1,721,022 research outputs found
SPPADBASE: the first on-line searchable database of PCR primers for phytopathogenic fungi
Full text linkThe fast and unambiguous identification of microbial pathogens affecting plants or plant products is
an essential prerequisite for obtaining high-quality and safe production. Ecologically friendly practice
of the modern agriculture requires the adoption of diagnostic techniques able to detect minimum
inoculum levels of pathogens in soil, seeds, transplants or crops, to limit the raise of epidemics and
to address the adoption of rational and efficient control means. Moreover, there is an increasing
public and official awareness of the potential threat of bio-terrorism directed against food and
agriculture (Monke, 2004). Rapid detection techniques for bioweapon agents are a critical need for
the first-responder community.
Among the nucleic acid-based diagnostic techniques, those involving the Polymerase Chain
Reaction (PCR; Mullis and Faloona, 1987) are the most suited for early detection of phytopathogenic
agents, due to their high sensitivity and the potential for automation. Many sequence source types
could be selected and used as target for specific primer design. These may include, for instance,
Random Amplified Polymorphic DNAs (Williams et al., 1990; Welsh and McClelland, 1990), internal
transcribed spacer (ITS) regions of the ribosomal RNA genes (White et al., 1990) or other specific
gene sequences. Primer sets can be designed to target specificity at the genus, species, or physiological
race level, to distinguish a particular pathogen from closely related organisms.
A common and tedious task for researchers and technicians is to search for and retrieve
bibliographic references of published and validated specific primer sets for a given pathogen querying
the Internet, abstract collections and monthly journals’ tables of contents. Very few examples of
specific primer set collections for phytopathogenic agents have been released: a summary of primers for the diagnostic characterization of phytopathogenic bacteria seems to be the only one printed so far (Louws et al., 1999). Moreover, among 719 molecular biology databases publicly available
recorded by Galperin (2006) or among the 2470 BMC biomedical databases catalog available at
http://databases.biomedcentral.com/, no online repository of primer sets of this kind is accessible. To
overcome this lack of information, we released the first online searchable database of primer sets
useful for the detection and identification of plant pathogenic fungi
A critique of using epitaxial criterion to discriminate between protogenetic and syngenetic mineral inclusions in diamond
Full text link: Distinguishing syngenetic from protogenetic inclusions in natural diamonds is one of the most debated issues in diamond research. Were the minerals that now reside in inclusions in diamonds born before the diamond that hosts them (protogenesis)? Or did they grow simultaneously and by the same reaction (syngenesis)? Once previously published data on periclase [(Mg,Fe)O] and magnesiochromite (MgCr2O4) inclusions in diamond have been re-analysed, we show that the main arguments reported so far to support syngenesis between diamond and its mineral inclusions, definitely failed. Hence: (a) the epitaxial relationships between diamond and its mineral inclusion should no longer be used to support syngenesis, because only detecting an epitaxy does not tell us which was the nucleation substrate (there are evidences that in case of epitaxy, the inclusion acts as a nucleation substrate); (b) the morphology of the inclusion should no longer be used as well, as inclusions could be protogenetic regardless their shapes. Finally, we advance the hypothesis that the majority of inclusions in diamonds are protogenetic, e.g., they are constituent of rocks in which diamonds were formed and not products of reactions during diamond growth
In silico identification of the oosporein gene cluster in the genome of Victoriomyces antarcticus
No full textThe peculiar features of Victoriomyces antarcticus (Cephalothecaceae), including the production of red pigments, make this polar microfungus a promising candidate in biotechnology. However, the molecular basis of the majority of its biological aspects has to be yet understood. Here, we report the mitochondrial genome (31.08 Kb, GC % 27.04) and the nuclear genome (24 Mb, GC % 57.89) with annotation of V. antarcticus FBL 165T. Considering the genomes of V. antarcticus and the sequenced species within Sordariomycetes, the close evolutionary relationships of Cephalothecaceae with the Coniochaetaceae is confirmed in a phylogenomic framework. Sequence analyses indicated that V. antarcticus could act as saprobe, processing soil nutrients. In particular, among the CAZymes, the most abundant GHs were cellulases (GH5, GH6, GH45), endo-1,4-ß-glucanases (GH5, GH7), xylanases (GH10), and amylases (GH13_1, GH31, GH133),
which can be related to the decomposition of plant biomass. Moreover, a relatively low number (10) of chitinases (GH18) indicated limited lytic activities on the chitin. Among the SM biosynthesis gene clusters identified, a pks cluster had sequence homology as well as synteny conservation with a pks gene cluster present in Beauveria bassiana (Hypocreales) encoding the pathway for the production of the red pigment oosporin, a symmetrical 1-4 dibenzoquinone derivative with different biological activities. The putative oosporein biosynthesis in V. antarcticus begins with a pks, utilizing acetyl-CoA and malonyl-CoA to synthesize orsellinic acid, which is enzymatically hydroxylated and then oxidated to benzenetetrol. The dimerization of the benzenetetrol produces oosporein, which is transported across the cell membrane by a protein encoded in the gene cluster. While the regulation of gene expression remains to be elucidated, our data contribute to the understanding on the evolution of the oosporein gene cluster in Sordariomycetes
Draft genome and annotation of Aspergillus affinis (Circumdati): first insights into a biotech perspective
No full textAspergillus affinis (section Circumdati), a promising candidate for biomass bioconversion, produces ochratoxin A (OTA) that in possible contamination can be a threat to human health. However, little is known about its OTA biosynthetic genes. The whole-genome sequence of A. affinis may elucidate several aspects including its potential suitability in biomass bioconvesion at a pilot scale. Here, the nuclear and the mitochondrial (mt) genomes of A. affinis ATCC MYA-4773T were sequenced, assembled and annotated. OTA-producing Aspergillus species of the section Circumdati (A. ochraceus fc-1, A. persii NRRL 35669, A. steynii IBT 23096, A. westerdijkiae CBS 112803) with available complete genome sequences on databases were used for comparison. The mt genome (31.7 Kb,
GC % 25.3) contained core genes and accessory genes as well. Gene annotation for the nuclear genome (37 Mb, GC % 50.1) resulted in 11,386 genes, which were further classified according to GO terms and the CAZy databases. Among the 360 CAZymes identified, the GH family enzyme genes included cellulases (GH5, GH6), endo-1,4-ß-glucanases (GH5, GH7), xylanases (GH10), amylases (GH13_1, GH31), and inulinases (GH32), which may be of outstanding importance for white biotechnology. In general, the numbers of CAZy genes related to plant biomass degradation followed the phylogeny of Aspergillus section
Circumdati. Among the SM biosynthetic gene clusters predicted, the OTA biosynthetic pathway cluster contained genes encoding a pks (AaOTApks), a nrps (AaOTAnrps), a cytochrome P450 monooxygenase (AaOTAp450), a halogenase (AaOTAhal), and a basic leucine zipper transcription factor (AaOTAbZip). In addition, genes encoding hypothetical proteins were present although the genetic synteny conservation found in relation to the Aspergillus species here examined. OTA gene cluster contains target genes suitable for developing new genetic tools for rapid and accurate control methods of ochratoxigenic Aspergillus strains
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Gigaspora margarita with and without its endobacterium shows adaptive responses to oxidative stress
No full textArbuscular mycorrhizal (AM) fungi experience oxidative stress during the plantâfungal interaction, due to endogenous reactive oxygen species (ROS) produced by fungal metabolism and exogenous ROS produced by plant cells. Here, we examine the responses to H2O2 in Gigaspora margarita, an AM fungus containing the endobacterial symbiont Candidatus Glomeribacter gigasporarum (CaGg). Previous studies revealed that G. margarita with its endobacterium produces more ATP and has higher respiratory activity than a cured line that lacks the endobacterium. This higher bioenergetic potential leads to higher production of ROS and to a higher ROS-detoxifying capacity, suggesting a direct or indirect role of the endobacterium in modulating fungal antioxidant responses. To test the hypothesis that the fungalâendobacterial symbiosis may enhance the fitness of the AM fungus in the presence of oxidative stress, we treated the fungus with a sublethal concentration of H2O2 and performed RNA-seq analysis. Our results demonstrate that (i) irrespective of the endobacterium presence, G. margarita faces oxidative stress by activating multiple metabolic processes (methionine oxidation, sulfur uptake, the pentose phosphate pathway, activation of ROS-scavenger genes); (ii) in the presence of its endobacterium, G. margarita upregulates some metabolic pathways, like chromatin status modifications and iron metabolism; and (iii) contrary to our hypothesis, the cured line responds to H2O2 by activating the transcription of specific ROS scavengers. We confirmed the RNA-seq findings by measuring the glutathione and ascorbate concentration, which was the same in both lines after H2O2 treatment. We conclude that both fungal lines may face oxidative stress, but they activate alternative strategies
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Insights into the evolution of metazoan regenerative mechanisms: TGF superfamily member roles in tissue regeneration of the marine sponge Chondrosia reniformis Nardo, 1847
No full textTissue repair is an adaptive and widespread metazoan response. It is characterised by different cellular mechanisms and complex signalling networks that involve numerous growth factors and cytokines. In higher animals, transforming growth factor-β (TGF-β) signalling plays a fundamental role in wound healing. In order to evaluate the involvement of TGF superfamily members in lower invertebrate tissue regeneration, sequences for putative TGF ligands and receptors were isolated from the transcriptome of the marine sponge Chondrosia reniformis. We identified seven transcripts that coded for TGF superfamily ligands and three for TGF superfamily receptors. Phylogenetically, C. reniformis TGF ligands were not grouped into any TGF superfamily clades and thus presumably evolved independently, whereas the TGF receptors clustered in the Type I receptor group. We performed gene expression profiling of these transcripts in sponge regenerating tissue explants. Data showed that three ligands (TGF1, TGF3 and TGF6) were mainly expressed during early regeneration and seemed to be involved in stem cell maintenance, while other two (TGF4 and TGF5) were strongly upregulated during late regeneration and thus considered pro-differentiating factors. The presence of a strong TGF inhibitor, SB431542, blocked the restoration of the exopinacoderm layer in the sponge explants, confirming the functional involvement of the TGF-pathway in tissue regeneration also in these early evolved animals
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