bluuebunny/crossref_metadata_2025_split huggingface dataset:
First Report of Plum pox virus Recombinant Strain on Prunus spp. in Canada
Authors: Thompson D. , Varga A. , De Costa H. , Birch C. , Glasa M. , James D. 
Published: May 2009

In July of 2008, during the Canadian Plum pox virus (PPV) eradication survey, three Prunus spp. trees (B-5, B-6, and C-1) in a home owner's yard in Grimsby, ON, Canada were found to be infected with PPV by triple antibody sandwich (TAS)-ELISA using the 5B generic monoclonal detecting antibody (1) and reverse transcription (RT)-PCR using the well-validated universal primer set P1/P2. All three trees were grafted on an unknown plum rootstock cultivar. Tree B-5 contained grafts of unknown peach (P. persica) and plum (P. domestica) cultivars, tree B-6 contained the same peach graft as tree B-5 and an unknown apricot (P. armeniaca) cultivar, and tree C-1 was grafted with the same plum cultivar as tree B-5. Strain typing was done by TAS-ELISA using strain-specific monoclonal antibodies for D, M, C, and EA strains. Positive results were obtained with the M-specific test. Strain typing by RT-PCR also was done using primers specific for D, M, W, and recombinant (Rec) strains. Positive results were obtained with the M and Rec primers (4). The 605-bp fragment generated by the PPV Rec primers, which spans the recombination site, was cloned and sequenced. The nucleotide sequences obtained from B-5, B-6, and C-1 are 99% identical to each other and approximately 98 and 99% identical to the PPV Rec isolates BOR-3 and J4c, respectively. Correspondingly, percentage identities are approximately 90% for PPV M, 84% for PPV isolate D-Fan (a typical Canadian D isolate), and 69% for PPV W. The deduced amino acid sequence of B-5, B-6, and C-1 are 98 to 99% identical to each other, 99% identical to the PPV Rec isolates BOR-3 and J4c, 92% identical to isolates of PPV M, and only 84% identical to the typical Canadian D isolate PPV Fan. The P3-6K1 genomic region was amplified using primers that generate a 836-bp fragment (2). This region was 97 to 98% identical to the PPV Rec isolates BOR-3 and J4c, 96 to 97% identical to isolates of PPV D, but only 86% identical to isolates of PPV M. The data above confirm that the PPV isolates B-5, B-6, and C-1 belong to the strain PPV Rec (3). To our knowledge, this is the first report of PPV Rec in North America, and together with PPV D and W, it represents the third PPV strain found on this continent. An intensive survey of all Prunus spp. within a 1.5-km radius area surrounding the home owner's property failed to reveal any additional PPV-positive plants. The three positive plants were removed. References: (1) M. Cambra et al. EPPO Bull. 24:569, 1994. (2) M. Glasa et al. Arch. Virol. 147:563, 2002. (3) M. Glasa et al. J. Gen. Virol. 85:2671, 2004. (4) A. Šubr et al. Acta Virol. 48:173, 2004.
First Report of Peronospora sparsa Causing Downy Mildew (Dryberry) of Rubus fruticosus in Mexico
Authors: Rebollar-Alviter A. , Silva-Rojas H. V. , Zelaya-Molina L. X. , Ellis M. A. 
Published: May 2009

Michoacan State is the largest producer of blackberries (Rubus fruticosus) in Mexico with more than 4,000 ha in production. During the rainy season of 2007 (July to September), purple, angular, vein-delimited leaf spots along the midrib and major veins were observed. Affected young fruit lost their shine, became shriveled, and later dried. Some fruit split. Symptomatic leaflets from cv. Tupy were collected from the field in Tangancicuaro and Los Reyes counties. In the laboratory, 20 detached leaflets were washed with 10% bleach for 2 min, rinsed with sterile distilled water, and placed into sterile petri dishes containing 0.5% water agar. To promote sporulation of fungi, leaflets were incubated at 17°C with a 12-h photoperiod in a growth chamber. Sporangia and sporangiophores, which developed 20 days later on the underside of the leaves, were transferred to the underside of detached healthy leaves of the same cultivar with a sterile needle, and incubated as previously described. A set of noninoculated leaves were included as controls. Sporangiophores and sporangia developed on the underside of angular purple lesions on leaves 15 to 22 days after inoculation. Symptoms were identical to those observed on leaves in the field. The pathogenicity test was repeated twice with the same results. Sporangia were light brown, ovoid to elliptical, and measured 14 to 22 × 11 to 18 μm. Sporangiophores were dichotomously branched with slender curved ends. Symptoms on the leaves and fruit and oomycete morphology were similar to those described for downy mildew (2). To confirm pathogen identity, a product of ~500 bp of the nuclear ITS-rRNA was amplified from total DNA from symptomatic and asymptomatic leaves and fruit by nested PCR. The primers sets PS3/PS1 and PR3/PR4 were used for the first and second reaction, respectively (1,3). PCR products were sequenced in both directions and sequences were deposited in GenBank under Accession Nos. EU601168, EU601169, EU601170, and EU601171. Consensus sequences obtained in this study were compared with the same region of Peronospora sparsa (GenBank Accession Nos. EU391654 from Denmark and AF266783 from the UK). Similarity among these sequences varied between 99 and 100%. To our knowledge, this is the first report of downy mildew (dryberry) of blackberry caused by P. sparsa in Mexico. References: (1) B. J. Aegerter et al. Plant Dis. 86:1363, 2002. (2) W. D. Gubler. Page 15 in: Compendium of Raspberry and Blackberry Diseases and Insects. M. A. Ellis et al., eds. The American Phytopathological Society, St Paul MN, 1998. (3) H. Lindqvist et al. Plant Dis. 82:1304, 1998.
Iris yellow spot virus in Onion in Nevada and Northern California
Authors: Bag S. , Singh J. , Davis R. M. , Chounet W. , Pappu H. R. 
Published: May 2009

The disease caused by thrips-transmitted Iris yellow spot virus (IYSV; genus Tospovirus, family Bunyaviridae) has become a major constraint to bulb and seed onion crops in several parts of the country and the world (1,3). As part of an ongoing survey for IYSV incidence in onion in the western United States, commercial fields in Lyon County, Nevada and several commercial fields in the northern Californian counties of Colusa, San Benito, Sutter, and Yolo were surveyed during the summer of 2008. Symptomatic plants were found widespread in northern California, especially in seed-production fields. In Lyon County, NV, symptoms were observed only on volunteer onions in one commercial field. Symptoms on leaves and scapes included characteristic diamond-shaped lesions with or without green islands. Four samples from Nevada and fourteen from northern California were tested by double-antibody sandwich (DAS)-ELISA using a commercially available kit (Agdia Inc., Elkhart, IN). All tested samples were found positive in ELISA. IYSV infection was verified by reverse transcription (RT)-PCR. Total nucleic acids were prepared from symptomatic tissue, and primers specific to the small (S) RNA of IYSV were used to amplify an approximate 1.2-kb region of the S-RNA. This region included the complete nucleoprotein (N) gene (2). The amplicons from one sample each from Nevada and northern California were sequenced (GenBank Accession Nos. FJ713699 and FJ713700, respectively). Sequence analysis showed that the amplicons contained a single open reading frame of 822 bp, coding for a 273-amino acid N protein, and the gene shared 96 to 98% identity with known IYSV N gene sequences. To our knowledge, this is the first report of IYSV in onion in Nevada. In California, outbreaks of IYSV had been reported earlier in Imperial Valley and Antelope Valley in southern California (4), and the disease has been increasing in incidence in bulb and seed crops in northern California, as well. California and Nevada are major onion-producing states in the United States and regular surveys to determine the incidence and impact on yield are needed to develop an integrated disease management program. References: (1) D. H. Gent et al. Plant Dis. 90:1468, 2006. (2) H. R. Pappu et al. Arch. Virol. 151:1015, 2006. (3) H. R. Pappu and M. E. Matheron. Online publication. doi:10.1094/PHP-2008-0711-01-BR. Plant Health Progress, 2008. (4) G. J. Poole et al. Online publication. doi:10.1094/PHP-2007-0508-01-BR. Plant Health Progress, 2007.
First Report of Root-Knot Nematode Meloidogyne enterolobii on Guava in Vietnam
Authors: Iwahori H. , Truc N. T. N. , Ban D. V. , Ichinose K. 
Published: May 2009

In southern Vietnam, citrus is interplanted with guava (Psidium guajava L.) for the management of citrus greening disease. Guava seedlings exhibited decline symptoms including leaf browning, growth inhibition, leaf drop, and death. These symptomatic seedlings were accompanied by severely galled roots, possibly attributable to root-knot nematodes. We collected second-stage juveniles from the soil and picked adult females from roots to perform morphological observations. The perineal patterns of most specimens were similar to those in the original description of Meloidogyne enterolobii (3). However, some were similar to that of M. incognita. Such variability among perineal patterns precluded unequivocal identification. Therefore, DNA was extracted from these nematodes and their sequences were compared with those in the DNA sequence database. For the comparison, we employed the primer sets of Powers and Harris (1) to amplify a region between cytochrome oxidase II and the 16S ribosomal DNA gene of mitochondria by PCR. An approximate 700-bp fragment was obtained and analyzed, revealing more than 99.6% homology to M. mayaguensis, a synonym of M. enterolobii (2), when aligned with sequence data of isolates from France (GenBank Accession No. AJ421396), the United States (GenBank Accession No. AY446978), and China (GenBank Accession No. AY831967). These results indicate that the nematode species responsible for guava damage in southern Vietnam is M. enterolobii. To our knowledge, this is the first report of M. enterolobii in Vietnam. References: (1) T. O. Powers and T. S. Harris. J. Nematol. 25:1, 1993. (2) J. Xu et al. Eur. J. Plant Pathol. 110:309, 2004. (3) B. Yang and J. D. Eisenback. J. Nematol. 15:381, 1983.
RNA Interference of LIN5 in Tomato Confirms Its Role in Controlling Brix Content, Uncovers the Influence of Sugars on the Levels of Fruit Hormones, and Demonstrates the Importance of Sucrose Cleavage for Normal Fruit Development and Fertility
Authors: Zanor María Inés , Osorio Sonia , Nunes-Nesi Adriano , Carrari Fernando , Lohse Marc , Usadel Björn , Kühn Christina , Bleiss Wilfrid , Giavalisco Patrick , Willmitzer Lothar , Sulpice Ronan , Zhou Yan-Hong , Fernie Alisdair R. 
Published: May 2009

Abstract
It has been previously demonstrated, utilizing intraspecific introgression lines, that Lycopersicum Invertase5 (LIN5), which encodes a cell wall invertase, controls total soluble solids content in tomato (Solanum lycopersicum). The physiological role of this protein, however, has not yet been directly studied, since evaluation of data obtained from the introgression lines is complicated by the fact that they additionally harbor many other wild species alleles. To allow a more precise comparison, we generated transgenic tomato in which we silenced the expression of LIN5 using the RNA interference approach. The transformants were characterized by an altered flower and fruit morphology, displaying increased numbers of petals and sepals per flower, an increased rate of fruit abortion, and a reduction in fruit size. Evaluation of the mature fruit revealed that the transformants were characterized by a reduction of seed number per plant. Furthermore, detailed physiological analysis revealed that the transformants displayed aberrant pollen morphology and a reduction in the rate of pollen tube elongation. Metabolite profiling of ovaries and green and red fruit revealed that metabolic changes in the transformants were largely confined to sugar metabolism, whereas transcript and hormone profiling revealed broad changes both in the hormones themselves and in transcripts encoding their biosynthetic enzymes and response elements. These results are discussed in the context of current understanding of the role of sugar during the development of tomato fruit, with particular focus given to its impact on hormone levels and organ morphology.
The K-Segment of Maize DHN1 Mediates Binding to Anionic Phospholipid Vesicles and Concomitant Structural Changes
Authors: Koag Myong-Chul , Wilkens Stephan , Fenton Raymond D. , Resnik Josh , Vo Evanly , Close Timothy J. 
Published: May 2009

Abstract
Dehydrins (DHNs; late embryogenesis abundant D11 family) are a family of intrinsically unstructured plant proteins that accumulate in the late stages of seed development and in vegetative tissues subjected to water deficit, salinity, low temperature, or abscisic acid treatment. We demonstrated previously that maize (Zea mays) DHNs bind preferentially to anionic phospholipid vesicles; this binding is accompanied by an increase in α-helicity of the protein, and adoption of α-helicity can be induced by sodium dodecyl sulfate. All DHNs contain at least one “K-segment,” a lysine-rich 15-amino acid consensus sequence. The K-segment is predicted to form a class A2 amphipathic α-helix, a structural element known to interact with membranes and proteins. Here, three K-segment deletion proteins of maize DHN1 were produced. Lipid vesicle-binding assays revealed that the K-segment is required for binding to anionic phospholipid vesicles, and adoption of α-helicity of the K-segment accounts for most of the conformational change of DHNs upon binding to anionic phospholipid vesicles or sodium dodecyl sulfate. The adoption of structure may help stabilize cellular components, including membranes, under stress conditions.
Influence of pH on copper, lead and cadmium binding by an ombrotrophic peat
Authors: Villaverde P. , Gondar D. , Antelo J. , López R. , Fiol S. , Arce F. 
Published: May 2009

SummaryThe effect of pH on the adsorption of copper (Cu), lead (Pb) and cadmium (Cd) by a peat soil was studied, and the results compared with those corresponding to cation binding by a dissolved peat humic acid (HA), and interpreted with a NICA–Donnan model. A potentiometric titration technique was used to determine the adsorption isotherms for H+, at different ionic strengths, and for Cu2+, Pb2+ and Cd2+ at different pH values, in a peat soil. The effect of the ionic strength on proton binding was similar for the soil (solid) organic matter and for dissolved HA. The adsorption isotherms for cation–peat and the binding curves cation–dissolved HA are almost parallel, although more cation was adsorbed per kg of C in the dissolved HA. The effect of pH on cation binding is similar for dissolved organic matter and for the organic soil. At low metal concentration the amount of adsorbed metal followed the order Cu2+ > Pb2+ > Cd2+. The cation‐binding parameters obtained with the NICA–Donnan model allow excellent simulation of the effect of pH on the adsorption of Cu, Pb and Cd ions in the studied peat soil. The binding constants for the peat suspension were greater than the corresponding generic parameters for dissolved HA. Speciation calculations showed that for Cu and Pb, the most abundant fraction was the metal adsorbed on peat, whereas for Cd the most abundant fraction was dissolved metal.
Structural basis for red‐shifted emission of a GFP‐like protein from the marine copepod Chiridius poppei
Authors: Suto Kyoko , Masuda Hiromi , Takenaka Yasuhiro , Tsuji Frederick I. , Mizuno Hiroshi 
Published: May 2009

The fluorescence excitation and emission maxima of a GFP‐like protein from the marine copepod Chiridius poppei (CpYGFP) show a significant red shift (λex = 509 nm, λem = 517 nm) compared with those of GFP from Aequorea victoria (avGFP) and other GFP‐like proteins from marine copepods. We performed crystallographic and biochemical studies to understand why this shift occurs in CpYGFP. The structure of CpYGFP showed that the imidazole side chain of His52 is involved in stacking on the phenol moiety of the chromophore. We investigated the potential role of His52 in causing the red‐shifted spectral properties by performing mutational analyses of H52T, H52D and H52F. The emission wavelengths of H52T and H52D were blue‐shifted and that of H52F was red‐shifted relative to the wild type. Comparison of its structure of another copepod GFP (ppluGFP2) having an emission maximum at 502 nm showed that the imidazole ring of His54 (corresponding to His52 in CpYGFP) is flipped out of the stacking position with the chromophore. These findings suggest that π–π stacking interaction between His52 and the phenol moiety of the chromophore is the likely cause of the red‐shift in light emission.
Lifespan extension by suppression of autophagy genes in Caenorhabditis elegans
Authors: Hashimoto Yasufumi , Ookuma Sadatsugu , Nishida Eisuke 
Published: May 2009

Lifespan is regulated by a complex combination of environmental and genetic factors. Autophagy, which is a bulk degradation system of macromolecules and organelles, has an important role in various biological events. In Caenorhabditis elegans, several autophagy genes have been shown to have a role in promoting longevity, but many other autophagy genes have not been examined for their role in the lifespan regulation. Here we have systematically examined the effect of RNAi suppression of 14 autophagy genes on lifespan. While maternal RNAi of autophagy genes in wild‐type worms tended to reduce lifespan, maternal RNAi of each of seven autophagy genes in the insulin/IGF‐1 receptor daf‐2 mutants extended lifespan. Remarkably, RNAi of unc‐51/atg‐1, bec‐1/atg‐6 or atg‐9, from young adult, i.e. after development, extended lifespan in both wild‐type animals and daf‐2 mutants, although RNAi of one or two genes shortened it. Moreover, our analysis suggests that the lifespan extension, which is induced by RNAi of unc‐51, bec‐1 or atg‐9 after development, does not require the transcription factor daf‐16, the NAD+‐dependent protein deacetylase sir‐2.1 or the genes related to mitochondrial functions. Collectively, our results suggest that autophagy may not always be beneficial to longevity, but may also function to restrict lifespan in C. elegans.
Identification of novel virulence factors associated with signal transduction pathways in Alternaria brassicicola
Authors: Cho Yangrae , Kim Kwang‐Hyung , La Rota Mauricio , Scott Derrick , Santopietro Graciela , Callihan Meagan , Mitchell Thomas K. , Lawrence Christopher B. 
Published: May 2009

Summary Alternaria brassicicola is an important, necrotrophic fungal pathogen that causes black spot disease on Brassicas. In order to study pathogenicity mechanisms, gene deletion mutants were generated for 21 putative regulatory genes including kinases and transcription factors subjectively selected from the annotated A. brassicicola genome. Except for Ste12, the deletion of the SNF1 kinase, XlnR, and CreA homologues that control cell wall‐degrading enzyme production did not significantly affect virulence in contrast to other pathogenic fungi. Only deletion of XlnR but not CreA, Ste12 or SNF1 impaired the fungus' ability to utilize sole carbon sources suggesting Alternaria regulates expression of cell wall‐degrading enzymes in a novel manner. In addition, two novel virulence factors encoding a transcription factor (AbPro1) and a two‐component histidine kinase gene (AbNIK1) were discovered. Deletion of AbPro1 resulted in a 70% reduction in virulence and a 25% reduction in vegetative growth rates in vitro. Deletion of AbNIK1 resulted in a near complete loss of virulence, increased sensitivity to osmotic stress, and no changes in vegetative growth rates in vitro. Interestingly, addition of long polypeptides to spores of both Δabste12 and Δabnik1 during inoculations resulted in a complete restoration of pathogenicity through a yet to be defined mechanism.
Comparing methods of analysing datasets with small clusters: case studies using four paediatric datasets
Authors: Marston Louise , Peacock Janet L. , Yu Keming , Brocklehurst Peter , Calvert Sandra A. , Greenough Anne , Marlow Neil 
Published: May 2009

SummaryStudies of prematurely born infants contain a relatively large percentage of multiple births, so the resulting data have a hierarchical structure with small clusters of size 1, 2 or 3. Ignoring the clustering may lead to incorrect inferences. The aim of this study was to compare statistical methods which can be used to analyse such data: generalised estimating equations, multilevel models, multiple linear regression and logistic regression. Four datasets which differed in total size and in percentage of multiple births (n = 254, multiple 18%; n = 176, multiple 9%; n = 10 098, multiple 3%; n = 1585, multiple 8%) were analysed.With the continuous outcome, two‐level models produced similar results in the larger dataset, while generalised least squares multilevel modelling (ML GLS ‘xtreg’ in Stata) and maximum likelihood multilevel modelling (ML MLE ‘xtmixed’ in Stata) produced divergent estimates using the smaller dataset. For the dichotomous outcome, most methods, except generalised least squares multilevel modelling (ML GH ‘xtlogit’ in Stata) gave similar odds ratios and 95% confidence intervals within datasets. For the continuous outcome, our results suggest using multilevel modelling.We conclude that generalised least squares multilevel modelling (ML GLS ‘xtreg’ in Stata) and maximum likelihood multilevel modelling (ML MLE ‘xtmixed’ in Stata) should be used with caution when the dataset is small. Where the outcome is dichotomous and there is a relatively large percentage of non‐independent data, it is recommended that these are accounted for in analyses using logistic regression with adjusted standard errors or multilevel modelling. If, however, the dataset has a small percentage of clusters greater than size 1 (e.g. a population dataset of children where there are few multiples) there appears to be less need to adjust for clustering.
Analgesia for labour: a survey of Norwegian practice – with a focus on parenteral opioids
Authors: TVEIT T. O. , HALVORSEN A. , ROSLAND J. H. 
Published: May 2009

Background: During the last two decades, epidural analgesia has become ‘a gold standard’ for labour pain in most Western countries. Newer short‐acting opioids given systemically represent an alternative for adequate pain relief without using regional techniques. With this survey, we wish to explore how Norwegian hospitals practice labour analgesia, especially their use of systemic opioids.Methods: A questionnaire was sent to the head of all 46 registered Norwegian labour units in 2005. The questionnaire focused on epidural and the use of systemic opioids. In 2008, the same questionnaire was sent to the 19 largest units reporting >1000 births a year, seeking updated information.Results: Forty‐three of the 46 original questionnaires were returned. An epidural frequency of 25.9% was registered. For epidural treatment, bupivacaine was the preferred local anaesthetic, while sufentanil was the opioid of choice for the majority of units. Pethidine was the most commonly used opioid for systemic administration (77%). All units reported nurse administration of systemic opioids. The intramuscular route was most commonly used, either alone (58%) or in combination with an intravenous (i.v.) administration (34%). Only one unit used i.v. fentanyl. There were only minor changes with the repeated survey, except for one large unit, which reported over a 50% increase in the epidural frequency.Conclusion: In Norway, the frequency of epidural for labour analgesia is still relatively low, but seems to be increasing. Systemic opioids are often used instead of or as a supplement. Clinical practice seems to be conservative, and newer short‐acting opioids are seldom used systemically.