bluuebunny/crossref_metadata_2025 huggingface dataset:
Long‐term follow‐up of the hepatitis C HENCORE cohort: response to therapy and occurrence of liver‐related complications
Authors: Pradat P. , Tillmann H. L. , Sauleda S. , Braconier J.‐H. , Saracco G. , Thursz M. , Goldin R. , Winkler R. , Alberti A. , Esteban J.‐I. , Hadziyannis S. , Rizzetto M. , Thomas H. , Manns M. P. , Trepo C. ,   for the HENCORE group
Published: December 2006

Summary.  The aims of the study were to verify the long‐term effect of time on viral clearance in hepatitis C virus (HCV) patients and to find out factors possibly associated with disease progression. A total of 1641 patients recruited from eight European centres in 1996–1997 were re‐analysed 5–7 years after inclusion. The occurrence of decompensated cirrhosis, hepatocellular carcinoma (HCC) and liver transplantation was analysed in relation to different host and viral factors. Ninety‐three per cent of the HCV patients who had cleared the virus (spontaneously or after antiviral therapy) remained HCV‐RNA‐negative during follow up and may be considered as ‘cured’. Among patients who were sustained responders at inclusion, 2.3% developed liver complications during follow up, and 31% of non‐responders did. Advanced age at infection and presence of the human leucocyte antigen (HLA) DRB1*1201–3 allele were possibly associated with a higher rate of progression to decompensated cirrhosis or HCC. Decompensated cirrhosis might be further associated with male gender, non‐response to previous therapy, and lack of HLA DRB1*1301 allele, whereas HCC seems to be associated with the presence of the HLA DQ02 allele. Long‐term follow up of HCV patients indicates that virological response persists over time and is associated with a very low incidence of liver complications. Advanced age at inclusion, advanced age at infection, viral genotype 1, non‐response to previous therapy and possibly some specific HLA alleles are factors independently associated with a faster rate of progression towards liver complications. The large proportion of patients lost to follow up stresses the need for a strengthened and optimized management of HCV patients.
Does soil type drive social organization in southern hairy‐nosed wombats?
Authors: WALKER FAITH M. , TAYLOR ANDREA C. , SUNNUCKS PAUL
Published: December 2006

Spatiotemporal distributions of key resources are hypothesized to underpin sociobiological patterns. Burrow availability and quality is of paramount importance to fossorial animals. The southern hairy‐nosed wombat (Lasiorhinus latifrons) burrows in both hard and friable soils. Theoretical and empirical studies suggest that the harder substrate should promote closer geographical clustering of burrows than in softer soils. Clustered burrows are expected to be associated with larger group sizes. If sociality is driven by constraint rather than advantage, patterns of spatial and temporal distribution of animals within and among groups may show indications of avoidance or even antagonism, and ‘making the best of a bad job’ via positive kin associations to offset the disadvantages of high‐density living. To test these ideas, we compared warren relatedness and social structure of L. latifrons on friable soils (Nullarbor Plain) and hard calcrete (Brookfield Conservation Park, BCP). Individuals were sampled by noninvasive collection of hairs for genotyping to identify individuals and to estimate their space‐use and associative behaviour with respect to relatedness. Burrows in calcrete were indeed more clumped, and warren and group size larger. Differences in spatiotemporal organization and relatedness structure between sites were in the expected direction: (i) Nullarbor males associated and shared warrens less than at BCP; and (ii) Nullarbor spatial relatedness patterning data were not consistent with proposed female breeding dispersal, in contrast to those at BCP. Under Nullarbor (low density) conditions, cooperation or tolerance between males may be less advantageous, and accessing or digging burrows should be less of a constraint for juvenile females.
Local adaptation and pronounced genetic differentiation in an extremophile fish, Poecilia mexicana, inhabiting a Mexican cave with toxic hydrogen sulphide
Authors: PLATH M. , HAUSWALDT J. S. , MOLL K. , TOBLER M. , GARCÍA DE LEÓN F. J. , SCHLUPP I. , TIEDEMANN R.
Published: December 2006

We investigated genetic differentiation and migration patterns in a small livebearing fish, Poecilia mexicana, inhabiting a sulfidic Mexican limestone cave (Cueva del Azufre). We examined fish from three different cave chambers, the sulfidic surface creek draining the cave (El Azufre) and a nearby surface creek without the toxic hydrogen sulphide (Arroyo Cristal). Using microsatellite analysis of 10 unlinked loci, we found pronounced genetic differentiation among the three major habitats: Arroyo Cristal, El Azufre and the cave. Genetic differentiation was also found within the cave between different pools. An estimation of first‐generation migrants suggests that (i) migration is unidirectional, out of the cave, and (ii) migration among different cave chambers occurs to some extent. We investigated if the pattern of genetic differentiation is also reflected in a morphological trait, eye size. Relatively large eyes were found in surface habitats, small eyes in the anterior cave chambers, and the smallest eyes were detected in the innermost cave chamber (XIII). This pattern shows some congruence with a previously proposed morphocline in eye size. However, our data do not support the proposed mechanism for this morphocline, namely that it would be maintained by migration from both directions into the middle cave chambers. This would have led to an increased variance in eye size in the middle cave chambers, which we did not find. Restricted gene flow between the cave and the surface can be explained by local adaptations to extreme environmental conditions, namely H2S and absence of light. Within the cave system, habitat properties are patchy, and genetic differentiation between cave chambers despite migration could indicate local adaptation at an even smaller scale.
Recognizing diversity in coral symbiotic dinoflagellate communities
Authors: APPRILL AMY M. , GATES RUTH D.
Published: December 2006

A detailed understanding of how diversity in endosymbiotic dinoflagellate communities maps onto the physiological range of coral hosts is critical to predicting how coral reef ecosystems will respond to climate change. Species‐level taxonomy of the dinoflagellate genus Symbiodinium has been predominantly examined using the internal transcribed spacer (ITS) region of the nuclear ribosomal array (rDNA ITS2) and downstream screening for dominant types using denaturing gradient gel electrophoresis (DGGE). Here, ITS2 diversity in the communities of Symbiodinium harboured by two Hawaiian coral species was explored using direct sequencing of clone libraries. We resolved sixfold to eightfold greater diversity per coral species than previously reported, the majority of which corresponds to a novel and distinct phylogenetic lineage. We evaluated how these sequences migrate in DGGE and demonstrate that this method does not effectively resolve this diversity. We conclude that the Porites spp. examined here harbour diverse assemblages of novel Symbiodinium types and that cloning and sequencing is an effective methodological approach for resolving the complexity of endosymbiotic dinoflagellate communities harboured by reef corals.
Phylogeographic patterns inDrosophila montana
Authors: MIROL P. M. , SCHÄFER M. A. , ORSINI L. , ROUTTU J. , SCHLÖTTERER C. , HOIKKALA A. , BUTLIN R. K.
Published: December 2006

TheDrosophila virilisspecies group offers valuable opportunities for studying the roles of chromosomal re‐arrangements and mating signals in speciation. The 13 species are divided into two subgroups, the montana and virilis ‘phylads’. There is greater differentiation among species within the montana phylad in both karyotype and acoustic signals than exists among members of the virilis phylad.Drosophila montanais a divergent species which is included in the montana phylad. Here, we analyse the phylogeography ofD. montanato provide a framework for understanding divergence of acoustic signals among populations. We analysed mitochondrial sequences corresponding to the cytochrome oxidase I and cytochrome oxidase II genes, as well as 16 microsatellite loci, from 108 lines ofD. montanacovering most of the species’ range. The species shows a clear genetic differentiation between North American and Scandinavian populations. Microsatellite allele frequencies and mitochondrial DNA haplotypes gave significantFSTvalues between populations from Canada, USA and Finland. A Bayesian analysis of population structure based on the microsatellite frequencies showed four genetically distinct groups, corresponding to these three populations plus a small sample from Japan. A network based on mitochondrial haplotypes showed two Finnish clades of very different shape and variability, and another clade with all sequences from North America and Japan. AllD. montanapopulations showed evidence of demographic expansion but the patterns inferred by coalescent analysis differed between populations. The divergence times between Scandinavian and North American clades were estimated to range from 450 000 to 900 000 years with populations in Canada and the USA possibly representing descendants of different refugial populations. Long‐term separation ofD. montanapopulations could have provided the opportunity for differentiation observed in male signal traits, especially carrier frequency of the song, but relaxation of sexual selection during population expansion may have been necessary.
Parasite phylogeographical congruence with salmon host evolutionarily significant units: implications for salmon conservation
Authors: CRISCIONE CHARLES D. , BLOUIN MICHAEL S.
Published: December 2006

Comparative phylogeographical studies between parasites and their hosts or with biogeographical regions are useful to predict parasite dispersal potential over a broad geographical range. We used both microsatellite markers and mtDNA sequence data from a trematode parasite, Plagioporus shawi, to test for congruence across two evolutionarily significant unit (ESU) boundaries of its salmonid hosts (Oncorhynchus spp.). We find congruent patterns with the nuclear loci of P. shawi and the ESU boundaries of its salmonid hosts. This pattern indicates that broad‐scale phylogeographical patterns of a parasite can be predicted by the biogeographical history of their hosts. Furthermore, this pattern provides independent support for these ESU boundaries as biologically relevant barriers. The mtDNA shows some discordance with nuclear loci and a level of genetic differentiation greater than can be explained by genetic drift. Thus, the mtDNA cannot be used in isolation to infer the population history of P. shawi. The genetic differentiation at both the nuclear and mtDNA markers will be useful for salmon fisheries management by providing a tool to assign ocean‐migrating salmonids back to their freshwater population of origin.
A novel protein kinase family in Plasmodium falciparum is differentially transcribed and secreted to various cellular compartments of the host cell
Authors: Nunes Marta C. , Goldring J. P. Dean , Doerig Christian , Scherf Artur
Published: December 2006

Processes at the surface of Plasmodium falciparum‐infected erythrocytes such as antigenic variation and cytoadhesion may be modulated by active signalling between host and parasite. Potential candidates for this role include the putative kinases of the FIKK family. The novel Apicomplexa‐specific FIKK gene has expanded in P. falciparum to 20 sequence‐related members distributed between 11 chromosomes. Specific antibodies raised against different members indicated that most FIKK proteins locate to punctate foci in the erythrocyte cytoplasm that colocalized with Maurer's clefts proteins. One FIKK member dissociates at the trophozoite stage from the Maurer's clefts and relocates with the erythrocyte cytoskeleton. Another FIKK protein, despite having a PEXEL motif, remains located within the parasite. FIKK proteins possess the essential residues for phosphotransferase activity. We show that protein kinase activity was detected in immunoprecipitates obtained with two anti‐FIKK antibodies. Quantitative PCR analysis revealed differential gene transcription of the FIKK paralogues in asexual blood stages parasites. We observed significant changes in the transcription pattern between parasites with different adhesion phenotypes. Our data suggest a role of FIKK proteins in the remodelling of the erythrocyte surface and reveal the existence of an adaptable parasite system able to sense intra‐ and possibly extracellular changes.
Interplay between primase and replication factor C in the hyperthermophilic archaeonSulfolobus solfataricus
Authors: Wu Kangyun , Lai Xiaoqin , Guo Xin , Hu Jinchuan , Xiang Xiaoyu , Huang Li
Published: December 2006

The heterodimeric primase from the hyperthermophilic archaeonSulfolobus solfataricussynthesizes long RNA and DNA productsin vitro. How primer synthesis by primase is coupled to primer extension by DNA polymerase in this organism is unclear. Here we show that the small subunit of the clamp loader replication factor C (RFC) ofS. solfataricusinteracted with both the catalytic and non‐catalytic subunits of the primase by yeast two‐hybrid and co‐immunoprecipitation assays. Further, the primase–RFC interaction was also identified in the cell extract ofS. solfataricus. Deletion analysis indicated that the small subunit of RFC interacted strongly with the N‐terminal domain of the catalytic subunit of the primase. RFC stimulated dinucleotide formation but decreased the amount of primers synthesized by the primase. The inhibition of primer synthesis is consistent with the observation that RFC reduced the affinity of the primase for DNA templates. On the other hand, primase stimulated the ATPase activity of RFC. These findings suggest that the primase–RFC interaction modulates the activities of both enzymes and therefore may be involved in the regulation of primer synthesis and the transfer of primers to DNA polymerase in Archaea.
Antimicrobial peptides activate the Vibrio choleraeσE regulon through an OmpU‐dependent signalling pathway
Authors: Mathur Jyoti , Davis Brigid M. , Waldor Matthew K.
Published: December 2006

Vibrio cholerae, an enteric pathogen, is subject to assault by several membrane‐acting, host gut‐derived antimicrobial peptides (AP). We previously found that a major V. cholerae outer membrane protein, OmpU, confers resistance to polymyxin B and to a bioactive peptide (P2) derived from the human bactericidal/permeability‐increasing protein. Here, we report that the alternative sigma factor σE also plays a critical role in determining V. cholerae resistance to AP and that OmpU and σE lie in the same pathway. In fact, we found that OmpU is a key determinant of basal σE expression. We also found that sublethal AP exposure activates σE and the σE‐mediated periplasmic stress response. σE is not activated by P2 in V. cholerae cells lacking OmpU or DegS, a periplasmic protease that controls σE activity. The lack of AP‐elicited σE activation in a strain harbouring a point mutation in OmpU's putative DegS‐binding residues provides support for a link between OmpU and DegS‐mediated activation of σE. We propose that AP‐induced membrane perturbations change the conformation of OmpU to trigger a DegS‐dependent σE‐activating cascade. Thus, OmpU appears to act as a sensor component in a signal transduction pathway.
The small nucleoid protein Fis is involved in Vibrio cholerae quorum sensing
Authors: Lenz Derrick H. , Bassler Bonnie L.
Published: December 2006

Quorum sensing is a process of cell–cell communication that bacteria use to relay information to one another about the cell density and species composition of the bacterial community. Quorum sensing involves the production, secretion and population‐wide detection of small signalling molecules called autoinducers. This process allows bacteria to synchronize group behaviours and act as multicellular units. The human pathogen, Vibrio cholerae, uses quorum sensing to co‐ordinate such complex behaviours as pathogenicity and biofilm formation. The quorum‐sensing circuit of V. cholerae consists of two autoinducer/sensor systems, CAI‐1/CqsS and AI‐2/LuxPQ, and the VarS/A‐CsrA/BCD growth‐phase regulatory system. Genetic analysis suggests that an additional regulatory arm involved in quorum sensing exists in V. cholerae. All of these systems channel information into the histidine phosphotransfer protein, LuxU, and/or the response regulator, LuxO. LuxO, when phosphorylated, activates the expression of four genes encoding the Qrr (quorum regulatory RNAs) small RNAs (sRNAs). The Qrr sRNAs destabilize the hapR transcript encoding the master regulator of quorum sensing, HapR. Here we identify the nucleoid protein Fis as playing a major role in the V. cholerae quorum‐sensing circuit. Fis fulfils the predictions required to be the putative additional component that inputs information into the cascade: its expression is regulated in a growth phase‐dependent manner; it requires LuxO but acts independently of LuxU, and it regulates all four qrr genes and, in turn, HapR by directly binding to the qrr gene promoters and modulating their expression.
Probiotics and irritable bowel syndrome: a rationale for their use and an assessment of the evidence to date
Authors: Quigley E. M. M. , Flourie B.
Published: December 2006

Abstract  Probiotics, defined as live organisms that, when ingested in adequate amounts, exert a health benefit on the host, have been used for almost a century in the management of a variety of medical disorders, usually on the basis of little evidence. Advances in our understanding of the gut flora and of its relationship to the host, together with progress in microbiology, molecular biology and clinical research have identified important biological properties for probiotics and demonstrated efficacy in a number of gastrointestinal disorders. The clear delineation of a post‐infective variety of irritable bowel syndrome (IBS), as well as the description, in a number of studies, of evidence of low‐grade inflammation and immune activation in IBS, suggest a role for a dysfunctional relationship between the indigenous flora and the host in IBS and, accordingly, provide a clear rationale for the use of probiotics in this disorder. Other modes of action, including bacterial displacement and alterations in luminal contents, are also plausible. While clinical evidence of efficacy is now beginning to emerge, a review of available trials emphasises the importance of clear definition of strain selection, dose and viability. This is evidently an area of great potential in IBS and deserves further study at all levels.
The peptide hormone xenin induces gallbladder contractions in conscious dogs
Authors: Kamiyama Y. , Aihara R. , Nakabayashi T. , Mochiki E. , Asao T. , Kuwano H.
Published: December 2006

Abstract  Xenin is a 25‐amino acid peptide isolated from human gastric mucosa. The biological activities of xenin include modulating intestinal motility and affecting exocrine pancreatic secretion and gastric acid secretion. The physiological effect of xenin on the gastrointestinal tract, however, is incomplete. The objective of this study is to investigate the effects of xenin on the gastrointestinal tract motility of conscious dogs. Gastrointestinal tract and gallbladder contractions were monitored by chronically implanted force transducers. Synthetic xenin was injected intravenously during the interdigestive state with or without pretreatment with cholinergic blockers. The effects of xenin following cholecystectomy and truncal vagotomy were also investigated. Xenin induced gallbladder and jejunal contractions, although a dose‐dependent response was shown only with gallbladder contractions. These effects were inhibited by pretreatment with cholinergic blockers, but were not enhanced by truncal vagotomy. The jejunal contractions were completely inhibited by cholecystectomy. The only direct effect of xenin in terms of gastrointestinal motility was to induce gallbladder contractions in conscious dogs. The neural pathway mediating xenin's action was cholinergic, but not the vagal. This novel finding indicates a new role of xenin.
A semiselective medium for the isolation of Acidovorax valerianellae from soil and plant debris
Authors: Grondeau C. , Manceau C. , Samson R.
Published: December 2006

Bacterial black spot of corn‐salad (Valerianella locusta) caused by Acidovorax valerianellae appeared in France in the beginning of the 1990s. The disease is now widespread in the main area of corn‐salad production and is responsible for high depreciation and significant economic losses every year. A semiselective medium is described for the detection of the bacterium in various environments and to identify primary sources of inoculum. The medium TSAV (tryptic soy broth, 3 g L−1, agar 15 g L−1, 5‐fluorouracyl 5 mg L−1, novobiocin 5 mg L−1, propiconazole 5 mg L−1) increased chances of obtaining cultures of A. valerianellae from naturally infested soil and from root‐debris. Using TSAV, the pathogen was detected in root‐debris up to 39 days after the harvest of a diseased crop. As only a few days usually separates harvest from the next sowing date, soil is likely to be an important source of inoculum for the next crop.
Inheritance of resistance to carboxylic acid amide (CAA) fungicides in Plasmopara viticola
Authors: Gisi U. , Waldner M. , Kraus N. , Dubuis P. H. , Sierotzki H.
Published: December 2006

Mandipropamid is a new mandelic acid amide fungicide expressing high activity against foliar infecting oomycetes, including the grapevine downy mildew, Plasmopara viticola. Because cross‐resistance with the valinamide fungicides iprovalicarb and benthiavalicarb and the cinnamic acid amide fungicides dimethomorph and flumorph was postulated, all five compounds are classified as carboxylic acid amide (CAA) fungicides. To support this classification, cross‐resistance among these compounds with field isolates and the segregation of resistance in F1 and F2 progeny of P. viticola were evaluated. A bimodal distribution of sensitivity in field isolates and cross‐resistance among all CAAs for the vast majority of isolates were detected. Crosses between sensitive (s) and CAA‐resistant (r) isolates of opposite mating types, P1 and P2, yielded abundant oospores. All F1‐progeny isolates were sensitive to CAAs (s:r segregation 1:0), whereas in F2 progeny segregation of about 9:1 (s:r) was observed suggesting that resistance to CAA fungicides is controlled by two recessive nuclear genes. Mating type segregated in a ratio P1:P2 of c. 2:1 in F1 and 1:1 in F2 progeny. In the same crosses, resistance to the phenylamide fungicide mefenoxam segregated in a ratio of c. 1:3:2 (sensitive:intermediate:resistant), reflecting the monogenic, semidominant nature of resistance. The risk of resistance in P. viticola was classified as high for phenylamide and moderate for CAA fungicides. This is the first report on the inheritance of phenotypic traits in P. viticola.
Characterization of Rhizoctonia solani from potato in Great Britain
Authors: Woodhall J. W. , Lees A. K. , Edwards S. G. , Jenkinson P.
Published: December 2006

One hundred and thirty five isolates of Rhizoctonia solani were obtained from British potato crops between 2001 and 2003. Isolates were assigned to anastomosis group (AG) using conventional PCR assays for AG2‐1 or AG3 or through the observation of hyphal interactions, where appropriate. A previously published primer set was modified in this study to enhance specificity for AG3PT. Most of the isolates (92·6%) belonged to AG3PT whilst some (6·7%) belonged to AG2‐1. Only one isolate recovered (0·7%) belonged to AG5. Isolates of AG2‐1 were diverse, with variation in both the length of the rDNA intergenic spacer 1 (IGS1) region and the categories of hyphal interaction observed between pairings of AG2‐1 isolates. No variation in the length of the rDNA IGS1 region was observed amongst the AG3 isolates collected. Tests carried out on potato stems with a sub‐set of the isolates revealed a wide range of aggressiveness amongst AG2‐1 isolates. Sequencing of the rDNA internal transcribed spacer (ITS) region of the AG2‐1 isolates and construction of a neighbour joining tree with other AG2‐1 sequences available indicated that AG2‐1 isolates with the short IGS1 region were closely related. This is the first investigation which provides evidence of the relative AG composition of R. solani populations causing disease in potato crops in Great Britain.
Comparison of conventional and molecular methods for the detection of Rosellinia necatrix in avocado orchards in southern Spain
Authors: Ruano‐Rosa D. , Schena L. , Ippolito A. , López‐Herrera C. J.
Published: December 2006

White root rot, caused by Rosellinia necatrix, is one of the most important diseases in avocado orchards and is particularly widespread on the Mediterranean seaboard of southern Spain. In this study, the presence of the pathogen in soil samples collected from the base of 47 plants showing different symptoms of canopy decline was assessed with a molecular detection method based on real‐time Scorpion PCR. Results were compared with symptoms in the canopy and with the traditional method of isolation of R. necatrix from roots and/or bark. The fungus was isolated from 24 samples by the traditional method and from 37 soil samples by the molecular method (cycle threshold values 25·8 to 47·1), demonstrating the higher sensitivity and reliability of the molecular method. A single real‐time PCR amplification was sufficient to detect R. necatrix in naturally infested soils. The avoidance of nested PCR has important practical implications because of the reduced costs and risk of cross contamination. Also, it enables faster sample analysis and is more appropriate for quantitative detection. A modified molecular method was also developed to detect R. necatrix in roots and in soils with very low populations of the pathogen.
Epidemiological aspects of mango malformation disease caused by Fusarium mangiferae and source of infection in seedlings cultivated in orchards in Egypt
Authors: Youssef S. A. , Maymon M. , Zveibil A. , Klein‐Gueta D. , Sztejnberg A. , Shalaby A. A. , Freeman S.
Published: December 2006

Mango malformation, caused by the fungus Fusarium mangiferae, is one of the major diseases of this crop occurring worldwide. This study was conducted to investigate aspects of the epidemiology, survival and spread of the pathogen in general and specifically in seedlings, the majority of which are cultivated in infected orchards in Egypt. Survival of conidia of a representative isolate (506/2) declined very rapidly in soil under summer conditions (1·6 weeks for 50% population decline), but significantly less in controlled and winter conditions (17·9 and 15·0 weeks, respectively, for 50% population decline). Likewise, inoculum survival in naturally infected panicles on the soil surface declined faster than in those buried at 30‐cm depths. Natural infections were evaluated on fruits and seeds in a heavily infected and a healthy orchard. In infected trees, the skins of all sampled fruits within a 2‐m radius of infected panicles were infected, but the pathogen was not detected in the seeds, seed coats or flesh. The pathogen was not detected in any parts of fruits from a healthy orchard. Vegetatively malformed mango seedlings, growing under infected trees bearing infected panicles, were sampled in two locations in Egypt to determine whether infection in seedlings was systemic (evenly distributed within plant tissue) or whether the pathogen originated from malformed panicles. According to PCR‐specific primer amplification, the pathogen was detected in 97% of seedling apical meristems, declining gradually to 5% colonization in roots. It was concluded that inoculum of the pathogen originates from infected panicles and affects seedlings from the meristem, with infections descending to lower stem sections and roots. Minor infections of roots may occur from inoculum originating from infected panicles, but the pathogen is not seedborne.
Genetic diversity of Pseudomonas syringae pv. lachrymans strains isolated from cucumber leaves collected in Poland
Authors: Olczak‐Woltman H. , Masny A. , Bartoszewski G. , Płucienniczak A. , Niemirowicz‐Szczytt K.
Published: December 2006

Several strains of Pseudomonas syringae pathovar (pv.) lachrymans and related bacterial pathogens were isolated from cucumber (Cucumis sativus) leaves collected in central and southern Poland in 2001 and 2002. Twenty five original strains, together with five reference strains of P. syringae pv. lachrymans, pv. syringae and pv. tomato, were genetically characterized by PCR‐RFLP (polymerase chain reaction − restriction fragment length polymorphism), ADSRRS (amplification of DNA fragments surrounding rare restriction sites), and PCR‐MP (PCR − melting profiles) fingerprinting techniques. Genetic similarity analyses of the PCR‐RFLP and ADSRRS fingerprints showed that strains of P. syringae pv. lachrymans form distinct clusters. The results also indicated that the ADSRRS and the PCR‐MP fingerprinting techniques may serve as more efficient tools for evaluating genetic similarity among pathovars and strains of P. syringae than PCR‐RFLP. The 25 strains showed diverse pathogenicity to cucumber seedlings and biochemical tests were varied. The syrB gene was identified in four cucumber strains, characterized as P. syringae pv. syringae.
Sympatric ascochyta complex of wild Cicer judaicum and domesticated chickpea
Authors: Frenkel O. , Shtienberg D. , Abbo S. , Sherman A.
Published: December 2006

The aim of this study was to isolate, identify and characterize ascochyta blight pathogens from Cicer judaicum, a wild annual Cicer species which grows in Israel and other Mediterranean countries in sympatric distribution with legume crops, and determine their virulence and aggressiveness to other wild and domesticated legumes. Native C. judaicum plants exhibited symptoms resembling ascochyta diseases of grain legume crops. Two distinct pathogens were isolated and identified as Phoma pinodella and Didymella rabiei using morphological and molecular tools; their infectivity was verified using Koch's postulates. The virulence of these pathogens was examined on 13 legume species, of which P. pinodella was virulent to Pisum sativum, P. fulvum, C. judaicum, C. arietinum, C. reticulatum, C. pinnatifidum and C. bijugum. Didymella rabiei infected all these Cicer species, but not the other legume species tested. Aggressiveness of the pathogens was tested on wild and domesticated chickpea and pea. Didymella rabiei isolated from C. judaicum had significantly higher (P < 0·001) aggressiveness than P. pinodella from C. judaicum on both wild and domesticated chickpea. Disease severity on the former species ranged from 62·5% to 70% and on the latter from 41% to 56%. Phoma pinodella isolates from C. judaicum were more aggressive on C. arietinum and P. sativum than on C. judaicum and P. fulvum. Results of the current study suggest that C. judaicum may serve as an alternative host to ascochyta pathogens that endanger chickpea and possibly other crops and wild species growing in close proximity.
Management of nematodes and a stalk borer by increasing within‐field sugarcane cultivar diversity
Authors: Cadet P. , Berry S. D. , Leslie G. W. , Spaull V. W.
Published: December 2006

The aim of this study was to determine whether an increase in plant diversity could modify the structure of the nematode community in favour of less pathogenic species and whether it affected the lepidopteran stalk borer, Eldana saccharina. Four sugarcane cultivars were planted either singly or as a mixture in the furrow. Nematodes were enumerated when the crops were 6 months old for five successive 10 to 13 month old crop cycles. Results showed that the mixture of cultivars had little significant impact on the overall abundance of the plant‐parasitic or free‐living nematodes. However, the nematode community structure within the mixture was slightly different to that observed on any single cultivar planted on its own and there was a higher than expected proportion of Helicotylenchus dihystera during the first three crops. With successive crops and in all treatments, there was an overall trend of increasing proportions of Meloidogyne javanica in the nematode community. However, the way that the change in the species‐balance occurred in the mixed cultivar plots suggested a resistance to the evolving dominance of M. javanica. These results showed that sugarcane cultivars interacted within the rhizosphere when planted in a mixture because the observed nematode community in the mixture differed from that expected. The level of damage caused by E. saccharina was slightly lower in the mixture than expected from the actual cultivar composition.
Modelling the spread ofXanthomonas campestrispv.campestrisin module‐raised brassica transplants
Authors: Roberts S. J. , Brough J. , Hunter P. J.
Published: December 2006

A series of experiments was performed to quantify the rate of dispersal ofXanthomonas campestrispv.campestrisin module‐raised brassica transplants, in a simulated commercial plant‐raising system. Seeds were sown in ‘308’ module seed trays and set out in blocks in the glasshouse. Primary inoculum was introduced as inoculated seeds sown in one or more cells. Trays were watered via an overhead‐gantry irrigation system, hand‐watered or capillary‐watered. Disease symptoms were monitored visually and the presence of the pathogen on samples of plants was monitored by leaf washing, dilution and plating on selective medium. Spread of symptoms was greatest in the gantry‐watered trays, was very limited in hand‐watered trays and was almost non‐existent in capillary‐watered trays. Dispersal of bacteria followed a similar pattern, but the proportion of plants contaminated was much greater than the proportion showing symptoms, and approached 100% after six weeks in the gantry‐watered trays within 50 plants distance from a single primary infector. Models relating the proportion of plants with symptoms, or contaminated, to the distance from primary infector and time since sowing were fitted to the data. Predictions of the proportions of plants contaminated in commercial‐scale blocks of transplants suggested that high levels of disease in the field could be explained by rapid rates of pathogen spread during plant‐raising, and that the widely‐used tolerance standard for seed health testing (0·01%) should be revised to 0·004%. In addition to seed health testing, control should focus on raising transplants under conditions that minimise the rates of disease spread and pathogen dispersal.
An oligonucleotide microarray‐based assay for identification of phytoplasma 16S ribosomal groups
Authors: Nicolaisen M. , Bertaccini A.
Published: December 2006

A method using consensus PCR followed by oligonucleotide microarray hybridization was developed for identification of phytoplasma 16Sr ribosomal groups. The array consisted of 21– to 33‐nt‐long oligonucleotides which were designed to hybridize to individual 16Sr groups. Two oligonucleotides were designed to detect all phytoplasma groups. The array could efficiently identify samples from 16SrI, 16SrII, 16SrIII, 16SrV, 16SrVI, 16SrVII, 16SrIX, 16SrX and 16SrXII ribosomal groups. This microarray‐based test represents a rapid method for detection of phytoplasmas in unknown samples and for identification of most 16Sr groups.
In vitro somatic growth and reproduction of phenylamide‐resistant and ‐sensitive isolates of Phytophthora erythroseptica from infected potato tubers in Idaho
Authors: Porter L. D. , Miller J. S. , Nolte P. , Price W. J.
Published: December 2006

Pink rot of potato, most commonly caused by Phytophthora erythroseptica, is a major field and post‐harvest problem in southern Idaho, USA, particularly since 1998 when isolates resistant to the phenylamide fungicide metalaxyl‐M (mefenoxam) were detected. Isolates of P. erythroseptica were collected from infected tubers in 2001 and 2002 from six Idaho counties and tested for resistance to metalaxyl‐M on amended agar. Metalaxyl‐M resistant (MR) and metalaxyl‐M‐sensitive (MS) isolates were identified in six counties; 160 isolates were highly resistant, seven moderately resistant and 57 sensitive to metalaxyl‐M with mean EC50 values of 182, 23 and 0·5 mg L−1 ai metalaxyl‐M, respectively. Mycelial growth rates and oospore production in agar were assessed for 20 MS and 20 MR isolates at 10, 15, 20, 25 and 30°C. Growth rates of MR isolates were between 2·5 and 3·1 times greater (P < 0·05) than those of MS isolates at 10, 15, 20 and 25°C, and oospore production was between 6·8 and 20·5 times greater (P < 0·0001) for MR than for MS isolates at the same temperatures. Colony growth in V8 broth at 18°C was greater for MR than MS isolates (P < 0·0032). However, zoospore production at 18°C was greater for MS than for MR isolates (P < 0·0109), and zoospore production mm−1 of colony circumference was also greater for MS than for MR isolates, 14 191 and 9959, respectively (P = 0·0109). Sexual reproduction of MR isolates in nature may be greater than MS isolates, but MS isolates may be more asexually fit based on the fitness parameters studied.
Erosional and depositional characteristics of regional overwash deposits caused by multiple hurricanes
Authors: WANG PING , HORWITZ MARK H.
Published: December 2006

Regional‐scale washover deposits along the Florida Gulf and Atlantic coasts induced by multiple hurricanes in 2004 and 2005 were studied through coring, trenching, ground‐penetrating radar imaging, aerial photography, and prestorm and poststorm beach‐profile surveys. Erosional and depositional characteristics in different barrier‐island sub‐environments, including dune field, interior wetland and back‐barrier bay were examined. Over the eroded dune fields, the washover deposits are characterized by an extensive horizontal basal erosional surface truncating the old dune deposits and horizontal to slightly landward‐dipping stratification. Over the marshes in the barrier‐island interior, the washover deposits are characterized by steep tabular bedding, with no erosion at the bottom. Overwash into the back‐barrier bay produced the thickest deposits characterized by steep, prograding sigmoidal bedding. No significant erosional feature was observed at the bottom. Washover deposits within the dense interior mangrove swamp demonstrate both normal and reversed graded bedding. The washover deposits caused by hurricanes Frances (2004) and Jeanne (2004) along the southern Florida Atlantic coast barrier islands are substantially different from those along the northern Florida barrier islands caused by Ivan (2004) and Dennis (2005) in terms of regional extension, erosional features and sedimentary structures. These differences are controlled by different overall barrier‐island morphology, vegetation type and density, and sediment properties. The homogeneity of sediment along the northern Florida coast makes distinguishing between washover deposits from Ivan and Dennis difficult. In contrast, along the Atlantic coast barrier islands, the two overwash events, as demonstrated by two phases of graded bedding of the bimodal sediments, are easily distinguishable.
Histidine kinases play important roles in the perception and signal transduction of hydrogen peroxide in the cyanobacterium, Synechocystis sp. PCC 6803
Authors: Kanesaki Yu , Yamamoto Hiroshi , Paithoonrangsarid Kalyanee , Shumskaya Maria , Suzuki Iwane , Hayashi Hidenori , Murata Norio
Published: December 2006

Oxidative stress caused by reactive oxygen species and, in particular, to hydrogen peroxide (H2O2) has a major impact on all biological systems, including plants and microorganisms. We investigated the H2O2‐inducible expression of genes in the cyanobacterium Synechocystis sp. PCC 6803 using genome‐wide DNA microarrays. Our systematic screening of a library of mutant lines with defects in histidine kinases (Hiks) by RNA slot‐blot hybridization and DNA‐microarray analysis suggested that four Hiks, namely, Hik33, Hik34, Hik16 and Hik41, are involved in the perception and transduction of H2O2 signals that regulate the gene expression of 26 of the 77 H2O2‐inducible genes with induction factors higher than 4.0. Among the four Hiks, Hik33 was the main contributor and was responsible for 22 of the 26 H2O2‐inducible genes under the control of the Hiks. By contrast to Hik33, PerR encoding putative peroxide‐sensing protein is involved in the regulation of only nine H2O2‐inducible genes.
Subfunctionalization of PhyB1 and PhyB2 in the control of seedling and mature plant traits in maize
Authors: Sheehan Moira J. , Kennedy Lisa M. , Costich Denise E. , Brutnell Thomas P.
Published: December 2006

Phytochromes are the primary red/far‐red photoreceptors of higher plants, mediating numerous developmental processes throughout the life cycle, from germination to flowering. In seed plants, phytochromes are encoded by a small gene family with each member performing both distinct and redundant roles in mediating physiological responses to light cues. Studies in both eudicot and monocot species have defined a central role for phytochrome B in mediating responses to light in the control of several agronomically important traits, including plant height, transitions to flowering and axillary branch meristem development. Here we characterize Mutator‐induced alleles of PhyB1 and a naturally occurring deletion allele of PhyB2 in Zea mays (maize). Using single and double mutants, we show that the highly similar PhyB1 and PhyB2 genes encode proteins with both overlapping and non‐redundant functions that control seedling and mature plant traits. PHYB1 and PHYB2 regulate elongation of sheath and stem tissues of mature plants and contribute to the light‐mediated regulation of PhyA and Cab gene transcripts. However, PHYB1 and not PHYB2 contributes significantly to the inhibition of mesocotyl elongation under red light, whereas PHYB2 and to a lesser extent PHYB1 mediate the photoperiod‐dependent floral transition. This sub functionalization of PHYB activities in maize has probably occurred since the tetraploidization of maize, and may contribute to flowering time variation in modern‐day varieties.
Spatial variation in H2O2 response of Arabidopsis thaliana root epidermal Ca2+ flux and plasma membrane Ca2+ channels
Authors: Demidchik Vadim , Shabala Sergey N. , Davies Julia M.
Published: December 2006

Hydrogen peroxide is an important regulatory agent in plants. This study demonstrates that exogenous H2O2 application to Arabidopsis thaliana root epidermis results in dose‐dependent transient increases in net Ca2+ influx. The magnitude and duration of the transients were greater in the elongation zone than in the mature epidermis. In both regions, treatment with the cation channel blocker Gd3+ prevented H2O2‐induced net Ca2+ influx, consistent with application of exogenous H2O2 resulting in the activation of plasma membrane Gd3+‐sensitive Ca2+‐influx pathways. Application of 10 mm H2O2 to the external plasma membrane face of elongation zone epidermal protoplasts resulted in the appearance of a hyperpolarization‐activated Ca2+‐permeable conductance. This conductance differed from that previously characterized as being responsive to extracellular hydroxyl radicals. In contrast, in mature epidermal protoplasts a plasma membrane hyperpolarization‐activated Ca2+‐permeable channel was activated only when H2O2 was present at the intracellular membrane face. Channel open probability increased with intracellular [H2O2] and at hyperpolarized voltages. Unitary conductance decreased thus: Ba2+ > Ca2+ (14.5 pS) > Mg2+ > Zn2+ (20 mm external cation, 1 mm H2O2). Lanthanides and Zn2+ (but not TEA+) suppressed the open probability without affecting current amplitude. The results suggest spatial heterogeneity and differential sensitivity of Ca2+ channel activation by reactive oxygen species in the root that could underpin signalling.
Sequencing of a novel HLA‐A allele, A*6836†, showing a Bw4 epitope
Authors: Balas A. , García‐Sánchez F. , Vicario J. L.
Published: December 2006

A novel A*6836 allele was completely characterized by sequence‐based typing (SBT) in a cord blood sample from an Ecuadorian donor. A*6836 discloses six clustered amino acid residue changes at the α‐1 domain, codons 76–83, regarding its closer A*680102 allele. Therefore, A*6836 would be a new human leukocyte antigen (HLA)‐A molecule showing a Bw4‐epitope.
Relation between the mode of binding of nitrite and the energy distribution between the two photosystems
Authors: Singh Pooja , Jajoo Anjana , Sahay Archna , Bharti Sudhakar
Published: December 2006

The reversibility of nitrite‐induced inhibition in relation to energy distribution between the two photosystems was studied in spinach thylakoid membranes. Measurements of electron transfer rate catalyzed by photosystem I (PS I) and photosystem II (PS II), chlorophyll a (Chl a) fluorescence induction kinetics, S2 state multiline spectra, and room temperature electron paramagnetic resonance (EPR) signals indicated that nitrite anions bind PS II in two ways: dissociable (loose) and non‐dissociable (tight). The inhibition caused by the dissociable binding was reversible in washed (nitrite‐treated samples washed with nitrite‐free medium) samples, while the inhibition caused by the non‐dissociable binding was irreversible. At 77 K, an increase in absorption cross section of PS I (as inferred from the excitation spectra of Chl a fluorescence) and a decrease in absorption cross section of PS II in nitrite‐treated sample when compared with sample washed with nitrite‐free medium and control sample suggested that nitrite plays a role in regulating the distribution of absorbed excitation energy between the two photosystems. We propose, for the first time, that the removal of loosely bound nitrite leads to migration of light‐harvesting complex II back to the PS II, and thus the mode of binding of nitrite regulates the extent of migration of antenna molecules between the two photosystems.
Biochemical and molecular characterizations of nicotine demethylase in tobacco
Authors: Xu Dongmei , Shen Yanxin , Chappell Joe , Cui Mingwu , Nielsen Mark
Published: December 2006

Plant cytochrome P450 (CYP) enzymes are involved in the biosynthesis of many primary and secondary metabolites including phenylpropanoids, alkaloids, terpenoids, lipids, cyanogenic glycosides, and glucosinolates. However, while hundreds ofCYPgenes have been identified in plant genomes, relatively few have been functionally characterized. We report here the cloning and characterization of a CYP enzyme from tobacco (Nicotiana tabacumL.) that demethylates nicotine to form nornicotine, a precursor to the nitrosamineN′‐nitrosonornicotine (NNN). Microsomal demethylase activity was first shown to be induced in leaves treated with the growth regulator ethylene, required molecular oxygen and reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) for full activity, and exhibited aKmof 3.9 μMfor nicotine and a maximum turnover rate (Vmax) of 8.9 pkat mg−1protein. Equally important, microsomal activity was reduced greatly by several inhibitors of CYP‐mediated reactions. Using a polymerase chain reaction based strategy with degenerate primers designed to conserve P450 motifs and mRNA from ethylene‐treated leaves, putative gene fragments representing 32 different P450 gene families were isolated and numerous full‐length genes were cloned. Employing GeneChip®(Affymetrix Inc., Santa Clara, CA) microarray hybridizations, the steady‐state mRNA level of two highly related full‐length cDNAs and one cDNA fragment were demonstrated to be highly expressed in ethylene‐treated vs. control plant material. Microsomes from yeast over‐expressing the two full‐length cDNAs along with two other highly homologousP450genes demonstrated that only one cDNA, D121‐AA8 (GenBank accession no. DQ205656) encoded for demethylation activity comparable to that foundin planta. Molecular modeling was used to identify putative active site residues and for comparisons to other putative demethylase cDNAs.