bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of antibodies against Rift Valley fever virus in Kenyan wildlife
Authors: EVANS A. , GAKUYA F. , PAWESKA J. T. , ROSTAL M. , AKOOLO L. , VAN VUREN P. J. , MANYIBE T. , MACHARIA J. M. , KSIAZEK T. G. , FEIKIN D. R. , BREIMAN R. F. , KARIUKI NJENGA M. 
Published: November 2007

SUMMARYRift Valley fever virus (RVFV) is an arbovirus associated with periodic outbreaks, mostly on the African continent, of febrile disease accompanied by abortion in livestock, and a severe, fatal haemorrhagic syndrome in humans. However, the maintenance of the virus during the inter-epidemic period (IEP) when there is low or no disease activity detected in livestock or humans has not been determined. This study report prevalence of RVFV-neutralizing antibodies in sera (n=896) collected from 16 Kenyan wildlife species including at least 35% that were born during the 1999–2006 IEP. Specimens from seven species had detectable neutralizing antibodies against RVFV, including African buffalo, black rhino, lesser kudu, impala, African elephant, kongoni, and waterbuck. High RVFV antibody prevalence (>15%) was observed in black rhinos and ruminants (kudu, impala, buffalo, and waterbuck) with the highest titres (up to 1:1280) observed mostly in buffalo, including animals born during the IEP. All lions, giraffes, plains zebras, and warthogs tested were either negative or less than two animals in each species had low (⩽1:16) titres of RVFV antibodies. Of 249 sera collected from five wildlife species during the 2006–2007 outbreak, 16 out of 19 (84%) of the ruminant (gerenuk, waterbuck, and eland) specimens had RVFV-neutralizing titres ⩾1:80. These data provide evidence that wild ruminants are infected by RVFV but further studies are required to determine whether these animals play a role in the virus maintenance between outbreaks and virus amplification prior to a noticeable outbreak.
Performance of an interferon-gamma release assay for diagnosing latent tuberculosis infection in children
Authors: OKADA K. , MAO T. E. , MORI T. , MIURA T. , SUGIYAMA T. , YOSHIYAMA T. , MITARAI S. , ONOZAKI I. , HARADA N. , SAINT S. , KONG K. S. , CHHOUR Y. M. 
Published: November 2007

SUMMARYNewly developed interferon-gamma release assays have become commercially available to detect tuberculosis (TB) infection in adults. However, little is known about their performance in children. We compared test results between the QuantiFERON-TB® Gold test (QFT) and tuberculin skin test (TST) in young children living with pulmonary TB patients in Cambodia. Of 195 children tested with both QFT and TST, the TST-positive rate of 24% was significantly higher than the QFT-positive rate of 17%. The agreement between the test results was considerable (κ-coefficient 0·63). Positive rates increased from 6% to 32% for QFT and from 15% to 43% for TST, according to the sputum smear grades of the index cases. The presence of Bacille Calmette-Guérin (BCG) scars did not significantly affect the results of TST or QFT in a logistic regression analysis. In conclusion, QFT can be a substitute for TST in detecting latent TB infection in childhood contacts aged ⩽5 years, especially in those who may have a false-positive TST due to BCG vaccination or non-tuberculous mycobacterial infection.
Synthetic microarray data generation with RANGE and NEMO
Authors: Long James , Roth Mitchell 
Published: November 2007

AbstractMotivation: For testing and sensitivity analysis purposes, it is beneficial to have known transcription networks of sufficient size and variability during development of microarray data and network deconvolution algorithms. Description of such networks in a simple language translatable to Systems Biology Markup Language would allow generation of model data for the networks.Results: Described herein is software (RANGE: RAndom Network GEnerator) to generate large random transcription networks in the NEMO (NEtwork MOtif) language. NEMO is recognized by a grammar for transcription network motifs using lex and yacc to output Systems Biology Markup Language models for either specified or randomized gene input functions. These models of known networks may be input to a biochemical simulator, allowing the generation of synthetic microarray data.Availability: http://range.sourceforge.netContact: jlong@alaska.edu
Growth variability in Atlantic mackerel (Scomber scombrus) and Spanish mackerel (Scomber japonicus) off Portugal
Authors: Martins Maria Manuel 
Published: November 2007

Abstract
Martins, M. M. 2007. Growth variability in Atlantic mackerel (Scomber scombrus) and Spanish mackerel (Scomber japonicus) off Portugal. – ICES Journal of Marine Science, 64. Year-class effects may be very important when analysing fish growth. This work aims to compare growth in weight and in length between year classes of Atlantic and Spanish mackerel found off the Portuguese coast. The analysis included Atlantic mackerel data from year classes 1986–1993 and Spanish mackerel data from year classes 1988–1995. The analyses indicated significant differences between year classes in terms of mean weight-at-length and mean length-at-age. Atlantic mackerel year classes also showed significant differences in mean weight-at-length between males and females, and Spanish mackerel year classes showed significant differences between sexes for mean length-at-age. No significant effects were found for the two-way interaction between year class and sex. Growth variability may be linked with variability in environmental factors as well as density-dependence.
First Report of Soybean dwarf virus in Soybean in Northern Illinois
Authors: Thekkeveetil T. , Hobbs H. A. , Wang Y. , Kridelbaugh D. , Donnelly J. , Hartman G. L. , Domier L. L. 
Published: November 2007

Soybean dwarf virus (SbDV), a member of the Luteoviridae, is transmitted persistently by colonizing aphids and causes significant yield losses in soybean (Glycine max L.) in Japan. In the United States, SbDV is endemic in red and white clover (Trifolium pratense L. and T. repens L.) (1,3). Even so, SbDV has been detected in soybean only in Virginia (2) and Wisconsin (4). A study conducted in Illinois during 2001 and 2002 detected SbDV in clover but not soybean (3). During August of 2006, two surveys for virus diseases in soybean were conducted in Illinois. In the first survey, 30 soybean leaf samples were collected without regard for symptoms from each of 10 fields in each of five northern Illinois counties (Carroll, Jo Daviess, Ogle, Stephenson, and Winnebago). In the second survey, 10 random soybean leaf samples and 10 samples with virus-like symptoms were collected from each of 30 soybean rust sentinel plots spread throughout Illinois. Total RNA was extracted from pools of 90 to 100 plants and analyzed by quantitative real-time reverse transcriptase (QRT)-PCR using a fluorescently labeled minor groove binding probe (VIC-5′-AGCATATCCAAAGACGC-3′-MGBNFQ, nt 2358-2374) and flanking primers (5′-TGGCTATTATAGAATGGTGCGTAAAC-3′, nt 2327-2351; and 5′-GCCATGGAAATGAGGGAATG-3′, nt 2395-2376). From the first survey, pools from Carroll, Jo Daviess, and Ogle were positive for SbDV. Analysis of individual leaf samples from positive pools by double-antibody sandwich-ELISA (Agdia, Elkhart, IN) showed that one sample in each county was positive for SbDV. On the basis of the number of randomly sampled plants, the incidence of SbDV infection in northern Illinois was approximately 0.3%. In the second survey, SbDV was detected in one pool containing symptomatic plants from five soybean rust sentinel plots. Further QRT-PCR analysis showed that the sentinel plot in Bureau County was positive for SbDV. Because of the sampling protocols used, it was not possible to determine symptom phenotypes of SbDV-positive samples. Sequence analysis of the combined coat protein (CP) and readthrough domain (RTD) encoding region (nt 3019-5094) of SbDV isolates from Bureau (GenBank Accession No. EU095847) and Carroll (GenBank Accession No. EU095846) counties showed that the predicted amino acid sequences were 96 and 95% identical to a Japanese dwarfing isolate of SbDV (GenBank Accession No. AB038150), respectively. The predicted CP amino acid sequences of the Illinois isolates were identical and RTD amino acid sequences differed at six positions. To our knowledge, this is the first report of infection of soybean plants in Illinois with SbDV. References: (1) V. D. Damsteegt et al. Phytopathology 89:374, 1999. (2) A. Fayad et al. Phytopathology (Abstr.) 90(suppl.):S132, 2000. (3) B. Harrison et al. Plant Dis. 89:28, 2005. (4) A. Phibbs et al. Plant Dis. 88:1285, 2004.
First Report of Waitea circinata var. circinata Causing Brown Ring Patch on Poa trivialis in California
Authors: Chen C. M. , Douhan G. W. , Wong F. P. 
Published: November 2007

Rough bluegrass (Poa trivialis L.) is a C3 (cool-season) turfgrass used on golf course putting greens. It is often used to overseed C4 (warm-season) turf for fall through early-summer use. In March 2007, at maximium daytime air temperatures of approximately 30 to 35°C, irregular, thin, yellow rings approximately 10 to 20 cm in diameter were reported on P. trivialis in putting greens from two golf courses in the Coachella Valley of southern California. Affected plants had a blight of the leaves and stems and a rot of the crown, with initial symptoms being a yellowing of the tissue followed by the development of a dark, water-soaked appearance of the whole plant. Plants turned reddish brown as the water-soaked tissue dessicated. A Rhizoctonia-like fungus was found to be colonizing the leaves, stems, and upper roots and thatch. Three isolates were obtained from the diseased turf samples. All were identified as Waitea circinata var. circinata based on colony morphology (2) and rDNA internal transcribed spacer (ITS) region sequences (1). The sequences of the three isolates were more than 99% similar to those of W. circinata var. circinata deposited in the NCBI database (1,2). To confirm pathogenicity, each isolate was inoculated onto 4-week-old P. trivialis (2 mg of seed per cm2) grown in 10-cm-diameter pots containing steam-sterilized UC-mix at 28°C. Five 8-mm-diameter plugs of each isolate were taken from 7-day-old cultures grown on potato dextrose agar (PDA) and placed in direct contact with the bases of the stems. The pots were then incubated in a moist chamber at 28°C. Five noncolonized PDA plugs were used as a negative control. Three pots were used for each of the three isolates and the check treatment. For all isolates, chlorosis of leaf and stems were observed 5 days after inoculation and the tissue appeared water soaked after 7 days with the production of abundant aerial mycelia being observed. All plants, except the negative controls, died after 10 days. W. circinata var. circinata was reisolated from symptomatic tissue from the inoculated plants. W. circinata var. circinata was previously reported as the causal agent of brown ring patch on creeping bentgrass (Agrostis palustris) in Japan (2) and as a pathogen of annual bluegrass (P. annua) in the United States (1). To our knowledge, this is the first report of W. circinata var. circinata infecting P. trivialis in California. References: (1) K. de la Cerda et al. Plant Dis. 91:791, 2007. (2) T. Toda et al. Plant Dis. 89:536, 2005.
Identification and Characterization of Nucleotide-Binding Site-Leucine-Rich Repeat Genes in the Model Plant Medicago truncatula
Authors: Ameline-Torregrosa Carine , Wang Bing-Bing , O'Bleness Majesta S. , Deshpande Shweta , Zhu Hongyan , Roe Bruce , Young Nevin D. , Cannon Steven B. 
Published: November 2007

Abstract
The nucleotide-binding site (NBS)-Leucine-rich repeat (LRR) gene family accounts for the largest number of known disease resistance genes, and is one of the largest gene families in plant genomes. We have identified 333 nonredundant NBS-LRRs in the current Medicago truncatula draft genome (Mt1.0), likely representing 400 to 500 NBS-LRRs in the full genome, or roughly 3 times the number present in Arabidopsis (Arabidopsis thaliana). Although many characteristics of the gene family are similar to those described on other plant genomes, several evolutionary features are particularly pronounced in M. truncatula, including a high degree of clustering, evidence of significant numbers of ectopic translocations from clusters to other parts of the genome, a small number of more evolutionarily stable NBS-LRRs, and numerous truncations and fusions leading to novel domain compositions. The gene family clearly has had a large impact on the structure of the genome, both through ectopic translocations (potentially, a means of seeding new NBS-LRR clusters), and through two extraordinarily large superclusters. Chromosome 6 encodes approximately 34% of all TIR-NBS-LRRs, while chromosome 3 encodes approximately 40% of all coiled-coil-NBS-LRRs. Almost all atypical domain combinations are in the TIR-NBS-LRR subfamily, with many occurring within one genomic cluster. This analysis shows the gene family not only is important functionally and agronomically, but also plays a structural role in the genome.
Starch Serves as Carbohydrate Storage in Nematode-Induced Syncytia
Authors: Hofmann Julia , Szakasits Dagmar , Blöchl Andreas , Sobczak Miroslaw , Daxböck-Horvath Sabine , Golinowski Wladyslaw , Bohlmann Holger , Grundler Florian M.W. 
Published: November 2007

AbstractThe plant parasitic nematode Heterodera schachtii induces specific syncytial feeding sites in the roots of Arabidopsis thaliana from where it withdraws all required nutrients. Therefore, syncytia have to be well supplied with assimilates and generate strong sinks in the host plant's transport system. Import mechanisms and consequent accumulation of sucrose in syncytia were described recently. In this work, we studied the starch metabolism of syncytia. Using high-performance liquid chromatography and microscopic analyses, we demonstrated that syncytia store carbohydrates by starch accumulation. Further, we monitored the expression of genes involved in the starch metabolic pathway by gene chip analysis and quantitative reverse transcription-PCR. Finally, we provide functional proof of the importance of starch synthesis for nematode development using T-DNA insertion lines. We conclude that syncytia accumulate starch as a carbohydrate buffer to compensate for changing solute uptake by the nematode and as long-term storage during juvenile development.
Trehalose-6-Phosphate Synthase/Phosphatase Regulates Cell Shape and Plant Architecture in Arabidopsis
Authors: Chary S. Narasimha , Hicks Glenn R. , Choi Yoon Gi , Carter David , Raikhel Natasha V. 
Published: November 2007

AbstractThe vacuole occupies most of the volume of plant cells; thus, the tonoplast marker δ-tonoplast intrinsic protein-green fluorescent protein delineates cell shape, for example, in epidermis. This permits rapid identification of mutants. Using this strategy, we identified the cell shape phenotype-1 (csp-1) mutant in Arabidopsis thaliana. Beyond an absence of lobes in pavement cells, phenotypes included reduced trichome branching, altered leaf serration and stem branching, and increased stomatal density. This result from a point mutation in AtTPS6 encoding a conserved amino-terminal domain, thought to catalyze trehalose-6-phosphate synthesis and a carboxy-terminal phosphatase domain, is catalyzing a two-step conversion to trehalose. Expression of AtTPS6 in the Saccharomyces cerevisiae mutants tps1 (encoding a synthase domain) and tps2 (encoding synthase and phosphatase domains) indicates that AtTPS6 is an active trehalose synthase. AtTPS6 fully complemented defects in csp-1. Mutations in class I genes (AtTPS1–AtTPS4) indicate a role in regulating starch storage, resistance to drought, and inflorescence architecture. Class II genes (AtTPS5–AtTPS11) encode multifunctional enzymes having synthase and phosphatase activity. We show that class II AtTPS6 regulates plant architecture, shape of epidermal pavement cells, and branching of trichomes. Thus, beyond a role in development, we demonstrate that the class II gene AtTPS6 is important for controlling cellular morphogenesis.
A Set of Modular Binary Vectors for Transformation of Cereals
Authors: Himmelbach Axel , Zierold Uwe , Hensel Götz , Riechen Jan , Douchkov Dimitar , Schweizer Patrick , Kumlehn Jochen 
Published: November 2007

Abstract
Genetic transformation of crop plants offers the possibility of testing hypotheses about the function of individual genes as well as the exploitation of transgenes for targeted trait improvement. However, in most cereals, this option has long been compromised by tedious and low-efficiency transformation protocols, as well as by the lack of versatile vector systems. After having adopted and further improved the protocols for Agrobacterium-mediated stable transformation of barley (Hordeum vulgare) and wheat (Triticum aestivum), we now present a versatile set of binary vectors for transgene overexpression, as well as for gene silencing by double-stranded RNA interference. The vector set is offered with a series of functionally validated promoters and allows for rapid integration of the desired genes or gene fragments by GATEWAY-based recombination. Additional in-built flexibility lies in the choice of plant selectable markers, cassette orientation, and simple integration of further promoters to drive specific expression of genes of interest. Functionality of the cereal vector set has been demonstrated by transient as well as stable transformation experiments for transgene overexpression, as well as for targeted gene silencing in barley.
Distinct Light and Clock Modulation of Cytosolic Free Ca2+ Oscillations and RhythmicCHLOROPHYLL A/B BINDING PROTEIN2Promoter Activity inArabidopsis
Authors: Xu Xiaodong , Hotta Carlos T. , Dodd Antony N. , Love John , Sharrock Robert , Lee Young Wha , Xie Qiguang , Johnson Carl H. , Webb Alex A.R. 
Published: November 2007

AbstractPlants have circadian oscillations in the concentration of cytosolic free calcium ([Ca2+]cyt). To dissect the circadian Ca2+-signaling network, we monitored circadian [Ca2+]cyt oscillations under various light/dark conditions (including different spectra) in Arabidopsis thaliana wild type and photoreceptor and circadian clock mutants. Both red and blue light regulate circadian oscillations of [Ca2+]cyt. Red light signaling is mediated by PHYTOCHROME B (PHYB). Blue light signaling occurs through the redundant action of CRYPTOCHROME1 (CRY1) and CRY2. Blue light also increases the basal level of [Ca2+]cyt, and this response requires PHYB, CRY1, and CRY2. Light input into the oscillator controlling [Ca2+]cyt rhythms is gated by EARLY FLOWERING3. Signals generated in the dark also regulate the circadian behavior of [Ca2+]cyt. Oscillations of [Ca2+]cyt and CHLOROPHYLL A/B BINDING PROTEIN2 (CAB2) promoter activity are dependent on the rhythmic expression of LATE ELONGATED HYPOCOTYL and CIRCADIAN CLOCK-ASSOCIATED1, but [Ca2+]cyt and CAB2 promoter activity are uncoupled in the timing of cab1 (toc1-1) mutant but not in toc1-2. We suggest that the circadian oscillations of [Ca2+]cyt and CAB2 promoter activity are regulated by distinct oscillators with similar components that are used in a different manner and that these oscillators may be located in different cell types in Arabidopsis.
Functional Definition of Outer Membrane Proteins Involved in Preprotein Import into Mitochondria
Authors: Lister Ryan , Carrie Chris , Duncan Owen , Ho Lois H.M. , Howell Katharine A. , Murcha Monika W. , Whelan James 
Published: November 2007

AbstractThe role of plant mitochondrial outer membrane proteins in the process of preprotein import was investigated, as some of the principal components characterized in yeast have been shown to be absent or evolutionarily distinct in plants. Three outer membrane proteins of Arabidopsis thaliana mitochondria were studied: TOM20 (translocase of the outer mitochondrial membrane), METAXIN, and mtOM64 (outer mitochondrial membrane protein of 64 kD). A single functional Arabidopsis TOM20 gene is sufficient to produce a normal multisubunit translocase of the outer membrane complex. Simultaneous inactivation of two of the three TOM20 genes changed the rate of import for some precursor proteins, revealing limited isoform subfunctionalization. Inactivation of all three TOM20 genes resulted in severely reduced rates of import for some but not all precursor proteins. The outer membrane protein METAXIN was characterized to play a role in the import of mitochondrial precursor proteins and likely plays a role in the assembly of β-barrel proteins into the outer membrane. An outer mitochondrial membrane protein of 64 kD (mtOM64) with high sequence similarity to a chloroplast import receptor was shown to interact with a variety of precursor proteins. All three proteins have domains exposed to the cytosol and interacted with a variety of precursor proteins, as determined by pull-down and yeast two-hybrid interaction assays. Furthermore, inactivation of one resulted in protein abundance changes in the others, suggesting functional redundancy. Thus, it is proposed that all three components directly interact with precursor proteins to participate in early stages of mitochondrial protein import.
Glycolytic Enzymes Associate Dynamically with Mitochondria in Response to Respiratory Demand and Support Substrate Channeling
Authors: Graham James W.A. , Williams Thomas C.R. , Morgan Megan , Fernie Alisdair R. , Ratcliffe R. George , Sweetlove Lee J. 
Published: November 2007

Abstract
In Arabidopsis thaliana, enzymes of glycolysis are present on the surface of mitochondria and free in the cytosol. The functional significance of this dual localization has now been established by demonstrating that the extent of mitochondrial association is dependent on respiration rate in both Arabidopsis cells and potato (Solanum tuberosum) tubers. Thus, inhibition of respiration with KCN led to a proportional decrease in the degree of association, whereas stimulation of respiration by uncoupling, tissue ageing, or overexpression of invertase led to increased mitochondrial association. In all treatments, the total activity of the glycolytic enzymes in the cell was unaltered, indicating that the existing pools of each enzyme repartitioned between the cytosol and the mitochondria. Isotope dilution experiments on isolated mitochondria, using 13C nuclear magnetic resonance spectroscopy to monitor the impact of unlabeled glycolytic intermediates on the production of downstream intermediates derived from 13C-labeled precursors, provided direct evidence for the occurrence of variable levels of substrate channeling. Pull-down experiments suggest that interaction with the outer mitochondrial membrane protein, VDAC, anchors glycolytic enzymes to the mitochondrial surface. It appears that glycolytic enzymes associate dynamically with mitochondria to support respiration and that substrate channeling restricts the use of intermediates by competing metabolic pathways.