bluuebunny/crossref_metadata_2025 huggingface dataset:
Pulsed-field ionization photoelectron and IR-UV resonant photoionization spectroscopy of Al-thymine
Authors: Krasnokutski Serge A. , Lei Yuxiu , Lee Jung Sup , Yang Dong-Sheng
Published: September 2008

Al-thymine (Al–C4H3N2O2CH3) is produced by laser vaporization of a rod made of Al and thymine powders in a molecular beam and studied by single-photon pulsed-field ionization-zero electron kinetic energy (ZEKE) photoelectron and IR-UV resonant two-photon ionization spectroscopy and density functional theory calculations. The ZEKE experiment determines the adiabatic ionization energy of the neutral complex and 22 vibrational modes for the corresponding ion with frequencies below 2000 cm−1. The IR-UV photoionization experiment measures two N–H and three C–H stretches for the neutral species. The theoretical calculations predict a number of low-energy isomers with Al binding to single oxygen or adjacent oxygen and nitrogen atoms of thymine. Among these isomers, the structure with Al binding to the O4 atom of the diketo tautomer is predicted to be the most stable one by the theory and is probed by both ZEKE and IR-UV measurements. This work presents the first application of the IR-UV resonant ionization to metal-organic molecule systems. Like ZEKE spectroscopy, the IR-UV photoionization technique is sensitive for identifying isomeric structures of metal association complexes.
Graphene interferometer
Authors: Gunlycke D. , White C. T.
Published: September 2008

Ballistic transport calculations, which are treated exactly within the nearest-neighbor tight-binding theory, on graphene strips connected to a pair of contacts are presented. In strips with high width-to-length ratio, the calculations reveal the presence of groups of resonances from a large number of nonequivalent conductance channels. While the energies of the collective resonances are, to first order, uniformly spaced and only depend on the contact separation, their contrast also depends on the strip width and contact interfaces.
The magnetic field induced strain without prestress and with stress in a polycrystalline Mn–Fe–Cu antiferromagnetic alloy
Authors: Zhang J. H. , Peng W. Y. , Hsu (Xu Zuyao) T. H.
Published: September 2008

In this paper magnetic field induced strain (MFIS) of an antiferromagnetic γMn–Fe(Cu) is investigated. It is discovered that there is a high reversible MFIS of 1.6% with positive strain parallel to applied magnetic field at 3.8 T and ultimate negative strain of −0.15% at 1 T in the same way parallel to applied magnetic field after a precompressive stress (strain). The qualitative analysis of positive strain without prestress and the negative strain with precompressive stress under the same condition of applied magnetic field is discussed.
Transition from Casimir to van der Waals force between macroscopic bodies
Authors: Palasantzas G. , van Zwol P. J. , De Hosson J. Th. M.
Published: September 2008

The transition of van der Waals to Casimir forces between macroscopic gold surfaces is investigated by atomic force microscopy in the plane-sphere geometry. It was found that the transition appears to take place at separations ∼10% the plasma wavelength λp for evaporated gold surfaces, which compares to theoretical predictions by incorporation of experimental optical data and roughness corrections. Moreover, the force data allow estimation of the Hamaker constant AH in the van der Waals regime, which is in good agreement with the Lifshitz theory predictions (even if roughness corrections are taken into account) and former surface force apparatus measurements.
Carbon clusters in N-doped ZnO by metal-organic chemical vapor deposition
Authors: Tang Kun , Gu Shulin , Zhu Shunming , Liu Wei , Ye Jiandong , Zhu Jianmin , Zhang Rong , Zheng Youdou , Sun Xiaowei
Published: September 2008

We employed transmission electron microscopy and Raman spectra to investigate the behavior of impurity carbon usually unintentionally introduced in N-doped ZnO by metal-organic chemical vapor deposition. Unintentional doped carbon may form graphite clusters along grain boundaries resulting in n-type domains and possibly be a big obstacle for the realization of p-type conductivity. The enhanced desorption rate of hydrocarbon radicals by high temperature and oxygen atom will significantly suppress carbon incorporation rate. The results provide understandings of the formation mechanism of carbon clusters and help us find some available routines to minimize carbon impurity for realization of p-type N-doped ZnO.
Rough conical-shaped TiO2-nanotube arrays for flexible backilluminated dye-sensitized solar cells
Authors: Lin Chin-Jung , Yu Wen-Yueh , Chien Shu-Hua
Published: September 2008

Conical-shaped anodic TiO2-nanotube (TiNT) arrays with length of a few tens of micrometer and rough tube walls were fabricated for use in flexible backilluminated dye-sensitized solar cells (DSSCs) which exhibited conversion efficiency of 4.3% under AM1.5 back side illumination. As compared to TiO2 nanoparticles/Ti-based DSSC, TiNT/Ti-based DSSC showed enhanced light-harvesting efficiency, rapid electron-transport rate, prolonged electron lifetime, and reduced dark current, leading to an increase in efficiency by ∼30%.
Investigations on the self propagating reactions of nickel and aluminum multilayered foils
Authors: Gunduz Ibrahim Emre , Fadenberger Konrad , Kokonou Maria , Rebholz Claus , Doumanidis Charalabos C.
Published: September 2008

The self-propagating reaction of nickel-aluminum thin film multilayers with a bilayer thickness of ∼43 nm was investigated using high-speed optical camera and infrared thermometry. The results indicate a two-stage reaction with two different characteristic temperatures. Following ignition, the flame front propagates near the reverse peritectic transformation temperature of Ni2Al3 into NiAl and liquid at 1406 K. The reaction continues with the growth of NiAl until the melting temperature of 1911 K is reached. The reaction mechanism and kinetics are discussed.
Galileo's Eye: A New Vision of the Senses in the Work of Galileo Galilei
Authors: Piccolino Marco , Wade Nicholas J
Published: September 2008

Reflections on the senses, and particularly on vision, permeate the writings of Galileo Galilei, one of the main protagonists of the scientific revolution. This aspect of his work has received scant attention by historians, in spite of its importance for his achievements in astronomy, and also for the significance in the innovative scientific methodology he fostered. Galileo's vision pursued a different path from the main stream of the then contemporary studies in the field; these were concerned with the dioptrics and anatomy of the eye, as elaborated mainly by Johannes Kepler and Christoph Scheiner. Galileo was more concerned with the phenomenology rather than with the mechanisms of the visual process. His general interest in the senses was psychological and philosophical; it reflected the fallacies and limits of the senses and the ways in which scientific knowledge of the world could be gathered from potentially deceptive appearances. Galileo's innovative conception of the relation between the senses and external reality contrasted with the classical tradition dominated by Aristotle; it paved the way for the modern understanding of sensory processing, culminating two centuries later in Johannes Müller's elaboration of the doctrine of specific nerve energies and in Helmholtz's general theory of perception.
A common variant in the 3′UTR of the
GRIK4
glutamate receptor gene affects transcript abundance and protects against bipolar disorder
Authors: Pickard B. S. , Knight H. M. , Hamilton R. S. , Soares D. C. , Walker R. , Boyd J. K. F. , Machell J. , Maclean A. , McGhee K. A. , Condie A. , Porteous D. J. , St. Clair D. , Davis I. , Blackwood D. H. R. , Muir W. J.
Published: September 2008

Underactivity of the glutamatergic system is an attractive model for the pathophysiology of several major mental illnesses. We previously described a chromosome abnormality disrupting the kainate class ionotropic glutamate receptor gene,
GRIK4
/
KA1
, in an individual with schizophrenia and learning disability (mental retardation). We also demonstrated in a case-control study that two physically separated haplotypes within this gene were significantly associated with increased risk of schizophrenia and decreased risk of bipolar disorder, respectively. The latter protective haplotype was located at the 3′ end of the gene. We now report the identification from carriers of the protective haplotype of a deletion variant within the 3′ untranslated region of the gene. The deletion allele also was found to be negatively associated with bipolar disorder in both initial (
P
= 0.00000019) and replication (
P
= 0.0107) case-control studies. Expression studies indicated that deletion-carrying mRNA transcripts were relatively more abundant. We postulate that this may be a direct consequence of the differences in the RNA secondary structures predicted for the insertion and deletion alleles. These data suggest a mechanism whereby the genetic protective effect is mediated through increased kainate receptor expression.
Tetrapyrrole profiling in
Arabidopsis
seedlings reveals that retrograde plastid nuclear signaling is not due to Mg-protoporphyrin IX accumulation
Authors: Moulin Michael , McCormac Alex C. , Terry Matthew J. , Smith Alison G.
Published: September 2008

Chloroplast biogenesis involves careful coordination of both plastid and nuclear gene expression, which is achieved in part by retrograde signaling from the chloroplast to the nucleus. This can be demonstrated by the fact that the herbicide, Norflurazon (NF), which causes bleaching of chloroplasts, prevents the light induction of photosynthesis-related genes in the nucleus. It has been proposed that the tetrapyrrole pathway intermediate Mg-protoporphyrin IX acts as the signaling molecule in this pathway and accumulates in the chloroplasts and cytosol of the cell after NF treatment. Here we present data that demonstrate that this model is too simplistic. We have developed a sensitive liquid chromatography-mass spectrometry (LC/MS) method to measure tetrapyrrole intermediates and have shown that no Mg-protoporphyrin IX, nor indeed any other chlorophyll-biosynthesis intermediate, can be detected in NF-treated plants under conditions in which nuclear gene expression is repressed. Conversely when endogenous Mg-protoporphyrin IX levels are artificially increased by supplementation with the tetrapyrrole precursor, 5-aminolevulinic acid, the expression of nuclear-encoded photosynthetic genes is induced, not repressed. We also demonstrate that NF-treatment leads to a strong down-regulation of tetrapyrrole biosynthesis genes, consistent with the absence of an accumulation of tetrapyrrole intermediates. Finally, there is no correlation between nuclear-gene expression and any of the chlorophyll biosynthetic intermediates over a range of growth conditions and treatments. Instead, it is possible that a perturbation of tetrapyrrole synthesis may lead to localized ROS production or an altered redox state of the plastid, which could mediate retrograde signaling.
Probing atomic ordering and multiple twinning in metal nanocrystals through their vibrations
Authors: Portales H. , Goubet N. , Saviot L. , Adichtchev S. , Murray D. B. , Mermet A. , Duval E. , Pileni M.-P.
Published: September 2008

Control of nanocrystal (NC) crystallinity currently raises great interest because of its potential benefits in both physics modeling and technological applications. Advances in methods for synthesizing perfect single-crystalline NCs are recent, so that the effect of crystallinity on NC properties has received only limited study and still needs to be properly investigated. Here, we report that crystallinity of gold NCs dramatically modifies their vibrations. Using low-frequency Raman scattering, we clearly demonstrate that single-domain NCs vibrate differently than their multiply twinned counterparts, through the splitting of the quadrupolar vibrations, which is only observed for the former. Using the resonant ultrasound approach, we calculate the vibrational frequencies of a gold sphere and show that elastic anisotropy induces a lift of degeneracy of the quadrupolar mode in good agreement with our experimental measurements. These findings open up challenging perspectives on using Raman spectroscopy to characterize nanocrystallinity.
Thresholds of hypoxia for marine biodiversity
Authors: Vaquer-Sunyer Raquel , Duarte Carlos M.
Published: September 2008

Hypoxia is a mounting problem affecting the world's coastal waters, with severe consequences for marine life, including death and catastrophic changes. Hypoxia is forecast to increase owing to the combined effects of the continued spread of coastal eutrophication and global warming. A broad comparative analysis across a range of contrasting marine benthic organisms showed that hypoxia thresholds vary greatly across marine benthic organisms and that the conventional definition of 2 mg O
2
/liter to designate waters as hypoxic is below the empirical sublethal and lethal O
2
thresholds for half of the species tested. These results imply that the number and area of coastal ecosystems affected by hypoxia and the future extent of hypoxia impacts on marine life have been generally underestimated.
Emergence of hormonal and redox regulation of galectin-1 in placental mammals: Implication in maternal–fetal immune tolerance
Authors: Than Nandor Gabor , Romero Roberto , Erez Offer , Weckle Amy , Tarca Adi L. , Hotra John , Abbas Asad , Han Yu Mi , Kim Sung-Su , Kusanovic Juan Pedro , Gotsch Francesca , Hou Zhuocheng , Santolaya-Forgas Joaquin , Benirschke Kurt , Papp Zoltan , Grossman Lawrence I. , Goodman Morris , Wildman Derek E.
Published: September 2008

Galectin-1 is an anti-inflammatory lectin with pleiotropic regulatory functions at the crossroads of innate and adaptive immunity. It is expressed in immune privileged sites and is implicated in establishing maternal–fetal immune tolerance, which is essential for successful pregnancy in eutherian mammals. Here, we show conserved placental localization of galectin-1 in primates and its predominant expression in maternal decidua. Phylogenetic footprinting and shadowing unveil conserved
cis
motifs, including an estrogen responsive element in the 5′ promoter of
LGALS1
, that were gained during the emergence of placental mammals and could account for sex steroid regulation of
LGALS1
expression, thus providing additional evidence for the role of galectin-1 in immune–endocrine cross-talk. Maximum parsimony and maximum likelihood analyses of 27 publicly available vertebrate and seven newly sequenced primate
LGALS1
coding sequences reveal that intense purifying selection has been acting on residues in the carbohydrate recognition domain and dimerization interface that are involved in immune functions. Parsimony- and codon model-based phylogenetic analysis of coding sequences show that amino acid replacements occurred in early mammalian evolution on key residues, including gain of cysteines, which regulate immune functions by redox status-mediated conformational changes that disable sugar binding and dimerization, and that the acquired immunoregulatory functions of galectin-1 then became highly conserved in eutherian lineages, suggesting the emergence of hormonal and redox regulation of galectin-1 in placental mammals may be implicated in maternal–fetal immune tolerance.
The Scholar as Nation-Builder, or as Advisor and Advocate: Remarks Delivered by Paul Robert Magocsi (Chair of Ukrainian Studies, University of Toronto) for the Special Panel “Paul Robert Magocsi on the Scholar as a Nation-Builder” at the ASN 2007 World Convention, Columbia University
Authors: Magocsi Paul Robert
Published: September 2008

The Czech philosopher Tomáš G. Masaryk was a scholar and nation-builder; the Romanian historian Nicolae Iorga was a scholar and nation-builder; the Ukrainian historian Mykhailo Hrushevs'kyi was a scholar and nation-builder; Paul Robert Magocsi is a scholar but not a nation-builder. Unlike the first three distinguished figures, the North American Magocsi never lived in any country among any people that was in need of being “built.” At best he may be considered an advocate or a promoter of a nationality; that is, a people in search of a distinct identity recognizable to themselves and to others.
Outcomes approaches to assessment: comparing non‐government and government case‐study schools in Western Australia
Authors: Griffiths Joanne , Vidovich Lesley , Chapman Anne
Published: September 2008

A key feature of recent curriculum reform in post‐industrialised liberal economies has been the ascendancy of outcomes‐based education policies. A 1995 review conducted in Western Australia (WA) recommended an outcomes‐based approach, and in response, the Curriculum Framework (CF) was released in 1998. The same year, the WA State government mandated that all schools, both non‐government and government, demonstrate compliance with the outcomes‐based CF for Years K–10 by 2004. This article compares case‐studies of non‐government and government schools in analysing assessment and reporting issues in relation to the enactment of outcomes‐based curriculum policy in the mid‐2000s. With significantly different localised contexts, including different degrees of institutional autonomy and different approaches to curriculum, assessment and reporting, interesting contrasts and commonalities arose as each school engaged with the new policy. The research draws on a hybrid approach to policy analysis, incorporating both critical theory and post‐structuralism with their different conceptualisations of power relationships. In‐depth semi‐structured interviews were conducted to examine and analyse the views of participants at each site. Although there is no intention to generalise from individual case‐studies, cross‐case analysis reveals the emergence of meta‐level themes – such as market choice, accountability and teacher professionalism – which are associated with ‘bigger picture’ issues of power and which may well provide insights for explorations of curriculum reform in other contexts.
The Death Receptor 3–TNF-like protein 1A pathway drives adverse bone pathology in inflammatory arthritis
Authors: Bull Melanie Jane , Williams Anwen Siân , Mecklenburgh Zarabeth , Calder Claudia Jane , Twohig Jason Peter , Elford Carole , Evans Bronwen Alice James , Rowley Tania F. , Slebioda Tomasz J. , Taraban Vadim Y. , Al-Shamkhani Aymen , Wang Eddie Chung Yern
Published: September 2008

Rheumatoid arthritis (RA) is a chronic inflammatory disease of synovial joints that is associated with cartilage and bone destruction. Death Receptor 3 (DR3), a tumor necrosis factor (TNF) receptor superfamily member, has recently been associated with the pathogenesis of RA. We demonstrate that absence of DR3 confers resistance to the development of adverse bone pathology in experimental antigen-induced arthritis (AIA). DR3ko mice exhibited a reduction in all histopathological hallmarks of AIA but, in particular, failed to develop subchondral bone erosions and were completely protected from this characteristic of AIA. In contrast, TNF-like protein 1A (TL1A), the ligand for DR3, exacerbated disease in a dose- and DR3-dependent fashion. Analysis of osteoclast number within AIA joint revealed a reduction in areas susceptible to bone erosion in DR3ko mice, whereas in vitro osteoclastogenesis assays showed that TL1A could directly promote osteoclastogenesis in mouse and man. Treatment with antagonistic anti-TL1A mAb protected animals in a systemic model of RA disease collagen-induced arthritis. We therefore conclude that the DR3–TL1A pathway regulates joint destruction in two murine models of arthritis and represents a potential novel target for therapeutic intervention in inflammatory joint disease.
Mind bomb 1 in the lymphopoietic niches is essential for T and marginal zone B cell development
Authors: Song Ran , Kim Young-Woong , Koo Bon-Kyoung , Jeong Hyun-Woo , Yoon Mi-Jeong , Yoon Ki-Jun , Jun Dong-Jae , Im Sun-Kyoung , Shin Juhee , Kong Myoung-Phil , Kim Kyong-Tai , Yoon Keejung , Kong Young-Yun
Published: September 2008

Notch signaling regulates lineage decisions at multiple stages of lymphocyte development, and Notch activation requires the endocytosis of Notch ligands in the signal-sending cells. Four E3 ubiquitin ligases, Mind bomb (Mib) 1, Mib2, Neuralized (Neur) 1, and Neur2, regulate the Notch ligands to activate Notch signaling, but their roles in lymphocyte development have not been defined. We show that Mib1 regulates T and marginal zone B (MZB) cell development in the lymphopoietic niches. Inactivation of the Mib1 gene, but not the other E3 ligases, Mib2, Neur1, and Neur2, abrogated T and MZB cell development. Reciprocal bone marrow (BM) transplantation experiments revealed that Mib1 in the thymic and splenic niches is essential for T and MZB cell development. Interestingly, when BM cells from transgenic Notch reporter mice were transplanted into Mib1-null mice, the Notch signaling was abolished in the double-negative thymocytes. In addition, the endocytosis of Dll1 was impaired in the Mib1-null microenvironment. Moreover, the block in T cell development and the failure of Dll1 endocytosis were also observed in coculture system by Mib1 knockdown. Our study reveals that Mib1 is the essential E3 ligase in T and MZB cell development, through the regulation of Notch ligands in the thymic and splenic microenvironments.
Comprehensive simulation of vertical plasma instability events and their serious damage to ITER plasma facing components
Authors: Hassanein A. , Sizyuk T.
Published: September 2008

Safe and reliable operation is still one of the major challenges in the development of the new generation of ITER-like fusion reactors. The deposited plasma energy during major disruptions, edge-localized modes (ELMs) and vertical displacement events (VDEs) causes significant surface erosion, possible structural failure and frequent plasma contamination. While plasma disruptions and ELM will have no significant thermal effects on the structural materials or coolant channels because of their short deposition time, VDEs having longer-duration time could have a destructive impact on these components. Therefore, modelling the response of structural materials to VDE has to integrate detailed energy deposition processes, surface vaporization, phase change and melting, heat conduction to coolant channels and critical heat flux criteria at the coolant channels. The HEIGHTS 3D upgraded computer package considers all the above processes to specifically study VDE in detail. Results of benchmarking with several known laboratory experiments prove the validity of HEIGHTS implemented models. Beryllium and tungsten are both considered surface coating materials along with copper structure and coolant channels using both smooth tubes with swirl tape insert. The design requirements and implications of plasma facing components are discussed along with recommendations to mitigate and reduce the effects of plasma instabilities on reactor components.
Indicators and scientific knowledge in regional Baltic Sea environmental policy
Authors: Backer Hermanni
Published: September 2008

Backer, H. 2008. Indicators and scientific knowledge in regional Baltic Sea environmental policy. – ICES Journal of Marine Science, 65: 1398–1401. Since the 1990s, indicators have emerged as key tools used by the Helsinki Commission (HELCOM) for drafting regional Baltic Sea management actions and monitoring their implementation. The central role played by indicators in recent years can readily be seen in the 2007 Baltic Sea Action Plan (BSAP), where they have been used for defining quantitative targets and management actions and for providing background information. Similarly, the currently available, annually updated, web-based indicators include performance indicators with quantitative reference and target values, and descriptive indicators without such values. In addition to good indicators, implementation of the ecosystem approach, as is the aim of the BSAP as well as the newly adopted European Marine Strategy Framework Directive, requires extensive implementation of the precautionary principle and related concepts.
Volcanism and the atmosphere: the potential role of the atmosphere in unlocking the reactivity of volcanic emissions
Authors: Mather Tamsin A
Published: September 2008

Recent measurements of reactive trace gas species in volcanic plumes have offered intriguing hints at the chemistry occurring in the hot environment at volcanic vents. This has led to the recognition that volcanic vents should be regarded not only as passive sources of volcanic gases to the atmosphere, but also as ‘reaction vessels’ that unlock otherwise inert volcanic and atmospheric gas species. The atypical conditions created by the mixing of ambient atmosphere with the hot gases emitted from magma give rise to elevated concentrations of otherwise unexpected chemical compounds. Rapid cooling of this mixture allows these species to persist into the environment, with important consequences for gas plume chemistry and impacts. This paper discusses some examples of the implications of these high-temperature interactions in terms of nitrogen, halogen and sulphur chemistry, and their consequences in terms of the global fixed nitrogen budget, volcanically induced ozone destruction and particle fluxes to the atmosphere. Volcanically initiated atmospheric chemistry was likely to have been particularly important before biological (and latterly anthropogenic) processes started to dominate many geochemical cycles, with important consequences in terms of the evolution of the nitrogen cycle and the role of particles in modulating the Earth's climate.
Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
Authors: Cheng Yong , King David C. , Dore Louis C. , Zhang Xinmin , Zhou Yuepin , Zhang Ying , Dorman Christine , Abebe Demesew , Kumar Swathi A. , Chiaromonte Francesca , Miller Webb , Green Roland D. , Weiss Mitchell J. , Hardison Ross C.
Published: September 2008

Tissue development and function are exquisitely dependent on proper regulation of gene expression, but it remains controversial whether the genomic signals controlling this process are subject to strong selective constraint. While some studies show that highly constrained noncoding regions act to enhance transcription, other studies show that DNA segments with biochemical signatures of regulatory regions, such as occupancy by a transcription factor, are seemingly unconstrained across mammalian evolution. To test the possible correlation of selective constraint with enhancer activity, we used chromatin immunoprecipitation as an approach unbiased by either evolutionary constraint or prior knowledge of regulatory activity to identify DNA segments within a 66-Mb region of mouse chromosome 7 that are occupied by the erythroid transcription factor GATA1. DNA segments bound by GATA1 were identified by hybridization to high-density tiling arrays, validated by quantitative PCR, and tested for gene regulatory activity in erythroid cells. Whereas almost all of the occupied segments contain canonical WGATAR binding site motifs for GATA1, in only 45% of the cases is the motif deeply preserved (found at the orthologous position in placental mammals or more distant species). However, GATA1-bound segments with high enhancer activity tend to be the ones with an evolutionarily preserved WGATAR motif, and this relationship was confirmed by a loss-of-function assay. Thus, GATA1 binding sites that regulate gene expression during erythroid maturation are under strong selective constraint, while nonconstrained binding may have only a limited or indirect role in regulation.
A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L.
Authors: Chistiakov D. A. , Tsigenopoulos C. S. , Lagnel J. , Guo Y.‐M. , Hellemans B. , Haley C. S. , Volckaert F. A. M. , Kotoulas G.
Published: September 2008

European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) sustains a regional fishery and is commonly farmed in the Mediterranean basin, but has not undergone much long‐term genetic improvement. An updated genetic linkage map of the European sea bass was constructed using 190 microsatellites, 176 amplified fragment length polymorphisms and two single nucleotide polymorphisms. From the 45 new microsatellite markers (including 31 type I markers) reported in this study, 28 were mapped. A total of 368 markers were assembled into 35 linkage groups. Among these markers, 28 represented type I (coding) markers, including those located within the peptide Y, SOX10, PXN1, ERA and TCRB genes (linkage groups 1, 7, 16, 17 and 27 respectively). The sex‐averaged map spanned 1373.1 centimorgans (cM) of the genome. The female map measured 1380.0 cM, whereas the male map measured 1046.9 cM, leading to a female‐to‐male (F:M) recombination rate ratio of 1.32:1. The intermarker spacing of the second‐generation linkage map of the European sea bass was 3.67 cM, which is smaller than that of the first‐generation linkage map (5.03 cM). Comparative mapping of microsatellite flanking regions was performed with five model teleosts and this revealed a high percentage (33.6%) of evolutionarily conserved regions with the three‐spined stickleback.
SNP discovery in Litopenaeus vannamei with a new computational pipeline
Authors: Gorbach D. M. , Hu Z.‐L. , Du Z.‐Q. , Rothschild M. F.
Published: September 2008

Litopenaeus vannamei (Pacific white shrimp) have been farmed in the Americas for many years and are growing in popularity in Asia with the development of specific pathogen‐free stocks. The full genomic sequence of this species might not be available in the near future, so other tools are needed to discover the location of polymorphic sites for quantitative trait loci mapping, association studies and subsequent marker‐assisted selection. Currently, 25 937 L. vannamei expressed sequence tags (ESTs) are publicly available. These sequences were manually screened, masked for tandem repeats and inputted into CAP3 for clustering. The resulting 3532 contigs were analysed for possible single nucleotide polymorphisms (SNPs) with snpidentifier, a newly developed computer program for predicting SNPs. snpidentifier is designed for ESTs without accompanying chromatogram sequence quality information, and therefore it performs quality control checks on all data. snpidentifier sets a threshold such that the sequences used have a poor quality nucleotide (N) frequency <0.1, and it trims off the first 10 bases of every sequence to ensure higher sequence quality. For a base to be predicted as an SNP, the minor nucleotide (allele) frequency must be >0.1, it must be observed at least four times and the 15 bases on either side must exactly match the consensus sequence. Using these conservative parameters, 504 SNPs were predicted from 141 contigs for L. vannamei. A small sample of 18 individuals from three lines have been sequenced to verify prediction results and 17 of 39 (44%) of the tested SNPs have been confirmed.
Timber import and the risk of forest pest introductions
Authors: Skarpaas Olav , Økland Bjørn
Published: September 2008

Many invasive species are introduced by trade, and there is a need for studies of pre‐emptive measures to lower the risk of introductions, as post‐establishment management is often extremely costly or nearly impossible.

In this study, we present a generic model for the first step of the invasion process for trade‐imported pests, and further develop this model for potentially harmful bark beetles to assess the risk of introductions and alternative management options.

Our results suggest that introductions of bark beetles are likely, given present timber import practices, and that immigration may often go undetected by pheromone traps.

The most effective measures for reducing introduction risk were those aimed at isolating the storage from forest (storage enclosure, location) followed by those reducing the available resources for forest pests (debarking, timber irrigation, rapid processing), whereas delayed import was least effective.

Synthesis and applications: The generic model framework of species introductions presented here may easily be adapted to other import systems. The submodels of population dynamics and dispersal are also quite general, and we expect our qualitative results to hold in many cases, although the models were parameterized for bark beetles in this study. Our results suggest that detection of dispersal from storage to forests will be difficult, which implies that management actions should not be deferred until after detection in nature, as the pest species may then already be established and eradication may be too late. However, pre‐emptive measures reducing propagule pressure at one or several stages of the introduction process, in particular isolation measures, may strongly reduce introduction risk.
A conserved domain of previously unknown function in Gap1 mediates protein–protein interaction and is required for biogenesis of a serine‐rich streptococcal adhesin
Authors: Li Yirong , Chen Yabing , Huang Xiang , Zhou Meixian , Wu Ren , Dong Shengli , Pritchard David G. , Fives‐Taylor Paula , Wu Hui
Published: September 2008

Fap1‐like serine‐rich proteins are a new family of bacterial adhesins found in a variety of streptococci and staphylococci that have been implicated in bacterial pathogenesis. A gene cluster encoding glycosyltransferases and accessory Sec components is required for Fap1 glycosylation and biogenesis in Streptococcus parasanguinis. Here we report that the glycosylation‐associated protein, Gap1, contributes to glycosylation and biogenesis of Fap1 by interacting with another glycosylation‐associated protein, Gap3. Gap1 shares structural homology with glycosyltransferases. The gap1 mutant, like the gap3 mutant, produced an aberrantly glycosylated Fap1 precursor and failed to produce mature Fap1, suggesting that Gap1 and Gap3 might function in concert in the Fap1 glycosylation and biogenesis. Indeed, Gap1 interacted with Gap3 in vitro and in vivo. A Gap1 N‐terminal motif, within a highly conserved domain of unknown function (DUF1975) identified in many bacterial glycosyltransferases, was required for the Gap1–Gap3 interaction. Deletion of one, four and nine amino acids within the conserved motif gradually inhibited the Gap1–Gap3 interaction and diminished production of mature Fap1 and concurrently increased production of the Fap1 precursor. Consequently, bacterial adhesion to an in vitro tooth model was also reduced. These data demonstrate that the Gap1–Gap3 interaction is required for Fap1 biogenesis and Fap1‐dependent bacterial adhesion.
Ferritins control interaction between iron homeostasis and oxidative stress in Arabidopsis
Authors: Ravet Karl , Touraine Brigitte , Boucherez Jossia , Briat Jean‐François , Gaymard Frédéric , Cellier Françoise
Published: September 2008

Ferritin protein nanocages are the main iron store in mammals. They have been predicted to fulfil the same function in plants but direct evidence was lacking. To address this, a loss‐of‐function approach was developed in Arabidopsis. We present evidence that ferritins do not constitute the major iron pool either in seeds for seedling development or in leaves for proper functioning of the photosynthetic apparatus. Loss of ferritins in vegetative and reproductive organs resulted in sensitivity to excess iron, as shown by reduced growth and strong defects in flower development. Furthermore, the absence of ferritin led to a strong deregulation of expression of several metal transporters genes in the stalk, over‐accumulation of iron in reproductive organs, and a decrease in fertility. Finally, we show that, in the absence of ferritin, plants have higher levels of reactive oxygen species, and increased activity of enzymes involved in their detoxification. Seed germination also showed higher sensitivity to pro‐oxidant treatments. Arabidopsis ferritins are therefore essential to protect cells against oxidative damage.
The majority of HLA‐DR3 alloreactive T cells is peptide specific, but does not recognize known DR3‐bound sequences
Authors: de Koster H.S. , Vermeulen C.J. , Koning F.
Published: September 2008

Abstract: Rejection of transplants is frequently caused by activation of alloreactive T cells that recognize HLA/peptide differences between patient and graft. This T‐cell response can be directed towards the HLA molecule, the HLA‐bound peptide or towards a combination. More insight in the involvement of peptides in this process may help to find ways to avoid rejection using for example antagonist peptides. In recent years many naturally processed HLA‐bound peptides have been identified. This raises the question of whether these, presumably abundant, peptides are involved in class ri‐specific allorecognition. To investigate this, we first determined the proportion of peptide‐specific alloreactive T cells in the alloresponse against HLA‐DR3. For this purpose we have tested a panel of DR3‐specific alloreactive T‐cell clones against a DM‐mutant (i.e. peptide loading deficient) cell line. We found that 59 out of 64 alloreactive T‐cell clones were dependent upon the presence of DM for an optimal response. However, only 2 DM‐dependent T‐cell clones recognize known peptide sequences. Thus we conclude that most DR3‐specific alloreactive T‐cell clones are peptide specific and that the currently known DR3‐bound peptides are not the main target for allorecognitioa Finally, we identified 4 T‐cell clones that recognized the DM‐mutant better than the wild‐type cell line. The response against the wild‐type cell line could not be restored with invariant chain derived peptides (CLIP). This provides additional evidence that DM can negatively select self‐peptides other than CLIP, which can result in selection against peptides involved in allorecognition.
Effects of childhood physical abuse on depression, problem drinking and perceived poor health status in adolescents living in rural Taiwan
Authors: Yen Cheng‐Fang , Yang Mei‐Sang , Chen Cheng‐Chih , Yang Ming‐Jen , Su Yi‐Ching , Wang Mei‐Hua , Lan Chu‐Mei
Published: September 2008

Aims:  The aim of the present study was to investigate the magnitude and independence of the effects of childhood physical abuse on adolescent depression, problem drinking and perceived poor mental health in Taiwanese indigenous and non‐indigenous adolescents living in rural areas controlling for individual and familial characteristics.

Methods:  A sample of adolescents was randomly selected from junior high schools in the rural areas of southern Taiwan. The associations between childhood physical abuse and adolescent depression, problem drinking and perceived poor health status were examined on univariate and multivariate logistic regression.

Results:  Of the 1684 adolescents who completed the questionnaires, 374 (22.2%) reported that they had experienced physical abuse in childhood. Controlling for individual and familial factors, childhood physical abuse significantly increased the risk of depression, problem drinking and perceived poor health status in the present sample of adolescents on multivariate logistic regression.

Conclusion:  History of childhood physical abuse should be elicited from adolescents in treatment for depression, alcohol abuse or physical discomfort of unknown etiology. This finding may be of clinical benefit in terms of the design and implementation of intervention.
Exploring the burden of the primary family caregivers of schizophrenia patients in Taiwan
Authors: Hou Shu‐Ying , Ke Chiao‐Li Khale , Su Yi‐Ching , Lung For‐Wey , Huang Chun‐Jen
Published: September 2008

Aim: The purpose of the present study was to investigate the burden of the primary family caregivers of schizophrenia patients and the factors that affect caregiver burden.

Methods: A total of 126 pairs of patients and their primary family caregivers were recruited from the day care and acute wards of two teaching general hospitals. Demographic information was collected. All patients went through an interview with a senior psychiatrist using the Brief Psychiatric Rating Scale (BPRS). The Caregiver Burden Inventory–Brief Version and the Chinese Health Questionnaire (CHQ) were used to assess the caregiver burden and the caregivers' health condition. One‐way analysis of variance and Pearson correlation were used to analyze the relationship between demographic factors and caregiver burden. Multiple regression was used to analyze predictors of burden of caregivers. Statistical significance in this study was defined asP ≤ 0.05.

Results: The caregiver burden scores (25.9 ± 10.7; range, 3–61) indicated a moderate burden level. Among the five dimensions of burden, caregiver anxiety (2.13 ± 0.86) was the highest, followed by dependency of the patient (1.85 ± 1.02), feeling shame and guilt (1.56 ± 1.02), and family interference (1.43 ± 0.83). The burden level of stigmata (1.32 ± 1.24) was the lowest. The first three rankings of burden were ‘I worry about his/her safety when he/she is alone’ (2.26 ± 1.15), ‘I worry that she/he will become sick at any time’ (2.23 ± 1.10), and ‘I feel he/she depends on me very much’ (2.02 ± 1.29). Patient satisfaction with medical staff support (P = 0.00), CHQ scores of the caregivers (P = 0.00), and the BPRS scores of the patients (P = 0.01) were significantly associated with the caregiver burden scores.

Conclusions: The physical and mental health condition of the primary family caregiver of schizophrenia patients was the most important factor determining the caregiver burden level. Comprehensive multidisciplinary care of chronic schizophrenia patients is needed, care that supports the needs and improves the psychiatric symptoms of the patients, helps to decrease the caregiver burden level, and facilitates family participation in treatment.
Comparative cognitive effects of levetiracetam and topiramate in intractable epilepsy
Authors: Huang Chin‐Wei , Pai Ming‐Chyi , Tsai Jing‐Jane
Published: September 2008

Aim:  Anti‐epileptic drugs (AED) may cause cognitive impairment. Because intractable epilepsy (IE) represents a distinct group, the purpose of the present study was to study the comparative cognitive effects of the two efficacious AED, levetiracetam (LEV) and topiramate (TPM), on IE.

Methods:  This was a non‐randomized, blinded cognitive assessment and parallel design. The cognitive effects of LEV and TPM on 79 demographically comparable patients with IE were assessed at baseline (T1) and after 1 year of treatment (T2) using the Cognitive Abilities Screening Instrument.

Results:  Forty patients took TPM and 39 took LEV. At T1, seizure frequency, number of AED, and epilepsy duration were not significantly different. There were no significant differences in cognition between the two groups at T1 or T2. T2 orientation scores were lower than T1 scores in the TPM group (P < 0.05). In the TPM subgroup with T1 cognitive abnormalities, T2 scores for recent memory improved (P < 0.05).

Conclusion:  For patients with IE, LEV might preserve cognition, TPM's effects for patients with baseline cognitive abnormalities are worth observation.
Serial analysis of gene expression in a rat lung model of asthma
Authors: YIN Lei‐Miao , JIANG Gong‐Hao , WANG Yu , WANG Yan , LIU Yan‐Yan , JIN Wei‐Rong , ZHANG Zen , XU Yu‐Dong , YANG Yong‐Qing
Published: September 2008

Background and objective:  The pathogenesis and molecular mechanism underlying asthma remain undetermined. The purpose of this study was to identify genes and pathways involved in the early airway response (EAR) phase of asthma by using serial analysis of gene expression (SAGE).

Methods:  Two SAGE tag libraries of lung tissues derived from a rat model of asthma and controls were generated. Bioinformatic analyses were carried out using the Database for Annotation, Visualization and Integrated Discovery Functional Annotation Tool, Gene Ontology (GO) Tree Machine and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis.

Results:  A total of 26 552 SAGE tags of asthmatic rat lung were obtained, of which 12 221 were unique tags. Of the unique tags, 55.5% were matched with known genes. By comparison of the two libraries, 186 differentially expressed tags (P < 0.05) were identified, of which 103 were upregulated and 83 were downregulated. Using the bioinformatic tools these genes were classified into 23 functional groups, 15 KEGG pathways and 37 enriched GO categories.

Conclusions:  The bioinformatic analyses of gene distribution, enriched categories and the involvement of specific pathways in the SAGE libraries have provided information on regulatory networks of the EAR phase of asthma. Analyses of the regulated genes of interest may inform new hypotheses, increase our understanding of the disease and provide a foundation for future research.
Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur‐oxidizing prokaryotes
Authors: Loy Alexander , Duller Stephan , Baranyi Christian , Mußmann Marc , Ott Jörg , Sharon Itai , Béjà Oded , Le Paslier Denis , Dahl Christiane , Wagner Michael
Published: September 2008

Sulfur‐oxidizing prokaryotes (SOP) catalyse a central step in the global S‐cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB‐encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound‐exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment.
Influence of different Sinorhizobium meliloti inocula on abundance of genes involved in nitrogen transformations in the rhizosphere of alfalfa (Medicago sativa L.)
Authors: Babić Katarina Huić , Schauss Kristina , Hai Brigitte , Sikora Sanja , Redžepović Sulejman , Radl Viviane , Schloter Michael
Published: September 2008

Inoculation of leguminous seeds with selected rhizobial strains is practised in agriculture to ameliorate the plant yield by enhanced root nodulation and nitrogen uptake of the plant. However, effective symbiosis between legumes and rhizobia does not only depend on the capacity of nitrogen fixation but also on the entire nitrogen turnover in the rhizosphere. We investigated the influence of seed inoculation with two indigenous Sinorhizobium meliloti strains exhibiting different efficiency concerning plant growth promotion on nitrogen turnover processes in the rhizosphere during the growth of alfalfa. Quantification of six target genes (bacterial amoA, nirK, nirS, nosZ, nifH and archaeal amoA) within the nitrogen cycle was performed in rhizosphere samples before nodule formation, at bud development and at the late flowering stage. The results clearly demonstrated that effectiveness of rhizobial inocula is related to abundance of nifH genes in the late flowering phase of alfalfa. Moreover, other genes involved in nitrogen turnover had been affected by the inocula, e.g. higher numbers of amoA copies were observed during flowering when the more effective strain had been inoculated. However, the respective gene abundances differed overall to a greater extent between the three plant development stages than between the inoculation variants.