bluuebunny/crossref_metadata_2025_split huggingface dataset:
First Record of Bacterial Blight Caused by Pseudomonas syringae pv. syringae on Pyracantha coccinea and an Amelanchier sp. in Bulgaria
Authors: Bobev S. G. , Baeyen S. , Van Vaerenbergh J. , Maes M. 
Published: July 2008

During the spring and summer months of 2004 and 2005, sporadic damage on individual shrubs of Pyracantha coccinea and an Amelanchier sp. were observed at two locations in the region of Plovdiv, Bulgaria. Symptoms initially were expressed as blossom blight and subsequently expanded to the shoots and branches, forming cankers on the supplying wood. In both years, a fluorescent gram-negative bacterium was isolated from diseased tissues onto King's B medium. The bacterial strains were levan positive and oxidase and arginine dihydrolase negative. They were able to induce a typical hypersensitive response on tobacco plants (cv. Samsun), but failed to rot potato slices. Pathogenicity of the strains was confirmed by puncture-inoculating detached shoots from both hosts and immature cherry and pear fruits with a bacterial suspension (108 CFU/ml, 50 μl per wound, and 3 replicates). Controls were punctured with sterile water. The inoculated plant material was maintained at room temperature (22 to 25°C) in plastic pots and covered with polyethylene bags for the first 48 h after inoculation. The inoculated and control subjects were kept under the same conditions as before inoculation. Except for the controls, slowly expanding but well defined necrotic lesions around the inoculation points were observed within the next 5 to 7 days. Bacteria reisolated from symptomatic tissue were identical to the initial cultures. On the basis of the symptoms and results from all laboratory tests, the bacterium was considered to be Pseudomonas syringae pv. syringae (1). PCR amplification of the 752-bp syrB fragment (2) confirmed the identification. To our knowledge, this is the first occurrence of P. syringae pv. syringae on Pyracantha coccinea and an Amelanchier sp. in Bulgaria, and most probably, this pathogen will play a more significant role within the rosaceous group because of a rising number of the cultivated ornamental species. References: (1) N. W. Schaad et al., eds. Laboratory Guide for Identification of Plant Pathogenic Bacteria. 3rd ed. The American Phytopathological Society, St. Paul, MN, 2001. (2) K. N. Sorensen et al. Appl. Environ. Microbiol. 64:226, 1998.
First Report of Apium virus Y on Cilantro, Celery, and Parsley in California
Authors: Tian T. , Liu H.-Y. , Koike S. T. 
Published: July 2008

Recently, Apium virus Y (ApVY) was detected in field-grown cilantro (Coriandrum sativum), celery (Apium graveolens), and parsley (Petroselinum crispum) in California. In 2003, cilantro plants growing in three different fields in California (Monterey, San Joaquin, and San Luis Obispo counties) expressed symptoms of mosaic, vein clearing, and stunting. When plant sap was examined by transmission electron microscopy, flexuous, rod-shaped virus particles were observed. Total RNA was extracted from the symptomatic cilantro plants and used as a template in reverse transcription (RT)-PCR using universal potyvirus primers according to Chen et al. (1). The RT-PCR product was cloned into pGEM-T (Promega, Madison, WI) and the insert of 1,713 bp was sequenced (GenBank Accession No. EU515125). Nucleotide sequences from clones derived from three different infected cilantro plants were 89 to 97% identical to ApVY sequences encoding partial sequence of polyprotein in GenBank (Accession Nos. AY049716, EU127499, AF207594, AF203529, and EU255632). In 2007, celery plants showing necrotic line patterns and necrotic lesions on lower leaves and petioles were observed in several fields in two coastal counties in California (Monterey and Santa Clara counties). Flexuous, rod-shaped virus particles were also observed in the sap of those plants. ELISA for Cucumber mosaic virus and RT-PCR for Celery mosaic virus were negative. ApVY specific primers were designed on the basis of a consensus sequence of ApVY identified from cilantro in 2003; reverse primer 5′-GGCTCTTGCTATAGACAAATAGT-3′ and forward primer 5′-GAAGACCAAGCCAATGTGTGTA-3′. The sequence of RT-PCR products (GenBank Accession No. EU515126) amplified from infected celery had 90 to 98% nucleotide identity to ApVY. When the deduced amino acid sequences of NIb and CP regions from both cilantro and celery were used for comparison, they showed 95 to 99% identity with the known ApVY GenBank sequences mentioned above. More than 10 asymptomatic parsley plants growing in fields adjacent to the infected celery were also tested for ApVY and found to be infected. ApVY was previously identified in three Apiaceae weeds in Australia (2) and in celery in New Zealand (3). To our knowledge, this is the first report of ApVY on cilantro, celery, and parsley in California. References: (1) J. Chen et al. Arch. Virol. 146:757, 2001. (2) J. Moran et al. Arch. Virol. 147:1855, 2002. (3) J. Tang et al. Plant Dis. 91:1682, 2007.
Characterization of Iris yellow spot virus from Onion in Arizona
Authors: Pappu Hanu , Matheron Michael 
Published: July 2008

Iris yellow spot virus is an economically important pathogen affecting both bulb and seed onion crops in the US and several parts of the world. In January 2008, two commercial onion fields in Yuma County, Arizona, had plants with symptoms suggestive of IYSV infection. IYSV infection was confirmed by ELISA, and the virus infection was further verified by reverse transcription-polymerase chain reaction. Accepted for publication 29 May 2008. Published 11 July 2008.
A molecular phylogeny of fleas (Insecta: Siphonaptera): origins and host associations
Authors: Whiting Michael F. , Whiting Alison S. , Hastriter Michael W. , Dittmar Katharina 
Published: July 2008

AbstractSiphonaptera (fleas) is a highly specialized order of holometabolous insects comprising ∼2500 species placed in 16 families. Despite a long history of extensive work on flea classification and biology, phylogenetic relationships among fleas are virtually unknown. We present the first formal analysis of flea relationships based on a molecular matrix of four loci (18S ribosomal DNA, 28S ribosomal DNA, Cytochrome Oxidase II, and Elongation Factor 1‐alpha) for 128 flea taxa from around the world representing 16 families, 25 subfamilies, 26 tribes, and 83 flea genera with eight outgroups. Trees were reconstructed using direct optimization and maximum likelihood techniques. Our analysis supports Tungidae as the most basal flea lineage, sister group to the remainder of the extant fleas. Pygiopsyllomorpha is monophyletic, as are the constituent families Lycopsyllidae, Pygiopsyllidae, and Stivaliidae, with a sister group relationship between the latter two families. Macropsyllidae is resolved as sister group to Coptopsyllidae with moderate nodal support. Stephanociricidae is monophyletic, as are the two constituent subfamilies Stephanocircinae and Craneopsyllinae. Vermipsyllidae is placed as sister group to Jordanopsylla. Rhopalopsyllidae is monophyletic as are the two constituent subfamilies Rhopalopsyllinae and Parapsyllinae. Hystrichopsyllidae is paraphyletic with Hystrichopsyllini placed as sister to some species of Anomiopsyllini and Ctenopariini placed as sister to Carterettini. Ctenophthalmidae is grossly paraphyletic with the family broken into seven lineages dispersed on the tree. Most notably, Anomiopsyllini is paraphyletic. Pulicidae and Chimaeropsyllidae are both monophyletic and these families are sister groups. Ceratophyllomorpha is monophyletic and includes Ischnopsyllidae, Ceratophyllidae, and Leptopsyllidae. Leptopsyllidae is paraphyletic as are its constituent subfamilies Amphipsyllinae and Leptopsyllinae and the tribes Amphipsyllini and Leptopsyllini. Ischnopsyllidae is monophyletic. Ceratophyllidae is monophyletic, with a monophyletic Dactypsyllinae nested within Ceratophyllinae, rendering the latter group paraphyletic. Mapping of general host associations on our topology reveals an early association with mammals with four independent shifts to birds.© The Willi Hennig Society 2008.
Finding an upper limit for gap costs in direct optimization parsimony
Authors: Spagna Joseph C. , Álvarez‐Padilla Fernando 
Published: July 2008

AbstractExploring a large number of parameter sets in sensitivity analyses of direct optimization parsimony can be costly in terms of time and computing resources, and there is little a priori guidance available for reasonable limits to these search parameters. For this reason, we sought a general‐purpose upper limit for gap costs in the direct optimization program POY to streamline this process. To test the performance of POY as gap costs increase, we simulated data onto a pre‐set topology using a GTR + I + G model modified to include gaps by adding them according to a negative‐binomial model. Gaps were then removed and the data were analysed in POY at increasing gap costs. Increasing gap costs consistently resulted in reduced phylogenetic accuracy across trees of different relative branch lengths. Decoupling gap insertion and gap extension costs recovered a fraction of the accuracy lost by having both high gap insertion and gap extension costs, but only in trees with long internal nodes. To determine whether loss of phylogenetic accuracy was node‐specific, we designed a small dataset with a constrained node, where all possible combinations of cost substitution and different percentages of gap versus nucleotide changes were explored. These analyses showed that the effects of gap insertion and extension are node‐specific, and the minimum threshold for convergence on gap‐supported nodes is similar to the threshold for accuracy loss found in the larger simulated datasets. Subsequent analyses of empirical data revealed that a similar pattern of loss with gap cost increase can occur with ribosomal genes (18S, 28S, 16S and 12S) but this pattern was not seen in the intron data (myoglobin II) examined. In conjunction with previously published congruence‐based studies, the results suggest that POY sensitivity analyses can be streamlined and made more accurate if gap insertion and extension costs follow, as a guideline, a limit of four times the highest base‐transformation cost.© The Willi Hennig Society 2008.
Parsimony and explanatory power
Authors: Farris James S. 
Published: July 2008

AbstractParsimony can be related to explanatory power, either by noting that each additional requirement for a separate origin of a feature reduces the number of observed similarities that can be explained as inheritance from a common ancestor; or else by applying Popper’s formula for explanatory power together with the fact that parsimony yields maximum likelihood trees under No Common Mechanism (NCM). Despite deceptive claims made by some likelihoodists, most maximum likelihood methods cannot be justified in this way because they rely on unrealistic background assumptions. These facts have been disputed on the various grounds that ad hoc hypotheses of homoplasy are explanatory, that they are not explanatory, that character states are ontological individuals, that character data do not comprise evidence, that unrealistic theories can be used as background knowledge, that NCM is unrealistic, and that likelihoods cannot be used to evaluate explanatory power. None of these objections is even remotely well founded, and indeed most of them do not even seem to have been meant seriously, having instead been put forward merely to obstruct the development of phylogenetic methods.© The Willi Hennig Society 2008.
Large genetic divergence of new, morphologically similar species of sterile lichens from Europe (Lepraria, Stereocaulaceae, Ascomycota): concordance of DNA sequence data with secondary metabolites
Authors: Fehrer Judith , Slavíková‐Bayerová Štěpánka , Orange Alan 
Published: July 2008

AbstractLichenized fungi of the genus Lepraria are known for their paucity of morphological characters. Species identification is therefore largely based on secondary chemistry. We investigated different chemotypes of the morphologically highly similar L. jackii species complex by internal transcribed spacer (ITS) sequencing. In phylogenetic analyses including all available Lepraria species, samples belonging to different chemotypes of the L. jackii agg. corresponded to four highly divergent clusters. While true L. jackii was genetically uniform, the other three clades represented previously unrecognized species. They originated from different major speciation events, and two of them were not closely related to any other species. Assessment of intraspecific genetic variability revealed four different patterns with respect to geographic scale. ITS sequences proved to be the most reliable and distinctive characters for species recognition in the Lepraria jackii complex and were in accordance with chemical and ecogeographic data. Frequent occurrence of long branches, relatively few resolved relationships despite high genetic variability, and the discovery and description of a considerable part of the Lepraria species within the last 10 years suggest that the genus is probably much larger than currently known. The diversification of this asexual group in the potential absence of recombination is discussed.© The Willi Hennig Society 2008.
TNT, a free program for phylogenetic analysis
Authors: Goloboff Pablo A. , Farris James S. , Nixon Kevin C. 
Published: July 2008

AbstractThe main features of the phylogeny program TNT are discussed. Windows versions have a menu interface, while Macintosh and Linux versions are command‐driven. The program can analyze data sets with discrete (additive, non‐additive, step‐matrix) as well as continuous characters (evaluated with Farris optimization). Effective analysis of large data sets can be carried out in reasonable times, and a number of methods to help identifying wildcard taxa in the case of ambiguous data sets are implemented. A variety of methods for diagnosing trees and exploring character evolution is available in TNT, and publication‐quality tree‐diagrams can be saved as metafiles. Through the use of a number of native commands and a simple but powerful scripting language, TNT allows the user an enormous flexibility in phylogenetic analyses or simulations.© The Willi Hennig Society 2008.
Phylum Tardigrada: an “individual” approach
Authors: Sands Chester J. , McInnes Sandra J. , Marley Nigel J. , Goodall‐Copestake William P. , Convey Peter , Linse Katrin 
Published: July 2008

AbstractPhylum Tardigrada consists of ∼1000 tiny, hardy metazoan species distributed throughout terrestrial, limno‐terrestrial and oceanic habitats. Their phylogenetic status has been debated, with current evidence placing them in the Ecdysozoa. Although there have been efforts to explore tardigrade phylogeny using both morphological and molecular data, limitations such as their few morphological characters and low genomic DNA concentrations have resulted in restricted taxonomic coverage. Using a protocol that allows us to identify and extract DNA from individuals, we have sequenced 18S rDNA from 343 tardigrades from across the globe. Using maximum parsimony and Bayesian analyses we have found support for dividing Order Parachela into three super‐families and further evidence that indicates the traditional taxonomic perspective of families in the class Eutardigrada are nonmonophyletic and require re‐working. It appears that conserved morphology within Tardigrada has resulted in conservative taxonomy as we have found cases of several discrete lineages grouped into single genera. Although this work substantially adds to the understanding of the evolution and taxonomy of the phylum, we highlight that inferences gained from this work are likely to be refined with the inclusion of further taxa—specifically representatives of the nine families yet to be sampled.© The Willi Hennig Society 2008.
Accumulation of the hormone abscisic acid (ABA) at the infection site of the fungus Cercospora beticola supports the role of ABA as a repressor of plant defence in sugar beet
Authors: SCHMIDT KLAUS , PFLUGMACHER MAIKE , KLAGES SIMONE , MÄSER ANJA , MOCK ANDREA , STAHL DIETMAR J. 
Published: July 2008

SUMMARYInducible plant defence responses in sugar beet (Beta vulgaris L.) leaves are repressed during the early phase of infection by the fungus Cercospora beticola. In this report, we show that the concentration of the plant hormone abscisic acid (ABA) increases in sugar beet leaves during C. beticola infection. After an initial burst of ABA induced by inoculation of the fungus, elevated ABA concentrations were detected during the fungal penetration and colonization phases 3–9 days after inoculation. Fifteen days after inoculation, with visible onset of the necrotic phase of infection, the strongly elevated ABA concentrations in infected leaves were at levels similar to drought‐stressed plants. A synthetic promoter composed of four copies of the ABA‐responsive element (ABRE) A2 and the coupling element CE3 of the ABA‐inducible barley gene HVA1 was strongly induced by ABA and C. beticola infection in transgenic sugar beet leaves. Analysis of the spatial pattern of promoter activity revealed that the ABA‐inducible promoter was locally activated at the fungal infection sites. Furthermore, expression of the basic leucine zipper transcription factor AREB1 was induced by drought stress and fungal infection in the sugar beet. Application of ABA reduced the promoter activity of the phenylalanine ammonia lyase (BvPAL) gene, and this effect was observed with the –34 to +248 BvPAL promoter region. This region is equivalent to the core promoter, which is necessary for the suppression of BvPAL expression by C. beticola, as recently shown. These data indicate that ABA accumulation and activation of the ABA‐dependent signalling cascade are the primary cause of suppression of BvPAL expression during infection of sugar beet leaves.
Paroxetine and fluoxetine in pregnancy: a prospective, multicentre, controlled, observational study
Authors: Diav‐Citrin Orna , Shechtman Svetlana , Weinbaum Dafna , Wajnberg Rebecka , Avgil Meytal , Di Gianantonio Elena , Clementi Maurizio , Weber‐Schoendorfer Corinna , Schaefer Christof , Ornoy Asher 
Published: July 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • In recent years there has been concern regarding the possibility that selective serotonin reuptake inhibitors (SSRIs) cause an increased rate of congenital cardiovascular anomalies.• As of today, there is still debate in the literature as to the possible effects of paroxetine and fluoxetine on the embryonic cardiovascular system. WHAT THIS STUDY ADDS • Based on prospective data from three Teratogen Information Services, we have demonstrated an increased rate of congenital cardiovascular anomalies among the offspring of fluoxetine‐ and paroxetine‐treated mothers.AIMSRecent studies have suggested a possible association between maternal use of selective serotonin reuptake inhibitors (SSRIs) in early pregnancy and cardiovascular anomalies. The aim of the present study was to evaluate the teratogenic risk of paroxetine and fluoxetine.METHODSThis multicentre, prospective, controlled study evaluated the rate of major congenital anomalies after first‐trimester gestational exposure to paroxetine, fluoxetine or nonteratogens.RESULTSWe followed up 410 paroxetine, 314 fluoxetine first‐trimester exposed pregnancies and 1467 controls. After exclusion of genetic and cytogenetic anomalies, there was a higher rate of major anomalies in the SSRI groups compared with the controls [paroxetine 18/348 (5.2%), fluoxetine 12/253 (4.7%) and controls 34/1359 (2.5%)]. The main risk applied to cardiovascular anomalies [paroxetine 7/348 (2.0%), crude odds ratio (OR) 3.47, 95% confidence interval (CI) 1.13, 10.58; fluoxetine 7/253 (2.8%), crude OR, 4.81 95% CI 1.56, 14.71; and controls 8/1359 (0.6%)]. On logistic regression analysis only cigarette smoking of ≥10 cigarettes day−1 and fluoxetine exposure were significant variables for cardiovascular anomalies. The adjusted ORs for paroxetine and fluoxetine were 2.66 (95% CI 0.80, 8.90) and 4.47 (95% CI 1.31, 15.27), respectively.CONCLUSIONThis study suggests a possible association between cardiovascular anomalies and first‐trimester exposure to fluoxetine.
Effect of sample size on cyst recovery by flotation methods: Recommendations for sample processing during EU monitoring of potato cyst nematodes (Globodera spp.)
Authors: Bellvert J. , Crombie K. , Horgan F. G. 
Published: July 2008

Under EC Council Directive 2007/33/EC member states of the European Union are recommended to take soil samples ranging from 100 mL to >1500 mL to monitor populations of potato cyst nematodes [PCN] (Globodera spp.) in targeted fields. This study examines the effects of varying sample size on sample processing and cyst extraction using two widely used laboratory methods. Cyst recovery was stable using the Fenwick can from 100 mL up to the physical limits of the can. Recovery was significantly lower for low density 50 mL samples; however, this was partly due to a statistical artefact since higher numbers of cysts were lost from successively larger samples with constant cyst numbers (i.e. decreasing densities). The Schuiling centrifuge had functional limits of <100 mL and >500 mL. Outside this range, cyst recovery from low density samples was significantly reduced. Cyst recovery from samples of varying size, but with equal numbers of cysts was only constant above 100 mL. However, samples ranging from 200–500 mL were optimal for the Schuiling centrifuge. Cyst extraction efficiency was similar using both methods for samples ranging from 150 mL to 1500 mL, where larger samples were divided into <500 mL portions. However, processing times (i.e. cyst extraction and microscopic examination) and water consumption increased significantly with increasing sample size and were significantly higher when using the Fenwick can.
The Nordic Baltic forum for plant health diagnostic laboratories and its use of ‘on‐site’ proficiency testing to improve laboratory testing1
Authors: Thrane C. , Boa E. 
Published: July 2008

During an Estonia‐UK‐Denmark twinning project, a new forum for Plant Health Diagnostic Laboratories in the Nordic‐Baltic region emerged. At the first meeting held in Estonia in July 2006, a new approach to proficiency testing was evaluated. Proficiency tests are key elements assessing the ability of a laboratory to perform a certain test in comparison with other laboratories. ‘On‐site’ proficiency testing means that experts are meeting to look at exactly the same samples under the same conditions on the same day. This is especially relevant for tests based on morphological interpretation as this minimizes the inherent differences in samples due to natural variation within a given species. The benefits of ‘on‐site’ proficiency testing outweigh the additional costs of organising a regional meeting which might include discussion of related scientific topics.Diagnostic capacity is an essential part of European Plant Health policies but staff may be spread out in different laboratories and countries. ‘On‐site’ proficiency testing helps create a stronger group identity for diagnosticians as well as maintaining quality control. In the plant health field there are also several difficulties in organising conventional proficiency tests. This is further discussed in the paper.