bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

SummaryEuropean 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

Summary 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

SummaryMany 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

SummaryFap1‐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

SummaryFerritin 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.
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

SummarySulfur‐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

SummaryInoculation 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.
Ammonia‐dependent differential regulation of the gene cluster that encodes ammonia monooxygenase in Nitrosococcus oceani ATCC 19707
Authors: El Sheikh Amal F. , Klotz Martin G. 
Published: September 2008

SummaryMolecular analysis of the ammonia monooxygenase‐encoding gene cluster in Nitrosococcus oceani revealed that the amo genes are differentially expressed from three promoters dependent on the external ammonia concentration. Whereas a distal amoRCABD operon promoter, pC1, is active only in the presence of ammonia, identified proximal amoC (pC2) and amoA (pA) sigma‐70‐type promoters are constitutive. Promoter region pC2 also contains a consensus sequence for binding of RpoN, usually involved in nitrogen starvation response. Additional regulation of transcript stability by anti‐termination and mRNA degradation are proposed and discussed.
Proteomics‐inferred genome typing (PIGT) demonstrates inter‐population recombination as a strategy for environmental adaptation
Authors: Denef Vincent J. , VerBerkmoes Nathan C. , Shah Manesh B. , Abraham Paul , Lefsrud Mark , Hettich Robert L. , Banfield Jillian F. 
Published: September 2008

SummaryAnalyses of ecological and evolutionary processes that shape microbial consortia are facilitated by comprehensive studies of ecosystems with low species richness. In the current study we evaluated the role of recombination in altering the fitness of chemoautotrophic bacteria in their natural environment. Proteomics‐inferred genome typing (PIGT) was used to genotype the dominant Leptospirillum group II populations in 27 biofilms sampled from six locations in the Richmond Mine acid mine drainage system (Iron Mountain, CA) over a 4‐year period. We observed six distinct genotypes that are recombinants comprised of segments from two ‘parental’ genotypes. Community genomic analyses revealed additional low abundance recombinant variants. The dominance of some genotypes despite a larger available genome pool, and patterns of spatiotemporal distribution within the ecosystem, indicate selection for distinct recombinants. Genes involved in motility, signal transduction and transport were over‐represented in the tens to hundreds of kilobase recombinant blocks, whereas core metabolic functions were significantly under‐represented. Our findings demonstrate the power of PIGT and reveal that recombination is a mechanism for fine‐scale adaptation in this system.
STANDARDISIERT DIE NIEDERDEUTSCHE GRAMMATIK DAS NIEDERDEUTSCHE?
Authors: Stellmacher Dieter 
Published: September 2008

ABSTRACTDas Niederdeutsche (Nd.) zählt unbestritten zu den historischen germanischen Einzelsprachen. Im Unterschied zu den meisten anderen Vertretern der germanischen Sprachfamilie hat das Nd. aber einen umfassenden Statuswandel erfahren und existiert ab dem 17./18. Jahrhundert nur noch als eine Dialektgruppe. Dieser Einschnitt in der Sprachgeschichte des Nd. hat Folgen für das Selbstverständnis der Nd.‐Sprecher und für die wissenschaftliche Arbeit am Nd. Wenn es auch heute ein Gegenstand der deutschen Dialektologie ist, so erfährt das Nd. doch eine von den anderen deutschen Dialekten verschiedene linguistische Bearbeitung. Dafür steht die 1998 erschienene Niederdeutsche Grammatik (Nd. Gr.), die als eine Gebrauchsgrammatik konzipiert ist, sodass die Frage nach ihrer präskriptiven Wirkung auf der Hand liegt. Das wird im Aufsatz an der von der Nd. Gr. vorgestellten Schreibung des Nd. und an morphologischen und syntaktischen Erscheinungen geprüft. Obwohl die Deskription grammatischer Erscheinungen Standardisierungen des modernen Nd. den Weg bereitet, kann von einer nd. Standardgrammatik (noch) nicht gesprochen werden. Hier wird die Wirkung der Nd. Gr. weiter zu beobachten sein. Ihr Beschreibungsschwerpunkt, das Nd. des Weser‐Trave‐Raumes, ist auf jeden Fall geeignet, das progressive Nord‐Nd. vom eher konservativen Süd‐Nd. noch stärker abzuheben. In dieser Sprachgeschichte bildet die Nd. Gr. einen markanten Orientierungspunkt, und zwar nicht nur für niederdeutsche Linguisten.
STANDARDISATION: THE NORTH BRITISH VIEW*1
Authors: Hogg Richard M. 
Published: September 2008

ABSTRACTGeorge Campbell was a major figure in the history of prescriptivism in the late eighteenth century. He is best known for his attack on Swift and his requirements that grammar must be reputable, national and present. This paper examines Campbell's idea in the wider context of his time, and in particular considers the implications for his work of the contemporary views about national identity. As a native of Aberdeen, Campbell had a double allegiance, to both Britain and to Scotland, and it is this which is explored here. I examine Campbell's role in the Scottish Enlightenment and more generally the position of intellectuals in that movement and I contrast that with the English grammarians of the time. Campbell's views fit squarely into the Common Sense School of philosophy. Although this school is often seen as representing middle class values, this has to be embedded into the intellectual context of the time.