , Itagaki T. , Oshima C.
Published: August 2007

The noise of field emission (FE) currents ranging from 10pAto100μA was measured under ∼7×10−10Pa. Stepwise features were routinely observed in damping curves of the FE current, indicating remarkable sensitivity of the FE current measuring system. The lowest frequency measurement of shot noise was recorded below 10Hz. Space-charge suppression of noise was not observed for FE currents up to 100μA. Adsorption of residual gas increased the intensity of noise and made the noise of field emission current be dominated by the flicker noise.
Influence of anthracene-2-thiol treatment on the device parameters of pentacene bottom-contact transistors
Authors: Bock C. , Pham D. V. , Kunze U. , Käfer D. , Witte G. , Terfort A.
Published: August 2007

In pentacene-based bottom-contact field-effect transistors, the authors study the influence of anthracene-2-thiol-modified gold electrodes on the morphology, the contact and sheet resistance, the trap density, and the charge-carrier activation energy. The data are compared to reference samples with untreated gold electrodes. Anthracene-2-thiol treatment leads to a reduced sheet resistance, a reduced activation energy, and an improved film morphology.
Liquid xenon detector joins the search for dark matter
Authors: Schwarzschild Bertram
Published: August 2007

The dark matter that dominates the material content of the cosmos is thought to be made up of WIMPs, weakly interacting particles perhaps 100 times heavier than protons.
Homemade panels significantly reduce noise in a busy hospital unit
Authors: Day Charles
Published: August 2007

The problem of excessive noise in hospitals is under-studied and poorly understood. But for one cancer ward, acousticians have found a simple, effective solution.
Stakeholders weigh costs of open-access publishing
Authors: Guinnessy Paul
Published: August 2007

As open access moves mainstream, publishers are concerned about who is going to fund their journals.
Cohen reorganizes DHS science with “customer-focused” research
Authors: Dawson Jim
Published: August 2007

Viewing scientists and researchers as “input mechanisms” for his directorate, the new science and technology undersecretary says he is open to all ideas but insists on technology that works.
The Formation of Stellar Galactic Nuclei through Dissipative Gas Dynamics
Authors: Bekki K.
Published: July 2007

It is a long-standing and remarkable problem as to howstellar galactic nuclei (SGN) were formed in the central region of galaxies. In order to elucidate the formation processes of SGN, we numerically investigate gas dynamics, star formation, and chemical evolution in the central 1–1000 pc of gas disks embedded by galactic stellar spheroids. The main results of the present numerical study are: (a) SGN can be formed from dissipative, repeated merging of massive stellar and gaseous clumps that have typical masses of 105–106 M⊙ and are developed from nuclear gaseous spiral arms owing to local gravitational instability. Typically ∼5% of the masses of their host spheroids can be transfered to the central∼50 pc and thus become SGN. (b) SGN have very flattened shapes, and rotational kinematics and central velocity dispersions much smaller than those of their host spheroids. These structural and kinematic characteristics do not depend on model parameters such as masses of spheroids (Msph) and initial gas mass fraction (fg). (c) Stellar populations of SGN can show a wide rage of ages and metallicities, because SGN are formed from massive clumps with different star-formation and chemical-evolution histories. The mean metallicities of SGN can be significantly higher than those of their host spheroids. (d) More massive, higher density SGN can be formed in spheroids with higher surface brightness. Furthermore there can be a threshold value (∼0.2) of fg below which massive SGN are less likely to be formed in the central gas disks of spheroids. (e) More massive spheroids can have more massive, more metal-rich and higher-density SGN, because star formation and chemical enrichment proceed more efficiently owing to the less dramatic suppression of star formation by supernovae feedback effects in more massive spheroids.

Based on these results, we discuss correlations between the physical properties of SGN and those of their host galaxies, structural and kinematic properties of SGN of dwarf elliptical galaxies and the origin of very massive star clusters such as ω Cen and ultra-compact dwarf galaxies.
No Way Back: Maximizing Survival Time Below the Schwarzschild Event Horizon
Authors: Lewis Geraint F. , Kwan Juliana
Published: July 2007

It has long been known that once you cross the event horizon of a black hole, your destiny lies at the central singularity, irrespective of what you do. Furthermore, your demise will occur in a finite amount of proper time. In this paper, the use of rockets in extending the amount of time before the collision with the central singularity is examined. In general, the use of such rockets can increase your remaining time, but only up to a maximum value; this is at odds with the ‘more you struggle, the less time you have' statement that is sometimes discussed in relation to black holes. The derived equations are simple to solve numerically and the framework can be employed as a teaching tool for general relativity.
Expanding Space: the Root of all Evil?
Authors: Francis Matthew J. , Barnes Luke A. , James J. Berian , Lewis Geraint F.
Published: July 2007

While it remains the staple of virtually all cosmological teaching, the concept of expanding space in explaining the increasing separation of galaxies has recently come under fire as a dangerous idea whose application leads to the development of confusion and the establishment of misconceptions. In this paper we develop a notion of expanding space that is completely valid as a framework for the description of the evolution of the universe and whose application allows an intuitive understanding of the influence of universal expansion. We also demonstrate how arguments against the concept in general have failed thus far, as they imbue expanding space with physical properties not consistent with the expectations of general relativity.
Effects of nutrient additions on intertidal seagrass (Zostera muelleri) habitat in Western Port, Victoria, Australia
Authors: Morris Liz , Jenkins Gregory , Hatton David , Smith Timothy
Published: August 2007

Loss of seagrass habitat in many parts of the world has been attributed to increases in nutrient loading to nearshore areas. The role of excess epiphyte, macroalgal or phytoplankton growth in shading of seagrass leaves and negatively affecting seagrass health is generally agreed to be a prevalent mechanism in seagrass decline worldwide. In the present study nutrient addition experiments were undertaken at three sites in Western Port, Victoria. Nutrients were added to the water column using the controlled release fertiliser Osmocote™ in late summer 2005. The experiments ran for one month at two of the sites (Blind Bight and Hastings) and at the third site (Crib Point) the experiment ran for three months. Control and nutrient addition plots were monitored for concentrations of inorganic nutrients, number of seagrass leaves, seagrass, epiphyte and loose algal biomass and invertebrate faunal assemblages. Nutrient additions had increased ash free dry weight of seagrass leaves and loose algae at two of the three sites studied. There was also an increase in gammarid amphipod densities at the Crib Point site. We consider that Western Port seagrass habitat is sensitive to increased loads of nutrients within the water column with the Blind Bight region most at risk.
Food web structure of a subtropical headwater stream
Authors: Huang I-Yu , Lin Yao-Sung , Chen Chang-Po , Hsieh Hwey-Lian
Published: August 2007

The food web structure of a headwater stream (Hapen Creek) in subtropical northern Taiwan, which is subject to regular typhoon disturbances, was characterised using stable isotope techniques. δ13C and δ15N signatures were used to examine (i) the relative contributions of allochthonous versus. autochthonous sources to the web, and (ii) the trophic organisation of the community including the predominant feeding guilds and the most prevalent feeding mode. This study presents food web attributes for one of the very few food webs studied to date in a subtropical region. Consumers utilised allochthonous and autochthonous carbon sources differently depending on their trophic positions. The majority of consumers exploited more autochthonous carbon sources. Consumers at higher trophic positions in the food web had more direct and greater association with benthic algae. Higher-order consumers also consumed allochthonous carbon in an indirect manner by assimilating lower-order insects. The results reveal the importance of invertebrate consumer snails and aquatic insects in the transfer of organic matter. Omnivores predominated in the food web; this may reflect an opportunistic foraging strategy that enables them to adapt to hydrological disturbances and a fluctuating food supply.
Partitioning the variation in stream fish assemblages within a spatio-temporal hierarchy
Authors: Stewart-Koster Ben , Kennard Mark J. , Harch Bronwyn D. , Sheldon Fran , Arthington Angela H. , Pusey Bradley J.
Published: August 2007

This paper describes the relative influence of (i) landscape scale environmental and hydrological factors, (ii) local scale environmental conditions including recent flow history, and (iii) spatial effects (proximity of sites to one another), on the spatial and temporal variation in local freshwater fish assemblages in the Mary River, south-eastern Queensland, Australia. Using canonical correspondence analysis, each of the three sets of variables explained similar amounts of variation in fish assemblages (ranging from 44 to 52%). Variation in fish assemblages was partitioned into eight unique components: pure environmental, pure spatial, pure temporal, spatially structured environmental variation, temporally structured environmental variation, spatially structured temporal variation, the combined spatial/temporal component of environmental variation and unexplained variation. The total variation explained by these components was 65%. The combined spatial/temporal/environmental component explained the largest component (30%) of the total variation in fish assemblages, whereas pure environmental (6%), temporal (9%) and spatial (2%) effects were relatively unimportant. The high degree of intercorrelation between the three different groups of explanatory variables indicates that our understanding of the importance to fish assemblages of hydrological variation (often highlighted as the major structuring force in river systems) is dependent on the environmental context in which this role is examined.
Survival of Microcystis aeruginosa and Scenedesmus obliquus under dark anaerobic conditions
Authors: Shi X. L. , Kong F. X. , Yu Y. , Yang Z.
Published: August 2007

The cyanobacterium Microcystis aeruginosa and the green alga Scenedesmus obliquus were incubated individually and together in the dark and under anaerobic conditions created by adding the reducing agent cysteine. Flow cytometry was used to monitor cell concentrations, fluorescence of chlorophyll-a (chl-a), and cell metabolic activity measured with an esterase-sensitive probe to detect fluorescein diacetate (FDA) hydrolysis of the two species. M. aeruginosa showed a slight increase in cell metabolic activity, no conspicuous death of cells, and absence of decay of chlorophyll-a fluorescence in individual and competition cases under dark anaerobic conditions. Cell metabolic activity and fluorescence of S. obliquus, on the contrary, decreased sharply, and cell concentrations fluctuated markedly with time in the unialgal cultures, but showed only a slight decline in the mixed cultures. M. aeruginosa appeared to be more tolerant to dark anaerobic conditions than S. obliquus, which may arise in eutrophic lakes beneath thick surface scums in the water column, or in the bottom sediments. Tolerance of these conditions may be important to the dominance of M. aeruginosa in eutrophic lakes.
Habitat type promotes rapid and extremely localised genetic differentiation in dolphins
Authors: Möller Luciana M. , Wiszniewski Joanna , Allen Simon J. , Beheregaray Luciano B.
Published: August 2007

The high potential for dispersal of many marine organisms often results in low population differentiation over large distances. Here, we report that dolphin communities living in very close geographic proximity (<16 km) but in two different environments – open coast and enclosed embayment – exhibit unexpected genetic differentiation at nine microsatellite loci. Results based on a fixation index and a Bayesian clustering approach suggested that gene flow between communities within an embayment is high, as is gene flow between coastal communities. However, lower gene flow between embayment and open coast communities translated into substantial genetic differentiation between dolphin communities from the two environments, and assignment of individuals into two populations. Along with patterns observed in 403 bp of the mitochondrial DNA control region, the results suggest that restriction of gene flow likely occurred in the last 6000 years, after coastal dolphins colonised the embayment. We hypothesise that factors such as fidelity to the local area and resource and behavioural specialisations may have played a major role in promoting and maintaining genetic subdivision between dolphins of the two environments. Importantly, our study shows that habitat type can rapidly promote extremely fine-scale genetic structure in a long-lived, highly mobile marine mammal.
The distribution and abundance of dictyoceratid sponges in relation to hydrodynamic features: identifying candidates and environmental conditions for sponge aquaculture
Authors: Bannister R. J. , Brinkman R. , Wolff C. , Battershill C. , de Nys R.
Published: August 2007

The distribution and abundance of dictyoceratid sponges was surveyed to a depth of 20 m at eleven locations within the Palm Island Group, Great Barrier Reef (GBR), Australia. These surveys were related to prevailing hydrodynamic conditions to identify candidates and environmental conditions for sponge aquaculture. Locations were classified as sheltered, intermediate and exposed using quantitative wave exposure and current force models. The species richness of dictyoceratid sponges was high with ten taxa, but the abundance of most species was low with patchy distributions. Two species, Coscinoderma sp. and Rhopaloeides odorabile, were abundant, and detailed surveys of these species were conducted at seven locations representing common habitats within the Palm Island Group. Coscinoderma sp. was present at all locations and although abundances differed significantly across locations, this was not related to hydrodynamic conditions. In contrast, R. odorabile was only present at exposed locations with low abundance. The higher abundance and broad distribution of Coscinoderma sp. supports its selection as an aquaculture candidate. In contrast, R. odorabile was less abundant and was restricted to high-energy environments making aquaculture more problematic. The present study demonstrates the importance of ecological data in the decision-making process for new species aquaculture.
Random linker-insertion mutagenesis to identify functional domains of herpes simplex virus type 1 glycoprotein B
Authors: Lin Erick , Spear Patricia G.
Published: August 2007

Herpes simplex virus glycoprotein B (gB) is one of four glycoproteins essential for viral entry and cell fusion. Recently, an x-ray structure of the nearly full-length trimeric gB ectodomain was determined. Five structural domains and two linker regions were identified in what is probably a postfusion conformation. To identify functional domains of gB, we performed random linker-insertion mutagenesis. Analyses of 81 mutants revealed that only 27 could fold to permit processing and transport of gB to the cell surface. These 27 mutants fell into three categories. Insertions into two regions excluded from the solved structure (the N terminus and the C-terminal cytoplasmic tail) had no negative effect on cell fusion and viral entry activity, identifying regions that can tolerate altered structure without loss of function. Insertions into a disordered region in domain II and the adjacent linker region also permitted partial cell fusion and viral entry activity. Insertions at 16 other positions resulted in loss of cell fusion and viral entry activity, despite detectable levels of cell surface expression. Four of these insertion sites were not included in the solved structure. Two were between residues exposed to a cavity that is too small to accommodate the 5-amino acid insertions, consistent with the solved structure being different from the native prefusion structure. Ten were between residues exposed to the surface of the trimer, identifying regions that may be critical for interactions with other viral proteins or cellular components or for transitions from the prefusion to postfusion state.
Divergent functions and distinct localization of the Notch ligands DLL1 and DLL3 in vivo
Authors: Geffers Insa , Serth Katrin , Chapman Gavin , Jaekel Robert , Schuster-Gossler Karin , Cordes Ralf , Sparrow Duncan B. , Kremmer Elisabeth , Dunwoodie Sally L. , Klein Thomas , Gossler Achim
Published: July 2007

The Notch ligands Dll1 and Dll3 are coexpressed in the presomitic mesoderm of mouse embryos. Despite their coexpression, mutations in Dll1 and Dll3 cause strikingly different defects. To determine if there is any functional equivalence, we replaced Dll1 with Dll3 in mice. Dll3 does not compensate for Dll1; DLL1 activates Notch in Drosophila wing discs, but DLL3 does not. We do not observe evidence for antagonism between DLL1 and DLL3, or repression of Notch activity in mice or Drosophila. In vitro analyses show that differences in various domains of DLL1 and DLL3 individually contribute to their biochemical nonequivalence. In contrast to endogenous DLL1 located on the surface of presomitic mesoderm cells, we find endogenous DLL3 predominantly in the Golgi apparatus. Our data demonstrate distinct in vivo functions for DLL1 and DLL3. They suggest that DLL3 does not antagonize DLL1 in the presomitic mesoderm and warrant further analyses of potential physiological functions of DLL3 in the Golgi network.
Intracellular Ca2+ Oscillations, a Potential Pacemaking Mechanism in Early Embryonic Heart Cells
Authors: Sasse Philipp , Zhang Jianbao , Cleemann Lars , Morad Martin , Hescheler Juergen , Fleischmann Bernd K.
Published: July 2007

Early (E9.5–E11.5) embryonic heart cells beat spontaneously, even though the adult pacemaking mechanisms are not yet fully established. Here we show that in isolated murine early embryonic cardiomyocytes periodic oscillations of cytosolic Ca2+ occur and that these induce contractions. The Ca2+ oscillations originate from the sarcoplasmic reticulum and are dependent on the IP3 and the ryanodine receptor. The Ca2+ oscillations activate the Na+-Ca2+ exchanger, giving rise to subthreshold depolarizations of the membrane potential and/or action potentials. Although early embryonic heart cells are voltage-independent Ca2+ oscillators, the generation of action potentials provides synchronization of the electrical and mechanical signals. Thus, Ca2+ oscillations pace early embryonic heart cells and the ensuing activation of the Na+-Ca2+ exchanger evokes small membrane depolarizations or action potentials.
Nuclear receptor ERRα and coactivator PGC-1β are effectors of IFN-γ-induced host defense
Authors: Sonoda Junichiro , Laganière Josée , Mehl Isaac R. , Barish Grant D. , Chong Ling-Wa , Li Xiangli , Scheffler Immo E. , Mock Dennis C. , Bataille Alain R. , Robert François , Lee Chih-Hao , Giguère Vincent , Evans Ronald M.
Published: August 2007

Macrophage activation by the proinflammatory cytokine interferon-γ (IFN-γ) is a critical component of the host innate response to bacterial pathogenesis. However, the precise nature of the IFN-γ-induced activation pathway is not known. Here we show using genome-wide expression and chromatin-binding profiling that IFN-γ induces the expression of many nuclear genes encoding mitochondrial respiratory chain machinery via activation of the nuclear receptor ERRα (estrogen-related receptor α, NR3B1). Studies with macrophages lacking ERRα demonstrate that it is required for induction of mitochondrial reactive oxygen species (ROS) production and efficient clearance of Listeria monocytogenes (LM) in response to IFN-γ. As a result, mice lacking ERRα are susceptible to LM infection, a phenotype that is localized to bone marrow-derived cells. Furthermore, we found that IFN-γ-induced activation of ERRα depends on coactivator PGC-1β (peroxisome proliferator-activated receptor γ coactivator-1β), which appears to be a direct target for the IFN-γ/STAT-1 signaling cascade. Thus, ERRα and PGC-1β act together as a key effector of IFN-γ-induced mitochondrial ROS production and host defense.
A three-helix homo-oligomerization domain containing BH3 and BH1 is responsible for the apoptotic activity of Bax
Authors: George Nicholas M. , Evans Jacquelynn J.D. , Luo Xu
Published: August 2007

Homo-oligomerization of Bax (or Bak) has been hypothesized to be responsible for cell death through the mitochondria-dependent apoptosis pathway. However, partly due to a lack of structural information on the Bax homo-oligomerization and apoptosis inducing domain(s), this hypothesis has remained difficult to test. In this study, we identified a three-helix unit, comprised of the BH3 (helix 2) and BH1 domains (helix 4 and helix 5), as the homo-oligomerization domain of Bax. When targeted to mitochondria, this minimum oligomerization unit induced apoptosis in Bax−/−Bak−/− mouse embryonic fibroblasts (DKO). Strikingly, the central helix of Bax (helix 5), when replacing the corresponding helix (helix 5) of Bcl-xL, an anti-apoptotic Bcl-2 family protein structurally homologous to Bax, converted Bcl-xL into a Bax-like molecule capable of forming oligomers and causing apoptosis in the DKO cells. Finally, a series of systematic mutagenesis analyses revealed that homo-oligomerization is both necessary and sufficient for the apoptotic activity of Bax. These results suggest that active Bax causes mitochondrial damage through homo-oligomers of a three-helix functional unit.
Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function
Authors: Isken Olaf , Maquat Lynne E.
Published: August 2007

Cells routinely make mistakes. Some mistakes are encoded by the genome and may manifest as inherited or acquired diseases. Other mistakes occur because metabolic processes can be intrinsically inefficient or inaccurate. Consequently, cells have developed mechanisms to minimize the damage that would result if mistakes went unchecked. Here, we provide an overview of three quality control mechanisms—nonsense-mediated mRNA decay, nonstop mRNA decay, and no-go mRNA decay. Each surveys mRNAs during translation and degrades those mRNAs that direct aberrant protein synthesis. Along with other types of quality control that occur during the complex processes of mRNA biogenesis, these mRNA surveillance mechanisms help to ensure the integrity of protein-encoding gene expression.
Top1- and Top2-mediated topological transitions at replication forks ensure fork progression and stability and prevent DNA damage checkpoint activation
Authors: Bermejo Rodrigo , Doksani Ylli , Capra Thelma , Katou Yuki-Mori , Tanaka Hirokazu , Shirahige Katsuhiko , Foiani Marco
Published: August 2007

DNA topoisomerases solve topological problems during chromosome metabolism. We investigated where and when Top1 and Top2 are recruited on replicating chromosomes and how their inactivation affects fork integrity and DNA damage checkpoint activation. We show that, in the context of replicating chromatin, Top1 and Top2 act within a 600-base-pair (bp) region spanning the moving forks. Top2 exhibits additional S-phase clusters at specific intergenic loci, mostly containing promoters. TOP1 ablation does not affect fork progression and stability and does not cause activation of the Rad53 checkpoint kinase. top2 mutants accumulate sister chromatid junctions in S phase without affecting fork progression and activate Rad53 at the M–G1 transition. top1 top2 double mutants exhibit fork block and processing and phosphorylation of Rad53 and γH2A in S phase. The exonuclease Exo1 influences fork processing and DNA damage checkpoint activation in top1 top2 mutants. Our data are consistent with a coordinated action of Top1 and Top2 in counteracting the accumulation of torsional stress and sister chromatid entanglement at replication forks, thus preventing the diffusion of topological changes along large chromosomal regions. A failure in resolving fork-related topological constrains during S phase may therefore result in abnormal chromosome transitions, DNA damage checkpoint activation, and chromosome breakage during segregation.
Canopy shade causes a rapid and transient arrest in leaf development through auxin-induced cytokinin oxidase activity
Authors: Carabelli Monica , Possenti Marco , Sessa Giovanna , Ciolfi Andrea , Sassi Massimiliano , Morelli Giorgio , Ruberti Ida
Published: August 2007

A plant grown under canopies perceives the reduction in the ratio of red (R) to far-red (FR) light as a warning of competition, and enhances elongation growth in an attempt to overgrow its neighbors. Here, we report that the same low R/FR signal that induces hypocotyl elongation also triggers a rapid arrest of leaf primordium growth, ensuring that plant resources are redirected into extension growth. The growth arrest induced by low R/FR depends on auxin-induced cytokinin breakdown in incipient vein cells of developing primordia, thus demonstrating the existence of a previously unrecognized regulatory circuit underlying plant response to canopy shade.
Heritability of alternative splicing in the human genome
Authors: Kwan Tony , Benovoy David , Dias Christel , Gurd Scott , Serre David , Zuzan Harry , Clark Tyson A. , Schweitzer Anthony , Staples Michelle K. , Wang Hui , Blume John E. , Hudson Thomas J. , Sladek Rob , Majewski Jacek
Published: August 2007

Alternative pre-mRNA splicing increases proteomic diversity and provides a potential mechanism underlying both phenotypic diversity and susceptibility to genetic disorders in human populations. To investigate the variation in splicing among humans on a genome-wide scale, we use a comprehensive exon-targeted microarray to examine alternative splicing in lymphoblastoid cell lines (LCLs) derived from the CEPH HapMap population. We show the identification of transcripts containing sequence verified exon skipping, intron retention, and cryptic splice site usage that are specific between individuals. A number of novel alternative splicing events with no previous annotations in either the RefSeq and EST databases were identified, indicating that we are able to discover de novo splicing events. Using family-based linkage analysis, we demonstrate Mendelian inheritance and segregation of specific splice isoforms with regulatory haplotypes for three genes:OAS1,CAST, andCRTAP. Allelic association was further used to identify individual SNPs or regulatory haplotype blocks linked to the alternative splicing event, taking advantage of the high-resolution genotype information from the CEPH HapMap population. In one candidate, we identified a regulatory polymorphism that disrupts a 5′ splice site of an exon in theCASTgene, resulting in its exclusion in the mutant allele. This report illustrates that our approach can detect both annotated and novel alternatively spliced variants, and that such variation among individuals is heritable and genetically controlled.
Gene copy number variation spanning 60 million years of human and primate evolution
Authors: Dumas Laura , Kim Young H. , Karimpour-Fard Anis , Cox Michael , Hopkins Janet , Pollack Jonathan R. , Sikela James M.
Published: August 2007

Given the evolutionary importance of gene duplication to the emergence of species-specific traits, we have extended the application of cDNA array-based comparative genomic hybridization (aCGH) to survey gene duplications and losses genome-wide across 10 primate species, including human. Using human cDNA arrays that contained 41,126 cDNAs, corresponding to 24,473 unique human genes, we identified 4159 genes that likely represent most of the major lineage-specific gene copy number gains and losses that have occurred in these species over the past 60 million years. We analyzed 1,233,780 gene-to-gene data points and found that gene gains typically outnumbered losses (ratio of gains/losses = 2.34) and these frequently cluster in complex and dynamic genomic regions that are likely to serve as gene nurseries. Almost one-third of all human genes (6696) exhibit an aCGH- predicted change in copy number in one or more of these species, and within-species gene amplification is also evident. Many of the genes identified here are likely to be important to lineage-specific traits including, for example, human-specific duplications of the AQP7 gene, which represent intriguing candidates to underlie the key physiological adaptations in thermoregulation and energy utilization that permitted human endurance running.
Staining Mouse Embryos for Alkaline Phosphatase Activity: Figure 1.
Authors: Nagy Andras , Gertsenstein Marina , Vintersten Kristina , Behringer Richard
Published: August 2007

This protocol describes a technique that is used to visualize human placental alkaline phosphatase (AP) activity in transgenic mice. AP activity staining is localized to the cell surface. Endogenous AP activity is eliminated by heat inactivation that spares the heat-stable human placental AP activity.
Baskets for In Situ Hybridization and Immunohistochemistry: Figure 1.
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M.
Published: August 2007

INTRODUCTION

For large in situ hybridization and immunohistochemistry experiments, changing solutions in vials becomes tedious, and baskets should be used. Commercially available baskets, such as 15-mm Netwell baskets (Corning), fit into 12-well tissue culture plates. Although they are expensive, they can, with extensive washing, be reused. However, these baskets are not readily adaptable to large-scale use, and their relatively shallow wells make cross-contamination between wells a real danger. This protocol describes a procedure for making homemade baskets with plastic microcentrifuge tubes and nylon mesh that are more adaptable to large-scale experiments. The baskets are narrow and deep and thus can be placed in a rack at high density. To change solutions, individual tubes or whole racks of tubes can be moved from one bath of solution to another. Because many tubes can be manipulated simultaneously, there is an enormous saving in work. It is also quite difficult to lose embryos in baskets; embryos in vials stand a good chance of being sucked into the aspirator during solution changes and lost.
Fetal Thymus Organ Culture: Figure 1.
Authors: Anderson Graham , Jenkinson Eric J.
Published: August 2007

INTRODUCTION

The generation of functionally competent T-cells from their progenitors involves a series of developmental events including proliferation, differentiation, and survival. T-cell development is a non-cell-autonomous event, and requires interactions with thymic stromal cells. Fetal thymus organ cultures provide an in vitro system in which isolated embryonic thymus lobes can be maintained in culture, allowing the study of T-cell development as well as thymic stromal cell function. This system remains the only in vitro system that supports a complete program of T-cell development, including positive and negative selection of the developing T-cell receptor repertoire. Modifications of the basic fetal thymus organ culture system, such as hanging drop cultures and reaggregate thymus organ cultures, provide useful systems to analyze thymus colonization and thymic stromal cell function, respectively.
A Rapid Protocol for Whole-Mount In Situ Hybridization on Xenopus Embryos
Authors: Monsoro-Burq Anne H.
Published: August 2007

INTRODUCTION

This in situ hybridization (ISH) protocol describes a simplified method using a digoxigenin-labeled antisense RNA probe on whole Xenopus embryos, suitable for both X. laevis and X. tropicalis. The protocol includes fixation, β-galactosidase staining (when lineage tracing is needed), and storage of the embryos prior to ISH. This method shortens the steps before hybridization, which limits RNA degradation in the sample, and preserves superficial structures. Hence, it is particularly suited for the analysis of ectoderm, neural, and mesodermal structures from blastula to early tadpole stages. Additional permeabilization steps are included to process later tadpole stages.
In Vivo Time-Lapse Imaging of Zebrafish Embryonic Development
Authors: Distel Martin , Köster Reinhard W.
Published: August 2007

INTRODUCTION

Intravital time-lapse imaging is a powerful technique for investigating continuous developmental processes without missing crucial events. Because of the rapid embryogenesis, external development, and transparency of zebrafish embryos, their developmental processes can be visualized in time-lapse studies in the context of the living organism. The following protocol describes a method for performing intravital time-lapse imaging of zebrafish embryos over several days using confocal or compound stereomicroscopes.
Preparing DNA from Cell Pellets for Genotyping
Authors: Sahota Amrik , Brooks Andrew I. , Tischfield Jay A.
Published: August 2007

INTRODUCTION

This protocol describes large-scale DNA extraction from cell pellets using either in-house or commercial (PUREGENE) reagents. The cell pellets are prepared from human lymphoblast cell lines (LCLs) that have been established using the Epstein-Barr virus (EBV).
Preparing DNA from Blood for Genotyping
Authors: Sahota Amrik , Brooks Andrew I. , Tischfield Jay A. , King Irena B.
Published: August 2007

INTRODUCTION

This protocol describes the extraction of genomic DNA from whole blood samples (fresh or frozen) and buffy coats. It provides methods for (1) large-scale extraction of DNA using either in-house or commercial (PUREGENE) reagents; (2) mid-scale extraction of DNA using the QIAamp DNA Blood Midi Kit (for 0.5-mL samples); and (3) small-scale extraction of DNA using the QIAamp DNA Blood Mini Kits (for 200-μL samples). Also included are methods for extracting DNA from blood samples that are compromised or clotted. Compromised blood samples include samples that spent more than 3 days in transit, samples that have been stored for more than 1 wk at 4°C, samples that have been stored at -20°C or -70°C, and samples that were collected incorrectly (e.g., not mixed properly). The procedures described here are not high throughput. Potential drawbacks of making them high-throughput are lower recoveries of DNA and possible variability in data quality, thus requiring additional quality assurance and control checks. DNA yields for these methods vary with the number of nucleated cells in the blood sample and the quality of the sample.
Growth allometry of immature insects: larvae do not grow exponentially
Authors: TAMMARU TOOMAS , ESPERK TOOMAS
Published: July 2007

The allometric relationship between growth rate and body mass has received considerable attention but different taxa have not been equally studied. In particular, a limited amount of information is available on growth allometry of insect larvae.

In life‐history studies, it is often assumed that insect larvae grow exponentially. This leads one to expect that potential rewards of extending growth periods are high in terms of increased adult body masses and fecundities. Therefore, it has been a challenge to find costs of large size that counterbalance the fecundity advantage of attaining larger sizes.

This study examines the intraspecific growth allometry of lepidopteran larvae. Original methodology is proposed to address problems arising from the complexity of the insect growth curve, and the high sensitivity of growth rates to environmental conditions. To facilitate generalizations, larvae of 11 unrelated lepidopteran species were subjected to an identical study design.

Instantaneous absolute growth rates of larvae were related to body size by an intraspecific allometric exponent in the range between 0·41 and 0·88. There were significant differences between the species but values of the exponent as high as 1 (exponential growth), and as low as 0 (linear growth) could safely be excluded.

Instantaneous relative growth rates of larvae were typically 35% lower in their last instar when compared to the penultimate one. Using the exponential growth curve (i.e. assuming the constancy of relative growth rates) in modelling insect life‐histories may therefore lead to substantially biased conclusions.
Condensin function at centromere chromatin facilitates proper kinetochore tension and ensures correct mitotic segregation of sister chromatids
Authors: Yong‐Gonzalez Vladimir , Wang Bi‐Dar , Butylin Pavel , Ouspenski Ilia , Strunnikov Alexander
Published: August 2007

The condensin complex is essential for sister chromatid segregation in eukaryotic mitosis. Nevertheless, in budding yeast, condensin mutations result in massive mis‐segregation of chromosomes containing the nucleolar organizer, while other chromosomes, which also contain condensin binding sites, remain genetically stable. To investigate this phenomenon we analyzed the mechanism of the cell‐cycle arrest elicited by condensin mutations. Under restrictive conditions, the majority of condensin‐deficient cells arrest in metaphase. This metaphase arrest is mediated by the spindle checkpoint, particularly by the spindle‐kinetochore tension‐controlling pathway. Inactivation of the spindle checkpoint in condensin mutants resulted in frequent chromosome non‐disjunction, eliminating the bias in chromosome mis‐segregation towards rDNA‐containing chromosomes. The spindle tension defect in condensin‐impaired cells is likely mediated by structural defects in centromere chromatin reflected by the partial loss of the centromere histone Cse4p. These findings show that, in addition to its essential role in rDNA segregation, condensin mediates segregation of the whole genome by maintaining the centromere structure in Saccharomyces cerevisiae.
Combined effects of fisheries and climate on a migratory long‐lived marine predator
Authors: Rolland V. , Barbraud C. , Weimerskirch H.
Published: July 2007

The impact of climate on marine ecosystems is now well documented, but remains complex. Climate change may interact with human activities to effect population dynamics. In addition, in migratory species conditions are different between the breeding and wintering grounds, resulting in more complex dynamics. All these possible effects should be considered to predict the future of endangered species, but very few studies have investigated such combined interactions.

As a case study, we assessed the relative impact of fisheries and of oceanographic conditions in breeding and wintering sites on adult survival and breeding success of a population of the endangered black‐browed albatross Thalassarche melanophrys in the Kerguelen Islands, Southern Indian Ocean. This study was based on long‐term monitoring of individually marked individuals (1979–2005) and identification by tracking studies and band recoveries of the oceanic feeding zones used during breeding and non‐breeding seasons.

Breeding success was variable until 1997 and then declined gradually, from 0·88 to 0·48 chicks per egg laid. It was favoured by positive sea‐surface temperature anomalies (SSTA) and trawl fishery during the breeding period, whereas it was negatively affected by positive SSTA around Tasmania, where the species winters. Adult survival was 0·918 ± 0·004 on average and increased with SSTA during incubation, but decreased significantly with high tuna longlining effort in the wintering zone.

Our analyses show that demographic parameters were influenced by both climate and fisheries in both breeding and wintering grounds, but with different effect size. Black‐browed albatross breeding success was more favoured by trawlers’ offal and discards than by any of the seasonally/spatially oceanographic conditions, whereas their survival was equally affected by tuna longline fishery through incidental by‐catch and spring SSTA.

Synthesis and applications. Our work underlines that a comprehensive knowledge of the life history of a species in all the habitats used is important to disentangle the respective roles of environmental conditions and human factors on population dynamics. Identification of these effects is required when proposing effective conservation measures, because the conservation of threatened species may depend on their wintering country's exclusive economic zones.
Revision of the subgenus Ceratitis (Pardalaspis) Bezzi, 1918 (Diptera, Tephritidae, Ceratitini)
Authors: MEYER MARC DE
Published: August 2007

Abstract. The fruit fly genus Ceratitis (Diptera: Tephritidae) comprises several important pest species attacking a wide range of unrelated fruits. In this paper the subgenus Ceratitis (Pardalaspis) Bezzi is revised. Ten species are recognized of which five are described as new: C.(P.)hamata sp.n., C.(P.)munroi sp.n., C.(P.)serrata sp.n., C.(P.)semipunctata sp.n. and C.(P.)zairensis sp.n. A key to both sexes is provided. All species are restricted to the Afrotropical Region and distributional and known host plant data are given.