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Junier, Pilar
Nom
Junier, Pilar
Affiliation principale
Fonction
Professeure assistante
Email
pilar.junier@unine.ch
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Voici les éléments 1 - 10 sur 13
- PublicationMétadonnées seulementMLgsc: A Maximum-Likelihood General Sequence Classifier(2015)
; ; We present software package for classifying protein or nucleotide sequences to user-specified sets of reference sequences. The software trains a model using a multiple sequence alignment and a phylogenetic tree, both supplied by the user. The latter is used to guide model construction and as a decision tree to speed up the classification process. The software was evaluated on all the 16S rRNA gene sequences of the reference dataset found in the GreenGenes database. On this dataset, the software was shown to achieve an error rate of around 1% at genus level. Examples of applications based on the nitrogenase subunit NifH gene and a protein-coding gene found in endospore-forming Firmicutes is also presented. The programs in the package have a simple, straightforward command-line interface for the Unix shell, and are free and open-source. The package has minimal dependencies and thus can be easily integrated in command-line based classification pipelines. - PublicationMétadonnées seulementGenome Sequence of Kosakonia radicincitans Strain YD4, a Plant Growth-Promoting Rhizobacterium Isolated from Yerba Mate (Ilex paraguariensis St. Hill.)(2015)
; - PublicationMétadonnées seulementGenetic diversity of Rhizobium present in nodules of Phaseolus vulgaris L. cultivated in two soils of the central region in Chile(2014-4-1)Although Phaseolus vulgaris L. is native from the Americas and is currently cultured in diverse areas, very little is know about the diversity of symbiotic nitrogen fixing Rhizobium (mycrosymbiont) in many of those cultures. Therefore, the aim of this study was to assess the genetic diversity of Rhizobium present in nodules of P. vulgaris in the central region of Chile. A method to extract DNA from surface-sterilized nodules was applied to two populations of the same seed variety grown in different fields. The 16S rRNA and nifH genes were amplified directly from the DNA extracted. DGGE analysis and clone libraries showed a restricted genetic diversity of the microsymbiotic populations that nodulate P. vulgaris. Both molecular markers revealed the presence of a microsymbiont closely related to Rhizobium etli in all the plants from the soils studied, indicating that the populations of Rhizobium spp. nodulating P. vulgaris in the central region of Chile displayed an extremely low genetic diversity. The level of genetic diversity in microsymbiont populations in plants grown in soils with different origin suggested that other factors rather than the indigenous soil rhizobial populations play a major role in the selection of the symbiotic partner in P. vulgaris.
- PublicationMétadonnées seulement
- PublicationMétadonnées seulementDetection of active oxalate-carbonate pathway ecosystems in the Amazon Basin: global implications of a natural potential C sink(2013-12-24)The oxalate-carbonate pathway (OCP) is a biogeochemical process, which has been described in Milicia excelsa tree ecosystems of Africa. This pathway involves biological and geological parameters at different scales: oxalate, as a by-product of photosynthesis, is oxidized by oxalotrophic bacteria leading to a local pH increase, and eventually to carbonate accumulation through time in previously acidic and carbonate-free tropical soils. Former studies have shown that this pedogenic process can potentially lead to the formation of an atmospheric carbon sink. Considering that 80 % of plant species are known to produce oxalate, it is reasonable to assume that Milicia excelsa is not the only tree that can support OCP ecosystems. The search for similar conditions on another continent led us to South America, in an Amazon forest ecosystem (Alto Beni, Bolivia). This area was chosen because of the absence of local inherited carbonate in the bedrock, as well as its expected acidic soil conditions. Eleven tree species and associated soils were tested positive for the presence of carbonate with a more alkaline soil pH close to the tree than at distance from it. A detailed study of Pentaplaris davidsmithii and Ceiba speciosa trees showed that oxalotrophy impacted soil pH in a similar way to at African sites (at least with 1 pH unit increasing). African and South American sites display similar characteristics regarding the mineralogical assemblage associated with the OCP, except for the absence of weddellite. The amount of carbonate accumulated is 3 to 4 times lower than the values measured in African sites related to Milicia excelsa ecosystems. Still, these secondary carbonates remain critical for the continental carbon cycle, as they are unexpected in the acidic context of Amazonian soils. Therefore, the present study demonstrates the existence of an active OCP in South America. The three critical components of an operating OCP are the presence of : i) local alkalinisation, ii) carbonate accumulations, and iii) oxalotrophic bacteria, which were identified associated to the oxalogenic tree Ceiba speciosa. If the question of a potential carbon sink related to oxalotrophic-oxalogenic ecosystems in the Amazon Basin is still pending, this study highlights the implication of OCP ecosystems on carbon and calcium biogeochemical coupled cycles. As previously mentioned for Milicia excelsa tree ecosystems in Africa, carbonate accumulations observed in the Bolivian tropical forest could be extrapolated to part or the whole Amazon Basin and might constitute an important reservoir that must be taken into account in the global carbon balance of the Tropics.
- PublicationMétadonnées seulementAssessment of a biological approach for the protection of copper alloys artefacts(Edinburgh: Historic Scotland and International Council of Museums, 2013)
; ; ; ; ; Wörle, MarieWe propose an innovative treatment by which the protection of copper-based artefacts can be provided by naturally occurring microorganisms. The properties of some fungi were exploited for the transformation of existing corrosion patinas into copper oxalates. The latter are known to be insoluble and chemically stable. Within the earlier EU-ARTECH and BAHAMAS projects, very promising results were obtained with an almost 100% conversion from copper hydroxysulfates and hydroxychlorides into copper oxalates. A fungal strain was used which had been isolated from vineyard soil heavily contaminated with copper. Further scientific investigations were carried out to determine the parameters of the process and allowing the formation of a reproducible and homogeneous patina of copper oxalates, called biopatina to highlight its biological origin. Particular attention was paid to the efficacy, durability and impact on colour of the newly developed treatment. Different copper and bronze coupons with either urban or marine patinas were prepared. Several analytical techniques were used for the characterisation of the patinas: Fourier Transform InfraRed microspectroscopy (µFTIR), colourimetry and Electrochemical Impedance Spectroscopy (EIS). The coupons were treated with either the biological treatment or reference materials (wax: Cosmoloid H80; silane: Dynasylan® F8263) and exposed to atmospheric corrosion (ISMAR-SMS Genoa Harbour, corrosivity class 5) in December 2011. The long-term behaviour and performance of the treatments under study was monitored and compared over a one year period using the same complement of analytical techniques used for the characterisation of the original patinas. These first measurements suggested a different weathering behaviour of the biopatina. In fact, in comparison to the silane and wax treatments the biopatina showed a lower colour variation, and a corrosion stabilisation process seemed to be in progress. A deeper analysis of colour and corrosion rate variation from different application methods was also achieved. The complete assessment of the different treatments will be finished this year. - PublicationMétadonnées seulementThe Response of Desulfotomaculum reducens MI-1 to U (VI) Exposure: A Transcriptomic Study(2011)
; - PublicationMétadonnées seulementUranium speciation and stability after reductive immobilization in aquifer sediments(2011)
; - PublicationMétadonnées seulementEffect of competing electron acceptors on the reduction of U (VI) by Desulfotomaculum reducens(2010)
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