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Proteomic analysis of Cupriavidus metallidurans CH34 as a model for soil bacteria under viable but non culturable status
No full textOffgel proteomics of Cupriavidus metallidurans CH34 in artificial soil under viable but not culturable state
No full textOffgel proteomics of Cupriavidus metallidurans CH34 in artificial soil under viable but not culturable state
Bacterial culturability and the viable but non-culturable (VBNC) state studied by a proteomic approach using an artificial soil
No full textGram-negative bacteria in soil rapidly adapt to various stresses, including nutrient limitation and desiccation, by
adopting the viable but non-culturable (VBNC) state as a survival strategy. Due to the physico-chemical and
microbiological complexity of soils, little is understood on the effects of nutrient availability and moisture level
on the transition from the VBNC state to culturability in soil. We evaluated the effects of gluconate or water on
the transition of the soil borne bacterium C. metallidurans strain CH34 from the VBNC state to culturability by
experiments of inoculation into artificial soils and bacterial metaproteomic analysis. Incubation without water or
nutrients reduced the bacterial culturability to zero in 12 d, and addition of both water or gluconate restored the
bacterial culturability to high levels within 24 h. The proteomic analysis showed that under water and nutrient
limitation, proteins related to the cell shape and protein synthesis were rapidly down-regulated and stressrelated
proteins were quickly up-regulated during the transition from culturability to VBNC state. Reversion
from the VBNC state to a culturable state with water or gluconate led to highly different bacterial proteomic
profiles of C. metallidurans. Gluconate availability restored main protein biosynthesis and energy metabolic
pathways, whereas water addition led to up-regulation of only six proteins, one of which degrade sigma factors
involved in expression of genes controlling bacterial resistance under nutrient limitation. Proteins regulated
during the transition between culturable and VBNC states could also be involved in the phenotypic VBNC for
other soil bacteria, and can highlight some of the microbial genetic mechanisms allowing the entering and
exiting from the VBNC state. Implications of the VBNC in microbial diversity and soil functionality are discussed
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Contact with soil-borne humic substances interfere with the prion identification by mass spectrometry
No full textWe studied the effects of humic substances (HS) extracted from soil on the identification of the recombinant ovine prion protein (RecPrP) by denaturing (sodium dodecyl sulfate polyacrylamide gel electrophoresis [SDS-PAGE]) and native PAGE (N-PAGE), and mass spectrometry (MS), at various HS to RecPrP contact ratios. The results showed that the contact with HS did not alter RecPrP electrophoretic mobility but affected protein identification by MS. Contact between RecPrP and HS resulted in a lower coverage percentage of specific RecPrP domains that led to a prion misidentification, more evident after N-PAGE than SDS-PAGE. The analysis of the nonidentified protein domains suggests that lower quality of RecPrP identification could be due to hydrophobic interactions between the prion protein and HS, but the mechanism by which HS hamper the correct identification of RecPrP remains to be established. Our results may have implications in the prion environmental risk assessment
Variations on the Author
Get PDF“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
Get PDFWe 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
Interactions between proteins and humic substances affect protein identification by mass spectrometry
No full textSoil proteomics is facing problems such as low yields of protein extraction from soil and low protein identification rates as compared to theoretical estimates of soil proteome. This work aimed to evaluate the effect of soil-borne humic substances (HS) on the identification of model proteins with different properties, such as myoglobin (Mb), α-glucosidase (αG), and β-glucosidase (βG), by using electrophoretic and ESI- and MALDI-mass spectrometry (MS) methodologies. Results showed that the contact between proteins and HS did not alter protein electrophoretic mobility but led to protein modifications that affected protein identification by MS. The decrease in protein identification parameters was more evident for Mb than for αG and βG, probably due to its lower molecular weight and less complex molecular structure. Analysis of MS data indicated that hydrophobic interactions could be responsible for the observed effects of contact between proteins and HS
Effect of plant nitrogen ultilizing efficiencies on Rhizospheric proteolytic bacterial communities of two maize inbred lines
No full textEffect of two maize lines with different N uptake efficienc
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