bluuebunny/crossref_metadata_2025 huggingface dataset:
The transition from thermally driven to ponderomotively driven stimulated Brillouin scattering and filamentation of light in plasma
Authors: Berger R. L. , Valeo E. J. , Brunner S.
Published: June 2005

The dispersion properties of ion acoustic waves and their nonlinear coupling to light waves through ponderomotive and thermal forces are sensitive to the strength of electron-ion collisions. Here, with the neglect of electron-electron collisions, the growth rate of stimulated Brillouin scattering (SBS) is obtained when the driven acoustic wave frequency and wavelength span the range of small to large compared to electron-ion collision frequency and mean free path, respectively. In all cases the thermal contributions to the SBS growth rate are insignificant if the ion acoustic wave frequency is greater than the electron-ion collision frequency and the wavelength is much shorter than the electron-ion mean free path. On the other hand, the purely growing filamentation instability remains thermally driven for shorter wavelengths than SBS even when the growth rate is larger than the acoustic frequency role.
Multiple species atom source for laser-cooling experiments
Authors: Stan C. A. , Ketterle W.
Published: May 2005

We describe the design of a single beam, multiple species atom source in which the flux of any component can be separately adjusted. Using this design we have developed a Na23–Li6 atom source for ultracold atom experiments. The fluxes of lithium and sodium are independently tunable, allowing operation as a single Na23 or Li6 source as well as a double source with equal atomic fluxes in each component.
Relating optimal growth to counterpropagating Rossby waves in shear instability
Authors: Heifetz Eyal , Methven John
Published: June 2005

The optimal dynamics of conservative disturbances to plane parallel shear flows is interpreted in terms of the propagation and mutual interaction of components called counterpropagating Rossby waves (CRWs). Pairs of CRWs were originally used by Bretherton to provide a mechanistic explanation for unstable normal modes in the barotropic Rayleigh model and baroclinic two-layer model. One CRW has large amplitude in regions of positive mean cross-stream potential vorticity (PV) gradient, while the second CRW has large amplitude in regions of negative PV gradient. Each CRW propagates to the left of the mean PV gradient vector, parallel to the mean flow. If the mean flow is more positive where the PV gradient is positive, the intrinsic phase speeds of the two CRWs will be similar. The CRWs interact because the PV anomalies of one CRW induce cross-stream velocity at the location of the other CRW, thus advecting the mean PV. Although a single Rossby wave is neutral, their interaction can result in phase locking and mutual growth. Here the general initial value problem for disturbances to shear flow is analyzed in terms of CRWs. For the discrete spectrum (which could alternatively be described using normal modes), the singular value decomposition of the dynamical propagator can be obtained analytically in terms of the CRW interaction coefficient and the intrinsic CRW phase speeds. Using this formalism, optimal perturbations, the disturbances which grow fastest in a given norm over a specified time interval, can readily be found. The most natural norm for CRWs is related to air parcel displacements or enstrophy. However, if an energy norm is taken, it is shown to grow due to both mutual amplification of air parcel displacements and the untilting of PV structures (the Orr mechanism) associated with decreasing phase difference between the CRWs. A generalization of the CRW description to the optimal dynamics of the complete spectrum solution is outlined. Although the dynamics then involves the interaction between an infinite number of “CRW kernels,” the form of the simple interaction between any two CRW kernels is the same as in the discrete case.
Dipole-radiation model for terahertz radiation from semiconductors
Authors: Peng H. J. , Aspnes D. E.
Published: June 2005

We present a simple dipole-radiation model for the generation of terahertz radiation from semiconductors under short-pulse excitation. Using a one-dimensional force model applied to bond charges and free carriers, we evaluate both current-surge and frequency-mixing contributions to obtain analytic expressions that provide an integrated description of previous results.
Evidence of ion diffusion at room temperature in microcrystals of the Bi2Sr2CaCu2O8+δ superconductor
Authors: Truccato M. , Lamberti C. , Prestipino C. , Agostino A.
Published: June 2005

We have studied Bi-2212 microcrystals aged at ambient conditions for 40 days. Combined x-ray absorption near edge structure and x-ray fluorescence measurements with micrometer space resolution show both an increase of Cu+ with respect to Cu2+ and an enrichment in Cu vs Bi and Sr cation content near the sample edges in the b-axis direction. A parallel study on an electrically contacted sample has indirectly detected the O loss, observing both a resistivity increase and an increase in sample thickness near the edges. We conclude that the O outdiffusion along the b axis is accompanied by Cu cation migration in the same direction.
Effects of weak ordering of InGaPN
Authors: Lin K. I. , Lee J. Y. , Wang T. S. , Hsu S. H. , Hwang J. S. , Hong Y. G. , Tu C. W.
Published: June 2005

The effect of weak ordering on InGaPN∕GaAs heterostructure grown by gas source molecular-beam epitaxy is quantitatively studied by room-temperature Raman, photoluminescence (PL), and photoreflectance spectroscopy in this work. The PL intensity decreases rapidly as the nitrogen concentration increases, implying that more nonradiative centers are generated by the ordering effect and the degradation of the samples. The band gap of InGaPN decreases dramatically as the nitrogen is incorporated. The Raman modes of InGaPN between 130 and 1000cm−1 are analyzed. Polarized Raman spectra reveal that the InGaPN layers become more ordered as more nitrogen is incorporated. A broad Raman structure that appeared around 730cm−1 is attributed to an InGaN-like LO-phonon mode. The transition of the crystal structure from the zinc blende to CuPt structure and the formation of GaN clusters are responsible for the ordering effect in the InGaPN layer.
Low-energy ion irradiation during film growth: Kinetic pathways leading to enhanced adatom migration rates
Authors: Adamovic D. , Münger E. P. , Chirita V. , Hultman L. , Greene J. E.
Published: June 2005

Embedded-atom molecular dynamics simulations are used to investigate the effects of low-energy self-ion irradiation of Pt adatoms on Pt(111). Here, we concentrate on self-bombardment dynamics, i.e., isolating and monitoring the atomic processes, induced by normally incident Pt atoms with energies E ranging from 5 to 50 eV, that can affect intra- and interlayer mass transport.. We find that adatom scattering, surface channeling, and dimer formation occur at all energies. Atomic intermixing events involving incident and terrace atoms are observed at energies ⩾15eV, while the collateral formation of residual surface vacancies is observed only with E>40eV. The overall effect of low-energy self-ion irradiation is to enhance lateral adatom and terrace atom migration.
Prism coupled terahertz waveguide sensor
Authors: Rau C. , Torosyan G. , Beigang R. , Nerkararyan Kh.
Published: June 2005

A simple THz waveguide element has been used as a sensitive sensor for adsorbates on surfaces. The evanescent wave from total internal reflection off a silicon prism was used to couple pulsed THz radiation frequency selectively into the waveguide. The coupled frequencies were determined via time domain spectroscopy and react sensitively to any changes of thickness or phase shift upon reflection. In particular, the sensitivity to phase shifts makes this waveguide sensor attractive for the detection of very thin adsorbates. Typical sensitivity and reliability limits for the detection of adsorbates are discussed.
1.55
μ
m
GaNAsSb photodetector on GaAs
Authors: Luo H. , Gupta J. A. , Liu H. C.
Published: June 2005

We report a GaNAsSb p-i-n photodetector operating in the 1.55-μm-wavelength region. The device consists of two undoped 70-Å GaN0.025As0.615Sb0.36 quantum wells sandwiched between p- and n- GaAs barriers grown by molecular-beam epitaxy on GaAs substrate. At 1.55μm, responsivities of 0.016 and 0.01A∕W are demonstrated for as-deposited and annealed samples, respectively, which correspond to absorption coefficients of 1.3×104 and 0.82×104cm−1.
Highly efficient in-plane channel drop filter in a two-dimensional heterophotonic crystal
Authors: Takano Hitomichi , Song Bong-Shik , Asano Takashi , Noda Susumu
Published: June 2005

Improvements in the channel drop efficiency of an in-plane drop filter in a two-dimensional photonic crystal slab are presented, using a device consisting of two photonic crystal slabs with different lattice constants. It is theoretically shown that drop efficiencies much higher than the maximum of 25% for a conventional configuration are achievable when utilizing reflections at the photonic crystal heterostructure interface. Additionally, the higher drop efficiency is found to be less sensitive to structural fluctuations. Drop operations with efficiencies of more than 80% are experimentally demonstrated by the fabricated devices.
Manipulation and sorting of magnetic particles by a magnetic force microscope on a microfluidic magnetic trap platform
Authors: Mirowski Elizabeth , Moreland John , Zhang Arthur , Russek Stephen E. , Donahue Michael J.
Published: June 2005

We have integrated a microfluidic magnetic trap platform with an external magnetic force microscope (MFM) cantilever. The MFM cantilever tip serves as a magnetorobotic arm that provides a translatable local magnetic field gradient to capture and move magnetic particles with nanometer precision. The MFM electronics have been programmed to sort an initially random distribution of particles by moving them within an array of magnetic trapping elements. We measured the maximum velocity at which the particles can be translated to be 2.2mm∕s±0.1mm∕s, which can potentially permit a sorting rate of approximately 5500particles∕min. We determined a magnetic force of 35.3±2.0pN acting on a 1μm diameter particle by measuring the hydrodynamic drag force necessary to free the particle. Release of the particles from the MFM tip is made possible by a nitride membrane that separates the arm and magnetic trap elements from the particle solution. This platform has potential applications for magnetic-based sorting, manipulation, and probing of biological molecules in a constant-displacement or a constant-force mode.
Strong photoabsorption by a single-quantum wire in waveguide-transmission spectroscopy
Authors: Takahashi Yasushi , Hayamizu Yuhei , Itoh Hirotake , Yoshita Masahiro , Akiyama Hidefumi , Pfeiffer Loren N. , West Ken W.
Published: June 2005

We measured the absorption spectrum of a single T-shaped 14×6nm lateral-sized quantum wire embedded in an optical waveguide using waveguide-transmission spectroscopy at 5 K. In spite of its small volume, the one-dimensional-exciton ground state shows a large absorption coefficient of 80cm−1, or a 98% absorption probability for a single pass of the 500μm long waveguide.
Interface atomic structure of epitaxial ErAs layers on (001) In0.53Ga0.47As and GaAs
Authors: Klenov Dmitri O. , Zide Joshua M. , Zimmerman Jeramy D. , Gossard Arthur C. , Stemmer Susanne
Published: June 2005

High-angle annular dark-field (HAADF) imaging in scanning transmission electron microscopy was used to determine the atomic structure of interfaces between epitaxial ErAs layers with the cubic rock salt structure and In0.53Ga0.47As and GaAs, respectively. All layers were grown by molecular-beam epitaxy. We show that the interfacial atomic arrangement corresponds to the so-called chain model, in which the zinc blende semiconductor is terminated with a Ga layer. Image analysis was used to quantify the expansion between the first ErAs plane and the terminating Ga plane. In the HAADF images, a high intensity transfer from the heavy Er columns into the background was observed in the ErAs layer, whereas the background in In0.53Ga0.47As was of much lower intensity.
Simultaneous electric and magnetic field induced nonvolatile memory
Authors: Quintero M. , Leyva A. G. , Levy P.
Published: June 2005

We investigate the electric field induced resistive switching effect and magnetic field induced fraction enlargement on a polycrystalline sample of a colossal magnetoresistive compound displaying intrinsic phase coexistence. Our data show that the electric effect (presumably related to the presence of inhomogeinities) is present in a broad temperature range (300–20 K), being observable even in a mostly homogeneous ferromagnetic state. In the temperature range in which low magnetic field determines the phase coexistence fraction, both effects, though related to different mechanisms, are found to determine multilevel nonvolatile memory capabilities simultaneously.
A conceptual basis for the wise use of wetlands in northern Australia — linking information needs, integrated analyses, drivers of change and human well-being
Authors: Finlayson C. Max , Bellio Maria Grazia , Lowry John B.
Published: June 2005

Australia’s north supports many wetlands. The biodiversity of these wetlands is highly regarded, but many are increasingly being affected by well recognised pressures that result in adverse change in their ecological character. The extent of the knowledge base and causes of adverse change in Australia’s tropical wetlands are reviewed with an emphasis on the linkage between direct and indirect drivers of change. Within the context of the existing knowledge base, an integrated model for collecting information on the ecological character of tropical wetlands is proposed. The model encompasses hierarchical and multi-scalar approaches to wetland inventory, assessment and monitoring and was developed largely from research undertaken in northern Australia. It is based around the concepts of wise use and maintenance of the ecological character of wetlands, which in turn emphasises the value of wetlands to people through the delivery of ecosystem services. A broader conceptual framework linking ecosystem services and human well-being to the condition of wetlands is introduced as a forerunner to considering research needs for tropical Australian wetlands. The integrated model and framework entail community consultation and the involvement of stakeholders in decisions about wetland research and management. In conclusion, it is emphasised that the maintenance of the ecological character of the wetlands of northern Australia is a task for wetland managers, users and owners in collaboration with scientists from many disciplines.
A preliminary typology of Australian tropical rivers and implications for fish community ecology
Authors: Erskine W. D. , Saynor M. J. , Erskine L. , Evans K. G. , Moliere D. R.
Published: June 2005

Australian tropical rivers are dependent on highly seasonal rainfall and runoff between November and April. They also transport low sediment and solute loads, except where catchments have been disturbed by mining, grazing and cropping. Aquatic habitats or channel units are the physical template influencing fish communities. Pools provide dry-season refuges for fish and channels provide pathways for movement between refuges when streamflows are re-established. A preliminary geomorphological typology of Australian tropical river reaches (excludes estuaries) is proposed that defines nine distinct river types: (1) bedrock rivers (upland channels and gorges); (2) bedrock-confined rivers; (3) avulsive rivers; (4) meandering rivers (confined meandering, laterally migrating unconfined and laterally stable unconfined); (5) straight rivers; (6) floodouts; (7) island- and ridge-anabranching rivers; (8) co-existent mud-braided and anabranching rivers; and (9) extensive freshwater wetlands and billabongs. Many of these have not been recognised overseas and are unique. Channel units differ greatly between river types and contribute to distinctive fish communities in different river types. As expected, fish diversity decreases upstream because of less diverse habitat and natural barriers to fish movement at steps, falls and turbulent cascades and rapids. Fish kills occur in most years and are caused by several different factors that reduce dissolved oxygen.
Freshwater-flow requirements of estuarine fisheries in tropical Australia: a review of the state of knowledge and application of a suggested approach
Authors: Robins Julie B. , Halliday Ian A. , Staunton-Smith Jonathan , Mayer David G. , Sellin Michelle J.
Published: June 2005

The freshwater-flow requirements of estuarine fisheries in tropical areas are reviewed, with reference to species important to fisheries in northern Australia. Fisheries production, in terms of catch, is often elevated during, or as a consequence of, years with higher river flow, but the causality of these relationships often remains unproven. Scientific information on the freshwater-flow requirements important to fisheries production is increasingly being sought during the planning, allocation and management of water resources within Australia and in other countries around the world. Frequently, such advice is based on the analysis of catch and freshwater flow (or rainfall), or on life-history information. Clarifying fisheries-specific goals of water management would assist in prioritising research into the freshwater-flow requirements of estuarine fisheries. A framework that integrates life-history information and correlative analyses is suggested to assist in understanding the freshwater-flow requirements of estuarine fisheries. The framework is also useful in identifying knowledge gaps and pertinent research questions. The approach is illustrated through its application to identifying key freshwater-flow events likely to be important for fisheries production in a dry tropical estuary in Queensland, Australia.
Correlations between apolipoprotein E ε4 gene dose and brain-imaging measurements of regional hypometabolism
Authors: Reiman Eric M. , Chen Kewei , Alexander Gene E. , Caselli Richard J. , Bandy Daniel , Osborne David , Saunders Ann M. , Hardy John
Published: June 2005

Patients with Alzheimer's disease (AD) have abnormally low positron emission tomography (PET) measurements of the cerebral metabolic rate for glucose (CMRgl) in regions of the precuneus and the posterior cingulate, parietotemporal, and frontal cortex. Apolipoprotein E (APOE) ε4 gene dose (i.e., the number of ε4 alleles in a person's APOE genotype) is associated with a higher risk of AD and a younger age at dementia onset. We previously found that cognitively normal late-middle-aged APOE ε4 carriers have abnormally low CMRgl in the same brain regions as patients with probable Alzheimer's dementia. In a PET study of 160 cognitively normal subjects 47–68 years of age, including 36 ε4 homozygotes, 46 heterozygotes, and 78 ε4 noncarriers who were individually matched for their gender, age, and educational level, we now find that ε4 gene dose is correlated with lower CMRgl in each of these brain regions. This study raises the possibility of using PET as a quantitative presymptomatic endophenotype to help evaluate the individual and aggregate effects of putative genetic and nongenetic modifiers of AD risk.
A heterodimer-selective agonist shows
in vivo
relevance of G protein-coupled receptor dimers
Authors: Waldhoer Maria , Fong Jamie , Jones Robert M. , Lunzer Mary M. , Sharma Shiv K. , Kostenis Evi , Portoghese Philip S. , Whistler Jennifer L.
Published: June 2005

There has been much speculation regarding the functional relevance of G protein-coupled receptor heterodimers, primarily because demonstrating their existence
in vivo
has proven to be a considerable challenge. Here we show that the opioid agonist ligand 6′-guanidinonaltrindole (6′-GNTI) has the unique property of selectively activating only opioid receptor heterodimers but not homomers. Importantly, 6′-GNTI is an analgesic, thereby demonstrating that opioid receptor heterodimers are indeed functionally relevant
in vivo
. However, 6′-GNTI induces analgesia only when it is administered in the spinal cord but not in the brain, suggesting that the organization of heterodimers is tissue-specific. This study demonstrates a proof of concept for tissue-selective drug targeting based on G protein-coupled receptor heterodimerization. Importantly, targeting opioid heterodimers could provide an approach toward the design of analgesic drugs with reduced side effects.
Survival adjustment of mature dendritic cells by IL-15
Authors: Dubois Sigrid P. , Waldmann Thomas A. , Müller Jürgen R.
Published: June 2005

The survival of CD8
+
/CD44
hi
memory phenotype T cells depends on an IL-15 activity on nonlymphoid cells. Here, we report that IL-15 and its receptor were induced on dendritic cells (DCs) by a combination of IFN-γ and NF-κB relA inducers. IL-15 conferred in an autocrine loop resistance to apoptosis that accompanied the maturation process in DCs
in vitro
. As an apparent result
in vivo
, mice deficient in IL-15 or its receptor harbor few DCs. Injecting DCs into IL-15
-/-
mice was associated with the appearance of CD8
+
/CD44
hi
T cells that depended on IL-15 expression but also correlated with the longevity of the DCs. These findings support the hypothesis that DCs mediate the effect of IL-15 on CD8
+
/CD44
hi
memory phenotype T cells.
Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets
Authors: Persson Staffan , Wei Hairong , Milne Jennifer , Page Grier P. , Somerville Christopher R.
Published: June 2005

Coexpression patterns of gene expression across many microarray data sets may reveal networks of genes involved in linked processes. To identify factors involved in cellulose biosynthesis, we used a regression method to analyze 408 publicly available Affymetrix
Arabidopsis
microarrays. Expression of genes previously implicated in cellulose synthesis, as well as several uncharacterized genes, was highly coregulated with expression of cellulose synthase (CESA) genes. Four candidate genes, which were coexpressed with CESA genes implicated in secondary cell wall synthesis, were investigated by mutant analysis. Two mutants exhibited
irregular xylem
phenotypes similar to those observed in mutants with defects in secondary cellulose synthesis and were designated
irx8
and
irx13
. Thus, the general approach developed here is useful for identification of elements of multicomponent processes.
Variation in efficiency of DNA mismatch repair at different sites in the yeast genome
Authors: Hawk Joshua D. , Stefanovic Lela , Boyer Jayne C. , Petes Thomas D. , Farber Rosann A.
Published: June 2005

Evolutionary studies have suggested that mutation rates vary significantly at different positions in the eukaryotic genome. The mechanism that is responsible for this context-dependence of mutation rates is not understood. We demonstrate experimentally that frameshift mutation rates in yeast microsatellites depend on the genomic context and that this variation primarily reflects the context-dependence of the efficiency of DNA mismatch repair. We measured the stability of a 16.5-repeat polyGT tract by using a reporter gene (
URA3-GT
) in which the microsatellite was inserted in-frame into the yeast
URA3
gene. We constructed 10 isogenic yeast strains with the reporter gene at different locations in the genome. Rates of frameshift mutations that abolished the correct reading frame of this gene were determined by fluctuation analysis. A 16-fold difference was found among these strains. We made mismatch-repair-deficient (
msh2
) derivatives of six of the strains. Mutation rates were elevated for all of these strains, but the differences in rates among the strains were substantially reduced. The simplest interpretation of this result is that the efficiency of DNA mismatch repair varies in different regions of the genome, perhaps reflecting some aspect of chromosome structure.
Experimental tests of a homology model for OxlT, the oxalate transporter of
Oxalobacter formigenes
Authors: Yang Qiang , Wang Xicheng , Ye Liwen , Mentrikoski Mark , Mohammadi Elham , Kim Young-Mog , Maloney Peter C.
Published: June 2005

Using the x-ray structure of the glycerol 3-phosphate transporter (GlpT), we devised a model for the distantly related oxalate transporter, OxlT. The model accommodates all earlier biochemical information on OxlT, including the idea that Lys-355 lies on the permeation pathway, and predicts that Lys-355 and a second positive center, Arg-272, comprise the binding site for divalent oxalate. Study of R272K, R272A, and R272Q derivatives verifies that Arg-272 is essential, and comparisons with GlpT show that both anion transporters bind substrates within equivalent domains. In 22 single-cysteine variants in TM7 and TM8, topology as marked by accessibility to Oregon green maleimide is predicted by the model, with similar concordance for 52 positions probed earlier. The model also reconciles cross-linking of a cysteine pair placed near the periplasmic ends of TM2 and TM7, and retrospective study of TM2 and TM11 confirms that positions supporting disulfide trapping lie at a helical interface. Our work describes a pathway to the modeling of OxlT and other transporters in the major facilitator superfamily and outlines simple experimental tests to evaluate such proposals.
Statistics of protein library construction
Authors: Firth Andrew E. , Patrick Wayne M.
Published: June 2005

Summary: We have investigated the statistics associated with constructing and sampling large protein-encoding libraries. Using fairly simple statistics we have written algorithms for estimating the diversity in libraries generated by the most commonly used protocols, including error-prone PCR, DNA shuffling, StEP PCR, oligonucleotide-directed randomization, MAX randomization, synthetic shuffling, DHR, ADO and SISDC.

Availability: Web interface and C++ source code available at http://guinevere.otago.ac.nz/stats.html

Contact:  aef@sanger.otago.ac.nz

Supplementary information: Complete mathematical notes, model assumptions and justification, users' guide and worked examples at above website.
Practical FDR-based sample size calculations in microarray experiments
Authors: Hu Jianhua , Zou Fei , Wright Fred A.
Published: June 2005

Motivation: Owing to the experimental cost and difficulty in obtaining biological materials, it is essential to consider appropriate sample sizes in microarray studies. With the growing use of the False Discovery Rate (FDR) in microarray analysis, an FDR-based sample size calculation is essential.

Method: We describe an approach to explicitly connect the sample size to the FDR and the number of differentially expressed genes to be detected. The method fits parametric models for degree of differential expression using the Expectation–Maximization algorithm.

Results: The applicability of the method is illustrated with simulations and studies of a lung microarray dataset. We propose to use a small training set or published data from relevant biological settings to calculate the sample size of an experiment.

Availability: Code to implement the method in the statistical package R is available from the authors.

Contact:  jhu@mdanderson.org
Evolution of cooperation by generalized reciprocity
Authors: Pfeiffer Thomas , Rutte Claudia , Killingback Timothy , Taborsky Michael , Bonhoeffer Sebastian
Published: June 2005

The evolution of cooperation by direct reciprocity requires that individuals recognize their present partner and remember the outcome of their last encounter with that specific partner. Direct reciprocity thus requires advanced cognitive abilities. Here, we demonstrate that if individuals repeatedly interact within small groups with different partners in a two person Prisoner's Dilemma, cooperation can emerge and also be maintained in the absence of such cognitive capabilities. It is sufficient for an individual to base their decision of whether or not to cooperate on the outcome of their last encounter—even if it was with a different partner.
Peak shift and epidemiology in a seasonal host–nematode system
Authors: Cattadori I.M , Boag B , Bjørnstad O.N , Cornell S.J , Hudson P.J
Published: June 2005

Insight into the dynamics of parasite–host relationships of higher vertebrates requires an understanding of two important features: the nature of transmission and the development of acquired immunity in the host. A dominant hypothesis proposes that acquired immunity develops with the cumulative exposure to infection, and consequently predicts a negative relationship between peak intensity of infection and host age at this peak. Although previous studies have found evidence to support this hypothesis through between-population comparisons, these results are confounded by spatial effects. In this study, we examined the dynamics of infection of the nematodeTrichostrongylus retortaeformiswithin a natural population of rabbits sampled monthly for 26 years. The rabbit age structure was reconstructed using body mass as a proxy for age, and the host age–parasite intensity relationship was examined for each rabbit cohort born from February to August. The age–intensity curves exhibited a typical concave shape, and a significant negative relationship was found between peak intensity of infection and host age at this peak. Adult females showed a distinct periparturient rise inT. retortaeformisinfection, with higher intensities in breeding adult females than adult males and non-breeding females. These findings are consistent with the hypothesis of an acquired immune response of the host to a parasite infection, supporting the principle that acquired immunity can be modelled using the cumulative exposure to infection. These findings also show that seasonality can be an important driver of host–parasite interactions.
Environmental variability in the early rearing environment generates behaviourally flexible cod: implications for rehabilitating wild populations
Authors: Braithwaite Victoria A , Salvanes Anne G.V
Published: June 2005

The release of hatchery-reared fishes for restoring threatened and endangered populations is one of the most controversial issues in applied ecology. A central issue has been to determine whether releases cause extinction of local wild populations. This may arise either through domesticated or non-local fishes hybridizing with wild fishes, or through inappropriate behavioural interactions; for example, many hatchery fishes show exaggerated aggressive and competitive behaviour and out-compete wild counterparts. The impact of the impoverished hatchery environment in shaping behaviour is only now receiving attention. Attempts to counteract hatchery-related behavioural deficiencies have utilized intensive training programmes shortly before the fishes are released. However, we show here that simple exposure to variable spatial and foraging cues in the standard hatchery environment generates fishes with enhanced behavioural traits that are probably associated with improved survival in the wild. It appears that fishes need to experience a varying and changeable environment to learn and develop flexible behaviour. Using variable hatchery rearing environments to generate suitable phenotypes in combination with a knowledge of appropriate local genotypes, rehabilitation of wild fishes is likely to succeed, where to date it has largely failed.
The zinc finger transcription factor Klf7 is required for TrkA gene expression and development of nociceptive sensory neurons
Authors: Lei Lei , Laub Friedrich , Lush Mark , Romero Mario , Zhou Jing , Luikart Bryan , Klesse Laura , Ramirez Francesco , Parada Luis F.
Published: June 2005

TrkA, the high affinity receptor for nerve growth factor (NGF), is essential for the development of nociceptive sensory and sympathetic neurons. The zinc finger transcription factor Klf7 interacts with an important cis element of the TrkA minimal enhancer and is coexpressed with TrkA in these neurons. We show that Klf7 binds to the endogenous TrkA minimal enhancer and can activate transcription from the TrkA minimal enhancer in a sequence-dependent manner. In Klf7-/- newborn mice, we find a significant reduction in sensory neurons due to increased apoptosis. The neuronal loss is restricted to nociceptive neurons that normally depend on TrkA for neurotrophic support, while other populations of somatosensory neurons appear normal. The reduction of TrkA expression in sensory neurons is a direct effect of Klf7 gene ablation, rather than a secondary effect of cell death. As a result, Klf7-/- mice have deficient response to noxious stimuli. Finally, removal of one TrkA allele exacerbates the loss of TrkA(+) neurons in Klf7-/- mice. Thus, Klf7 specifically regulates TrkA gene expression and is required for the development of a subset of nociceptive sensory neurons.
The developmental miRNA profiles of zebrafish as determined by small RNA cloning
Authors: Chen Po Yu , Manninga Heiko , Slanchev Krasimir , Chien Minchen , Russo James J. , Ju Jingyue , Sheridan Robert , John Bino , Marks Debora S. , Gaidatzis Dimos , Sander Chris , Zavolan Mihaela , Tuschl Thomas
Published: June 2005

MicroRNAs (miRNAs) represent a family of small, regulatory, noncoding RNAs that are found in plants and animals. Here, we describe the miRNA profile of the zebrafishDanio rerioresolved in a developmental and cell-type-specific manner. The profiles were obtained from larger-scale sequencing of small RNA libraries prepared from developmentally staged zebrafish, and two adult fibroblast cell lines derived from the caudal fin (ZFL) and the liver epithelium (SJD). We identified a total of 154 distinct miRNAs expressed from 343 miRNA genes. Other experimental/computational sources support an additional 10 miRNAs encoded by 19 genes. The miRNAs can be classified into 87 distinct families. Cross-species comparison indicates that 81 families are conserved in mammals, 17 of which also have at least one member conserved in an invertebrate. Our analysis reveals that the zygotes are essentially devoid of miRNAs and that their expression begins during the blastula period with a zebrafish-specific family of miRNAs encoded by closely spaced multicopy genes. Computational predictions of zebrafish miRNA targets are provided that take into account the depth of evolutionary conservation. Besides miRNAs, we identified a prominent class of repeat-associated small interfering RNAs (rasiRNAs).
Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila
Authors: Blanchette Marco , Green Richard E. , Brenner Steven E. , Rio Donald C.
Published: June 2005

To gain insight into splicing regulation, we developed a microarray to assay all annotated alternative splicing events in Drosophila melanogaster and identified the alternative splice events controlled by four splicing regulators: dASF/SF2, B52/SRp55, hrp48, and PSI. The number of events controlled by each of these factors was found to be highly variable: dASF/SF2 strongly affects >300 splicing events, whereas PSI strongly affects only 43 events. Pairwise analysis also revealed many instances of splice site usage affected by multiple factors and provides the framework to understand the network controlling the alternatively spliced mRNA isoforms that compose the Drosophila transcriptome.
Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase
Authors: Couture Jean-François , Collazo Evys , Brunzelle Joseph S. , Trievel Raymond C.
Published: June 2005

SET8 (also known as PR-SET7) is a histone H4-Lys-20-specific methyltransferase that is implicated in cell-cycle-dependent transcriptional silencing and mitotic regulation in metazoans. Herein we report the crystal structure of human SET8 (hSET8) bound to a histone H4 peptide bearing Lys-20 and the product cofactor S-adenosylhomocysteine. Histone H4 intercalates in the substrate-binding cleft as an extended parallel β-strand. Residues preceding Lys-20 in H4 engage in an extensive array of salt bridge, hydrogen bond, and van der Waals interactions with hSET8, while the C-terminal residues bind through predominantly hydrophobic interactions. Mutational analysis of both the substrate-binding cleft and histone H4 reveals that interactions with residues in the N and C termini of the H4 peptide are critical for conferring substrate specificity. Finally, analysis of the product specificity indicates that hSET8 is a monomethylase, consistent with its role in the maintenance of Lys-20 monomethylation during cell division.
Dynamic molecular linkers of the genome: the first decade of SMC proteins
Authors: Losada Ana , Hirano Tatsuya
Published: June 2005

Structural maintenance of chromosomes (SMC) proteins are chromosomal ATPases, highly conserved from bacteria to humans, that play fundamental roles in many aspects of higher-order chromosome organization and dynamics. In eukaryotes, SMC1 and SMC3 act as the core of the cohesin complexes that mediate sister chromatid cohesion, whereas SMC2 and SMC4 function as the core of the condensin complexes that are essential for chromosome assembly and segregation. Another complex containing SMC5 and SMC6 is implicated in DNA repair and checkpoint responses. The SMC complexes form unique ring- or V-shaped structures with long coiled-coil arms, and function as ATP-modulated, dynamic molecular linkers of the genome. Recent studies shed new light on the mechanistic action of these SMC machines and also expanded the repertoire of their diverse cellular functions. Dissecting this class of chromosomal ATPases is likely to be central to our understanding of the structural basis of genome organization, stability, and evolution.
Functional analyses of mouse ASK, an activation subunit for Cdc7 kinase, using conditional ASK knockout ES cells
Authors: Yamashita Nobuyuki , Kim Jung‐Min , Koiwai Osamu , Arai Ken‐ichi , Masai Hisao
Published: June 2005

ASK (activator of S phase kinase) is an activation subunit for mammalian Cdc7 kinase. We have generated mutant ES cell lines in which ASK can be conditionally inactivated. Upon loss of the ASK genes, the mutant ES cells rapidly cease cell growth. In keeping with its expected roles in activation of the essential S phase kinase, DNA synthesis is arrested and significant cell death is eventually induced in ASK‐deficient cells, demonstrating essential roles of ASK for viability of ES cells. Using these mutant cells, we have set up a system where ASK molecules can be functionally dissected. In keeping with previous results from yeasts, conserved motif‐M and motif‐C were shown to be essential for in vivo functions of ASK, whereas a long C‐terminal tail, found only in ASK‐related molecules in higher eukaryotes, is not required. Unexpectedly, the motif‐N, related to the BRCT motif and dispensable for viability in yeasts, is essential for the viability of ES cells. Further characterization reveals that motif‐N is required for the maximum phosphorylation of MCM in cells, whereas the autophosphorylation activity of Cdc7 is not significantly affected by its loss. These results may suggest that motif‐N of ASK may facilitate recruitment of substrates for Cdc7 kinase.
Error‐prone and inefficient replication across 8‐hydroxyguanine (8‐oxoguanine) in human and mouse ras gene fragments by DNA polymerase κ
Authors: Jałoszyński Paweł , Ohashi Eiji , Ohmori Haruo , Nishimura Susumu
Published: June 2005

Using fragments of human c‐Ha‐ras and mouse Ha‐ras1 genes containing 8‐hydroxyguanine (8‐OH‐G) in hypermutagenic codon 12, we analyzed the kinetics of DNA synthesis catalyzed by human Polκ. This translesion DNA polymerase, belonging to the Y‐family, was found to be moderately inhibited by the presence of 8‐OH‐G on either mouse or human templates. From our previous results, inhibition of various polymerases by 8‐OH‐G increases in the following order: Polη < Polκ < Polβ < Polα, showing that major replicative and repair polymerases are more sensitive to this lesion than enzymes belonging to the Y‐family. In the direct mutagenesis experiments, Polκ was found to be more mutagenic than Polη studied previously: it inserted dAMP more efficiently than dCMP opposite 8‐OH‐G. Polκ was also able to cause indirect mispair (‘action‐at‐a‐distance’ mutagenesis), this effect being more distinct on mouse templates. Two adjacent 8‐OH‐G residues in codon 12 inhibited Polκ moderately and induced misincorporation of dAMP. However, this effect was not comparable to the strong relaxation of the enzyme specificity, observed previously in the case of Polη. Polκ catalyzed incorporation (and misincorporation of dAMP) much more efficiently on mouse templates, human DNA fragments being distinctly worse substrates. Interestingly, in direct mutagenesis systems, the preference for dAMP over dCMP was nearly the same on mouse and human templates.
Membrane‐type 1 matrix metalloproteinase cytoplasmic tail binding protein‐1 (MTCBP‐1) acts as an eukaryotic aci‐reductone dioxygenase (ARD) in the methionine salvage pathway
Authors: Hirano Wakako , Gotoh Isamu , Uekita Takamasa , Seiki Motoharu
Published: June 2005

MTCBP‐1 was identified as a protein that binds the cytoplasmic tail of membrane‐type 1 matrix metalloproteinase (MT1‐MMP/MMP‐14). Since MTCBP‐1 has a putative β‐barrel structure, it is presumably a member of the recently proposed cupin superfamily that contains tremendously diverged functions of proteins in spite of their well‐conserved β‐barrel structure. MTCBP‐1 shows significant homology to the bacterial aci‐reductone dioxygenase (ARD) in the cupin family, which is an enzyme in the methionine salvage pathway (MTA cycle). Since it is difficult to speculate the functions of cupin proteins simply based on their sequence homology, we examined whether the eukaryotic ARD homologs surely function in the methionine metabolism. Under sulfur‐depleted conditions, yeast could grow when substrate of MTA cycle was provided. Disruption of the yeast ARD homolog, YMR009w gene, abolished ability of the cells to grow in this culture condition. Re‐expression of either the YMR009w or MTCBP‐1 gene restored the cell growth. Mutation analysis revealed that the glutamic acid residue in the β‐barrel fold and the N‐terminal extension from the β‐barrel fold were found to be important for the activity to restore the growth. Thus, MTCBP‐1 isolated as a binding protein for MT1‐MMP was demonstrated to function as an ARD‐like enzyme in the MTA cycle in yeast.
Angiogenesis within the developing mouse neural tube is dependent on sonic hedgehog signaling: possible roles of motor neurons
Authors: Nagase Takashi , Nagase Miki , Yoshimura Kotaro , Fujita Toshiro , Koshima Isao
Published: June 2005

Embryonic morphogenesis of vascular and nervous systems is tightly coordinated, and recent studies revealed that some neurogenetic factors such as Sonic hedgehog (Shh) also exhibit angiogenetic potential. Vascularization within the developing mouse neural tube depends on vessel sprouting from the surrounding vascular plexus. Previous studies implicated possible roles of VEGF/Flk‐1 and Angiopoietin‐1(Ang‐1)/Tie‐2 signaling as candidate molecules functioning in this process. Examining gene expressions of these factors at embryonic day (E) 9.5 and 10.5, we unexpectedly found that both VEGF and Ang‐1 were expressed in the motor neurons in the ventral neural tube. The motor neurons were indeed located in the close vicinity of the infiltrating vessels, suggesting involvement of motor neurons in the sprouting. To substantiate this possibility, we inhibited induction of the motor neurons in the cultured mouse embryos by cyclopamine, a Shh signaling blocker. The vessel sprouting was dramatically impaired by inhibition of Shh signaling, together with nearly complete loss of the motor neurons. Expression of Ang‐1, but not VEGF, within the neural tube was remarkably reduced in the cyclopamine treated embryos. These results suggest that the neural tube angiogenesis is dependent on Shh signaling, and mediated, at least in part, by the Ang‐1 positive motor neurons.
Analysis of sulfur and selenium assimilation in Astragalus plants with varying capacities to accumulate selenium
Authors: Sors Thomas G. , Ellis Danielle R. , Na Gun Nam , Lahner Brett , Lee Sangman , Leustek Thomas , Pickering Ingrid J. , Salt David E.
Published: June 2005

Several Astragalus species have the ability to hyperaccumulate selenium (Se) when growing in their native habitat. Given that the biochemical properties of Se parallel those of sulfur (S), we examined the activity of key S assimilatory enzymes ATP sulfurylase (ATPS), APS reductase (APR), and serine acetyltransferase (SAT), as well as selenocysteine methyltransferase (SMT), in eight Astragalus species with varying abilities to accumulate Se. Se hyperaccumulation was found to positively correlate with shoot accumulation of S‐methylcysteine (MeCys) and Se‐methylselenocysteine (MeSeCys), in addition to the level of SMT enzymatic activity. However, no correlation was observed between Se hyperaccumulation and ATPS, APR, and SAT activities in shoot tissue. Transgenic Arabidopsis thaliana overexpressing both ATPS and APR had a significant enhancement of selenate reduction as a proportion of total Se, whereas SAT overexpression resulted in only a slight increase in selenate reduction to organic forms. In general, total Se accumulation in shoots was lower in the transgenic plants overexpressing ATPS, PaAPR, and SAT. Root growth was adversely affected by selenate treatment in both ATPS and SAT overexpressors and less so in the PaAPR transgenic plants. Such observations support our conclusions that ATPS and APR are major contributors of selenate reduction in planta. However, Se hyperaccumulation in Astragalus is not driven by an overall increase in the capacity of these enzymes, but rather by either an increased Se flux through the S assimilatory pathway, generated by the biosynthesis of the sink metabolites MeCys or MeSeCys, or through an as yet unidentified Se assimilation pathway.
Calcium regulation of chloroplast protein import
Authors: Chigri Fatima , Soll Jürgen , Vothknecht Ute C.
Published: June 2005

The majority of chloroplast proteins is nuclear‐encoded and therefore synthesized on cytosolic ribosomes. In order to enter the chloroplast, these proteins have to cross the double‐membrane surrounding the organelle. This is achieved by means of two hetero‐oligomeric protein complexes in the outer and inner envelope, the Toc and Tic translocon. The process of chloroplast import is highly regulated on both sides of the envelope membranes. Our studies indicate the existence of an undescribed mode of control for this process so far, at the same time providing further evidence that the chloroplast is integrated into the calcium‐signalling network of the cell. In pea chloroplasts, the calmodulin inhibitor Ophiobolin A as well as the calcium ionophores A23187 and Ionomycin affect the translocation of those chloroplast proteins that are imported with an N‐terminal cleavable presequence. Import of these proteins is inhibited in a concentration‐dependent manner. Addition of external calmodulin or calcium can counter the effect of these inhibitors. Translocation of chloroplast proteins that do not possess a cleavable transit peptide, that is outer envelope proteins or the inner envelope protein Tic32, is not affected. These results suggest that the import of a certain subset of chloroplast proteins is regulated by calcium. Our studies furthermore indicate that this regulation occurs downstream of the Toc translocon either within the intermembrane space or at the inner envelope translocon. A potential promoter of the calcium regulation is calmodulin, a protein well known as part of the plant's calcium signalling system.