1,720,984 research outputs found
The Integrated Microbial Genome resource of analysis
No full textIntegrated Microbial Genomes and Metagenomes (IMG) is a biocomputational system that allows to provide information and support for annotation and comparative analysis of microbial genomes and metagenomes. IMG has been developed by the US Department of Energy (DOE)-Joint Genome Institute (JGI). IMG platform contains both draft and complete genomes, sequenced by Joint Genome Institute and other public and available genomes. Genomes of strains belonging to Archaea, Bacteria, and Eukarya domains are present as well as those of viruses and plasmids. Here, we provide some essential features of IMG system and case study for pangenome analysis
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
Legume tasters: symbiotic rhizobia host preference and smart inoculant formulations
Full text linkMutualistic interactions have great importance in ecology, with genetic infor-mation that takes shape through interactions within the symbiotic partners and between the partners and the environment. It is known that variation of the host-associated microbiome contributes to buffer adaptation challenges of the host’s physiology when facing varying environmental conditions. In agriculture, pivotal examples are symbiotic nitrogen-fixing rhizobia, known to contribute greatly to host (legume plants) adaptation and host productivity. A holistic view of increasing crop yield and resistance to biotic and abiotic stresses is that of microbiome engineering, the exploitation of a host-associated microbiome through its rationally designed manipulation with synthetic microbial commu-nities. However, several studies highlighted that the expression of the desired phenotype in the host resides in species-specific, even genotype-specific in-teractions between the symbiotic partners. Consequently, there is a need to dissect such an intimate level of interaction, aiming to identify the main ge-netic components in both partners playing a role in symbiotic differences/host preferences. In the present paper, while briefly reviewing the knowledge and the challenges in plant–microbe interaction and rhizobial studies, we aim to promote research on genotype x genotype interaction between rhizobia and host plants for a rational design of synthetic symbiotic nitrogen-fixing microbial communities to be used for sustainably improving leguminous plants yield
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
Editorial: Optimizing probiotic applications in agriculture: Exploring the role of growth and health promoter's microorganisms in plants and livestock animals
Full text linkAt the current state, the agricultural and livestock production would not be able to sustain the exponential increase of global population expected for the next 50 years. Furthermore, the change in dietary habits in favor of a higher meat consumption, will increase the food demand in the coming decades (Salter, 2017).
Intensive agricultural farming also involves the use of substances causing agrochemical pollution such as chemical fertilizers, pesticides, and plant growth regulators, to control damages that may arise from environmental conditions or biotic stresses toward crops. Furthermore, the large use of antibiotics to sustain livestock production would lead to the emerging of antibiotic resistant strains and to a decrease of the overall microbial biodiversity (Aidara-Kane et al., 2018).
The need for a sustainable increase of agricultural productivity has then become one of the most important challenges of the last 25 years. The slowing of environmental degradation (due to deforestation practices) and soil depletion (due to the overuse of agricultural land) are among the primary goals for forward-looking and non-impacting agricultural practices (Borrelli et al., 2017).
Probiotics are defined as beneficial microbes, conferring health benefits to the host whether it is a plant or an animal. In this sense, in the last years the exploitation of probiotic microorganisms for the plant wellness and growth has largely caught on, so much so that nowadays, bioinoculants based on plant growth promoting (PGP) microorganisms are fundamental in green agriculture (Maitra et al., 2022). PGP microorganisms are part of a complex microbial community which naturally colonize plants as endophytes diffusing in internal tissues and roots and as rhizobacteria diffusing in the rhizosphere and contributing to their biotic (such as pathogens) and abiotic stress tolerance like high salinity concentrations (Bellabarba et al., 2019).
PGP traits and abilities range over nitrogen fixation, phosphorus solubilization, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, indole acetic acid (IAA) and siderophores production, biocontrol agents against pathogens production. These are the characteristics mostly used to screen for PGP rhizobacteria (PGPR); however other features may be useful for their identification. Shi et al. showed that the capability to use metabolites commonly found in root exudates could be an alternative approach for the screening of potential PGPR, as rhizosphere and roots colonization is a fundamental prerequisite to exert their PGP role.
Among the PGP traits mostly screened, one of particular interest is the resistance to water deficiency, as this issue will become more and more prominent in the next few years because of climate change. Riva et al. tested different PGP bacterial strains as bioinoculants on tomato plants in normal and water deficit conditions, showing a significant effect of the strains tested to increase the number of productive plants in a short-term assay.
In the past years, PGP strains have been isolated from many different plants, in particular from plants of commercial interest. PGP bacteria may be highly different within the same plant species exhibiting different functional roles to increase plant productivity. Gushgary-Doyle et al. have characterized three N2 fixing switchgrass endophytes, at genomic and phenotypic level, highlighting the presence of multiple PGP features in each strain, from nutrient mobilization to plant hormone production.
However, also less common plant species could be a potential resource for novel PGP bacteria; Jain et al. explored the cultivable endophytic community of Arnebia euchroma, a plant typical of the cold Himalayan desert, isolating several microorganisms (bacteria and fungi) with different PGP capabilities that may help their host to withstand in cold environments.
The use of probiotic bacteria is not limited to plants but is now increasing its interest as a potential strategy to reduce the use of antibiotics and antimicrobials to increase performance and sustain the health of livestock animals.
As reviewed by Luise et al. the use of Bacillus strains as a probiotic strategy can have promising results in terms of growth performance and health; contributing in a reduced post-weaning diarrhea in piglets and the mortality in broilers. The correct definition of probiotic strains and doses would allow achieving the same performance and health parameters obtained using antimicrobials.
Furthermore, probiotics strains can be used together with specific prebiotics to obtain a synergic effect as proposed by Rodríguez-Sorrento et al. The authors observed that the supplementation of B. longum subsp. infantis combined with a mixture of inulin and fructooligosaccharides may have promising results against infections due to Salmonella enterica serovar Typhimurium and Escherichia coli F4, which are two of the most relevant pathogens for piglets. The symbiotic combination was able to influence the fermentation and the immune system activities in the gut of post-weaning piglets, depending on the pathogen infection.
Overall, considering the potential of probiotics for improving plant and animal health, a continuous development and research would be necessary to identify new bacterial strains or new combinations of probiotics. Studies for a deeper characterization of PGP microorganisms and their in-planta effects should be necessary to foresee the induced physiological effects in plant growth and development. Furthermore, account for the consequences of probiotics inoculation on pre-existing plant microbiota could allow the development of highly specific bioinoculants, selected on the basis of plant genome and its microbiome.
The research for their use in livestock animals should aim to offset the specific requirements during the different growing phases, as well as the specific sanitary conditions/pathogen infections. Furthermore, the continuous collaboration between scientific research, industry and in-field figures is encouraged to facilitate the development of a practical guide to lead to a transition into a more sustainable production of meat, based on a reduction of antimicrobials use
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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