1,720,986 research outputs found
A Compendium of Bioinformatic Tools for Bacterial Pangenomics to Be Used by Wet-Lab Scientists
No full textMaking use of mathematics and statistics, bioinformatics helps biologists to quickly obtain information from a huge amount of experimental data. Nowadays, a large number of web- and computer-based tools are available, allowing more unskilled scientists to be familiar with data analysis techniques. The present chapter gives an overview of the most easy-to-use tools and software packages for bacterial genes and genome analysis present on the Web, with the aim to mainly help wet-lab researcher at undergraduate and postgraduate levels to introduce them to bioinformatics analysis of biological data
Xanthomonas arboricola pv. corylina, causal agent of hazelnut bacterial blight: phenotypic and genomic characteristics of Chilean strains
No full textNowadays, the worldwide most important disease affecting hazelnut trees is caused by the highly host specific Xanthomonas arboricola pv. corylina (Xac). In fact, bacterial blight of Corylus avellanae (BBCa) reduces the vigour mainly of young hazelnut plants with devastating damages and yield losses either in orchards or in nurseries where the negative consequences on production are even worse. Recently, first reports of BBCa in European countries are on the rise, and serious outbreaks have been detected in Serbia, Italy and Chile. The prevalence of BBCa in Chile and favourable environmental factors in commercial orchards and nurseries are only partially known. Since in Chile the knowledge on pathogenicity and epidemiology of Xac is poorly understood, Xac Chilean strains from European hazelnut symptomatic plants, either from both commercial orchards and nurseries, were characterized with polyphasic approach in order to develop an integrated Xac control strategy. As the Xac lies within the Xanthomonas arboricola (Xa) species, which has a high genetic variability and has been intensively studied because of its strain specialization and host range complexity, the metabolic activity of 21 Xac strains and 19 Xa was evaluated using a Biolog GenIIITM analysis. 13 out of 19 Xa reference strains belonging to the pathovars celebensis, pruni, juglandis and populi were used as controls, while DISTAL 9081 strain of X. axonopodis pv. vitians as outgroup. The phenotypic analysis confirmed the data obtained by Rep-PCR: a) Xac strains showed a high genetic variability (approx. 45%); b) the Rep-PCR fingerprints of the Xa strains isolated from symptomatic hazelnut shoots and leaves gave similar results with a similarity value of approx. 50% among strains which were included in the corylina pathovar. Bioassays (hypersensitive response) and pathogenicity tests were also carried out
An interdisciplinary study of biodeterioration of the external marbles of Santa Maria del Fiore Cathedral, Florence (IT)
Full text linkStone-built cultural heritage exposed to urban environment represents a habitat where
heterogeneous microbial communities can grow causing structural and aesthetical modifications
and significant biodeterioration phenomena, the most common being colored patinas and crusts.
An in-depth investigation of microbial community composition and its metabolic potential is
essential to take the appropriate measures to control its growth. Conventional biocides remain
the most used practical solution to control microbial growth, nevertheless, they may be
dangerous for human health and the environment. The Cathedral of Santa Maria del Fiore
(SMFC) is a major architectural masterpiece in Florence (IT), and its conservation is a main
issue of worldwide concern. The whole edifice is externally covered with polychrome stone
panels consisting of white marbles, serpentinites and red limestones. Here we report a
multidisciplinary investigation on the state of conservation of SMFC white marbles which show,
in some extended areas, patinas and discoloration due to microbiological growth. This work
provides new details on the deterioration of SMFC marble and, for the first time, on the microbial
community involved. This preliminary knowledge will be used for planning field tests with
innovative low environmental impact biocides, such as essential oils, to contrast
biodeterioration
Exploring the Animal Waste Resistome: The Spread of Antimicrobial Resistance Genes Through the Use of Livestock Manure
Full text linkAntibiotic resistance is a public health problem of growing concern. Animal manure application to soil is considered to be a main cause of the propagation and dissemination of antibiotic residues, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs) in the soil-water system. In recent decades, studies on the impact of antibioticcontaminated manure on soil microbiomes have increased exponentially, in particular for taxonomical diversity and ARGs’ diffusion. Antibiotic resistance genes are often located on mobile genetic elements (MGEs). Horizontal transfer of MGEs toward a broad range of bacteria (pathogens and human commensals included) has been identified as the main cause for their persistence and dissemination. Chemical and bio-sanitizing treatments reduce the antibiotic load and ARB. Nevertheless, effects of these treatments on the persistence of resistance genes must be carefully considered. This review analyzed the most recent research on antibiotic and ARG environmental dissemination conveyed by livestock waste. Strategies to control ARG dissemination and antibiotic persistence were reviewed with the aim to identify methods for monitoring DNA transferability and environmental conditions promoting such diffusion
GASTROINTESTINAL MICROBIOTA OF THE SEYCHELLES GIANT TORTOISES
No full textStudies on gut microbiomes of different animals have provided many ecological and evolutionary information showing a strict link with health and disease conditions. Despite that, few studies concerned herbivorous reptiles. The aim of this study was to characterize the faecal microbial community of Aldabrachelys gigantea, herbivorous giant tortoises, living in two different environmental conditions: at Seychelles and at Parco Natura Viva Zoological Park (PNV) in Verona (Italy).
Individual fecal samples were collected from: 17 giant tortoises located in Curieuse Island (CI), 5 in Botanical Garden (BG) at Mahé in the Seychelles and 11 in PNV. Samples were collected in RNA later for microbiota NGS analysis and in agar slant to obtain isolates. Bacterial DNA was extracted using FastDNA SPIN Kit for Soil (MP Biomedicals) and the V3-V4 regions of the 16S rRNA gene were sequenced using the Illumina MisSeq platform. Amplification of good quality of DNA have been obtained from 17 samples (6 (CI), 3 (BG) and 8 (PNV) subjects). Bioinformatic analysis was carried out using the DADA2 pipeline and the Silva database as reference for taxonomy assignment was used. Alpha (Shannon, InvSimpson and Chao1) and beta (Bray Curtis distance) diversity indices were calculated and analysed using ANOVA and PERMANOVA model respectively.
A total of 25 Phyla (42 % Bacteroidetes, 32% Firmicutes), 167 Families (14% Ruminococcaceae, 14% Rikenellaceae) and 310 Genera (7% Treponema, 6% Rikenellaceae_RC9_gut_group) were identified among samples. A higher microbial diversity within a sample (alpha indices) was observed in the BG compared to the PNV (Shannon: 5.39 vs 4.43; InvSimpson: 80.7 vs 25; Chao1: 584 vs 377 p ≤ 0.05). For the beta diversity, the microbiological composition of the samples was different between the three locations (p =0.001).
Overall, the present study suggest that different environmental conditions can drive a shift of microbial profile of Aldabrachelys gigantea, which can be attributed to different diet or environmental conditions. Further investigations are needed
Assessment of Biolog EcoplateTM method for functional metabolic diversity of aerotolerant pig fecal microbiota
Full text linkIn the last decades, gut microbiota and its role in mammal host development and health have been increasingly investigated. Metabolites produced by gut microbiota can affect intestinal homeostasis and immune system maturity and activation, and in turn, they can influence the health and growth performance of livestock. Therefore, a better understanding of the functional metabolic capability of the gut microbiota would be appreciated by the scientific community. In this study, the BiologTM Ecoplates technology was applied for studying the metabolic potential of the aerotolerant microbial community of pig fecal samples, evaluating the interference of different storage conditions and cell concentrations. The length of time for which a fecal sample maintained detectable and unchanged microbial metabolic activity was also investigated. Two assays aimed to evaluate differences in the metabolic activities between fresh and snap-frozen fecal samples at different dilutions and at different lengths of times of preservation at −80°C were carried out. The biodiversity and the predicted functionality of the entire bacterial community through a targeted metagenomic approach were also explored. The results highlighted that snap freezing of fecal samples preserved the metabolic activity of the microbial community when compared to fresh feces. Sample storage at −80 °C did not significantly affect the metabolic activity of the microbial community, which was stable for 150 days. Furthermore, the highest metabolic activity was detected with 1:2 to 1:5 dilutions of the stock suspension. BiologTM Ecoplates technology is a rapid and useful method to explore microbial communities’ metabolism in animal fecal samples contributing to investigate host animal physiology
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
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
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