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161.
Giuseppe Firrao Marta Martini Paolo Ermacora Nazia Loi Emanuela Torelli Xavier Foissac Patricia Carle Bruce C. Kirkpatrick Lia Liefting Bernd Schneider Cristina Marzachì Sabrina Palmano 《Systematic and applied microbiology》2013
The phytoplasmas are currently named using the Candidatus category, as the inability to grow them in vitro prevented (i) the performance of tests, such as DNA-DNA hybridization, that are regarded as necessary to establish species boundaries, and (ii) the deposition of type strains in culture collections. The recent accession to complete or nearly complete genome sequence information disclosed the opportunity to apply to the uncultivable phytoplasmas the same taxonomic approaches used for other bacteria. In this work, the genomes of 14 strains, belonging to the 16SrI, 16SrIII, 16SrV and 16SrX groups, including the species “Ca. P. asteris”, “Ca. P. mali”, “Ca. P. pyri”, “Ca. P. pruni”, and “Ca. P. australiense” were analyzed along with Acholeplasma laidlawi, to determine their taxonomic relatedness. Average nucleotide index (ANIm), tetranucleotide signature frequency correlation index (Tetra), and multilocus sequence analysis of 107 shared genes using both phylogenetic inference of concatenated (DNA and amino acid) sequences and consensus networks, were carried out. The results were in large agreement with the previously established 16S rDNA based classification schemes. Moreover, the taxonomic relationships within the 16SrI, 16SrIII and 16SrX groups, that represent clusters of strains whose relatedness could not be determined by 16SrDNA analysis, could be comparatively evaluated with non-subjective criteria. “Ca. P. mali” and “Ca. P. pyri” were found to meet the genome characteristics for the retention into two different, yet strictly related species; representatives of subgroups 16SrI-A and 16SrI-B were also found to meet the standards used in other bacteria to distinguish separate species; the genomes of the strains belonging to 16SrIII were found more closely related, suggesting that their subdivision into Candidatus species should be approached with caution. 相似文献
162.
Although environmental modification by ecosystem engineers influences species distributions and abundances and ecological process rates, general determinants of the environmental states of engineered landscapes are not well understood. Here we develop a general, spatially implicit model of engineered landscapes that includes parameters driving engineer populations (demographics, environmental modification) and environmental decay. We show that average environmental states and heterogeneities of landscapes are the result of a balance between parameters determining engineering rates and decay rates that can be expressed as a net engineering ratio (NER). This ratio highlights the need to include environmental decay in ecosystem engineering studies. Moreover, it defines a significant engineer as one that can alter the environment despite decay and generates expectations for different kinds of effects on the engineer, other species and ecological processes depending on ratio values. Finally, it suggests that, in general, decay places limits as to what can be inferred about engineer population dynamics from environmental dynamics and vice versa. 相似文献
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165.
Lisa L. Bolin Shamim Ahmad Patricia A. Lobelle-Rich Tara G. Ooms Xavier Alvarez-Hernandez Peter J. Didier Laura S. Levy 《Journal of virology》2013,87(19):10874-10883
Feline leukemia virus (FeLV) is a naturally transmitted gammaretrovirus that infects domestic cats. FeLV-945, the predominant isolate associated with non-T-cell disease in a natural cohort, is a member of FeLV subgroup A but differs in sequence from the FeLV-A prototype, FeLV-A/61E, in the surface glycoprotein (SU) and long terminal repeat (LTR). Substitution of the FeLV-945 LTR into FeLV-A/61E resulted in pathogenesis indistinguishable from that of FeLV-A/61E, namely, thymic lymphoma of T-cell origin. In contrast, substitution of both FeLV-945 LTR and SU into FeLV-A/61E resulted in multicentric lymphoma of non-T-cell origin. These results implicated the FeLV-945 SU as a determinant of pathogenic spectrum. The present study was undertaken to test the hypothesis that FeLV-945 SU can act in the absence of other unique sequence elements of FeLV-945 to determine the disease spectrum. Substitution of FeLV-A/61E SU with that of FeLV-945 altered the clinical presentation and resulted in tumors that demonstrated expression of CD45R in the presence or absence of CD3. Despite the evident expression of CD45R, a typical B-cell marker, T-cell receptor beta (TCRβ) gene rearrangement indicated a T-cell origin. Tumor cells were detectable in bone marrow and blood at earlier times during the disease process, and the predominant SU genes from proviruses integrated in tumor DNA carried markers of genetic recombination. The findings demonstrate that FeLV-945 SU alters pathogenesis, although incompletely, in the absence of FeLV-945 LTR. Evidence demonstrates that FeLV-945 SU and LTR are required together to fully recapitulate the distinctive non-T-cell disease outcome seen in the natural cohort. 相似文献
166.
Eric Allan Wolfgang W. Weisser Markus Fischer Ernst-Detlef Schulze Alexandra Weigelt Christiane Roscher Jussi Baade Romain L. Barnard Holger Beßler Nina Buchmann Anne Ebeling Nico Eisenhauer Christof Engels Alexander J. F. Fergus Gerd Gleixner Marlén Gubsch Stefan Halle Alexandra M. Klein Ilona Kertscher Annely Kuu Markus Lange Xavier Le Roux Sebastian T. Meyer Varvara D. Migunova Alexandru Milcu Pascal A. Niklaus Yvonne Oelmann Esther Pašalić Jana S. Petermann Franck Poly Tanja Rottstock Alexander C. W. Sabais Christoph Scherber Michael Scherer-Lorenzen Stefan Scheu Sibylle Steinbeiss Guido Schwichtenberg Vicky Temperton Teja Tscharntke Winfried Voigt Wolfgang Wilcke Christian Wirth Bernhard Schmid 《Oecologia》2013,173(1):223-237
In order to predict which ecosystem functions are most at risk from biodiversity loss, meta-analyses have generalised results from biodiversity experiments over different sites and ecosystem types. In contrast, comparing the strength of biodiversity effects across a large number of ecosystem processes measured in a single experiment permits more direct comparisons. Here, we present an analysis of 418 separate measures of 38 ecosystem processes. Overall, 45 % of processes were significantly affected by plant species richness, suggesting that, while diversity affects a large number of processes not all respond to biodiversity. We therefore compared the strength of plant diversity effects between different categories of ecosystem processes, grouping processes according to the year of measurement, their biogeochemical cycle, trophic level and compartment (above- or belowground) and according to whether they were measures of biodiversity or other ecosystem processes, biotic or abiotic and static or dynamic. Overall, and for several individual processes, we found that biodiversity effects became stronger over time. Measures of the carbon cycle were also affected more strongly by plant species richness than were the measures associated with the nitrogen cycle. Further, we found greater plant species richness effects on measures of biodiversity than on other processes. The differential effects of plant diversity on the various types of ecosystem processes indicate that future research and political effort should shift from a general debate about whether biodiversity loss impairs ecosystem functions to focussing on the specific functions of interest and ways to preserve them individually or in combination. 相似文献
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168.
Olivier Escaffre Cyril Le Nou?n Michel Amelot Xavier Ambroggio Kristen M. Ogden Olivier Guionie Didier Toquin Hermann Müller Mohammed R. Islam Nicolas Eterradossi 《Journal of virology》2013,87(5):2767-2780
Infectious bursal disease virus (IBDV) causes an economically significant disease of chickens worldwide. Very virulent IBDV (vvIBDV) strains have emerged and induce as much as 60% mortality. The molecular basis for vvIBDV pathogenicity is not understood, and the relative contributions of the two genome segments, A and B, to this phenomenon are not known. Isolate 94432 has been shown previously to be genetically related to vvIBDVs but exhibits atypical antigenicity and does not cause mortality. Here the full-length genome of 94432 was determined, and a reverse genetics system was established. The molecular clone was rescued and exhibited the same antigenicity and reduced pathogenicity as isolate 94432. Genetically modified viruses derived from 94432, whose vvIBDV consensus nucleotide sequence was restored in segment A and/or B, were produced, and their pathogenicity was assessed in specific-pathogen-free chickens. We found that a valine (position 321) that modifies the most exposed part of the capsid protein VP2 critically modified the antigenicity and partially reduced the pathogenicity of 94432. However, a threonine (position 276) located in the finger domain of the virus polymerase (VP1) contributed even more significantly to attenuation. This threonine is partially exposed in a hydrophobic groove on the VP1 surface, suggesting possible interactions between VP1 and another, as yet unidentified molecule at this amino acid position. The restored vvIBDV-like pathogenicity was associated with increased replication and lesions in the thymus and spleen. These results demonstrate that both genome segments influence vvIBDV pathogenicity and may provide new targets for the attenuation of vvIBDVs. 相似文献
169.
José Rodrigues Coura Pedro Albajar Vi?as Lucia Maria Brum-Soares Andréa Silvestre de Sousa Sérgio Salles Xavier 《Memórias do Instituto Oswaldo Cruz》2013,108(8):1009-1013
A case-control study on the morbidity of Chagas heart disease was carried out in the
municipality of Barcelos in the microregion of the Rio Negro, state of Amazonas. One
hundred and six individuals, who were serologically positive for Trypanosoma
cruzi infection, as confirmed by at least two techniques with different
principles, were matched according to age and sex with an equal number of
seronegative individuals. The cases and controls were evaluated using an
epidemiological questionnaire and clinical, electrocardiograph and echocardiograph
examinations. In the seroepidemiological evaluation, 62% of the interviewees
recognised triatomines and most of them confirmed that they had seen these insects in
the piassava plantations of the riverside communities of the Negro River tributaries.
Of the seropositive patients, 25.8% affirmed that they had been stung by the
triatomines and 11.7% denied having been stung. The principal clinical manifestations
of the seropositive individuals were palpitations, chest pain and dyspnoea upon
effort. Cardiac auscultation revealed extrasystoles, bradycardia and systolic
murmurs. The electrocardiographic alterations were ventricular extrasystoles, left
and right bundle branch block, atrioventricular block and primary T wave alterations.
The echocardiogram was altered in 22.6% of the seropositive individuals and in 8.5%
of the seronegative individuals. 相似文献
170.
Stéphanie Suarez Agnès Ferroni Aurélie Lotz Keith A. Jolley Philippe Guérin Julie Leto Brunhilde Dauphin Anne Jamet Martin C.J. Maiden Xavier Nassif Jean Armengaud 《Journal of microbiological methods》2013
Whole-cell matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a rapid method for identification of microorganisms that is increasingly used in microbiology laboratories. This identification is based on the comparison of the tested isolate mass spectrum with reference databases. Using Neisseria meningitidis as a model organism, we showed that in one of the available databases, the Andromas database, 10 of the 13 species-specific biomarkers correspond to ribosomal proteins. Remarkably, one biomarker, ribosomal protein L32, was subject to inter-strain variability. The analysis of the ribosomal protein patterns of 100 isolates for which whole genome sequences were available, confirmed the presence of inter-strain variability in the molecular weight of 29 ribosomal proteins, thus establishing a correlation between the sequence type (ST) and/or clonal complex (CC) of each strain and its ribosomal protein pattern. Since the molecular weight of three of the variable ribosomal proteins (L30, L31 and L32) was included in the spectral window observed by MALDI-TOF MS in clinical microbiology, i.e., 3640–12000 m/z, we were able by analyzing the molecular weight of these three ribosomal proteins to classify each strain in one of six subgroups, each of these subgroups corresponding to specific STs and/or CCs. Their detection by MALDI-TOF allows therefore a quick typing of N. meningitidis isolates. 相似文献