1,721,163 research outputs found
Temporal variability of bacterioplankton is habitat driven
No full textTemporal dynamics of bacterioplankton are rarely investigated for multiple habitats and years within individual lakes, limiting our understanding of the variability of bacterioplankton community (BC) composition with respect to environmental factors. We assessed the BC composition of a littoral and two pelagic habitats (euphotic zone and hypolimnion) of Lake Tovel monthly from April 2014 to May 2017 by high throughput sequencing of the V3–V4 hypervariable region of the 16S rRNA gene. The three habitats differed in temperature, light, oxygen and hydrology. In particular, the littoral was the most hydrologically unstable because it receives most of the lake inflow, the hypolimnion was the most stable because of its hydrologically sheltered position, and the pelagic euphotic habitat was intermediate. Consequently, we hypothesized different temporal patterns of BC composition for all three habitats according to their environmental differences. We applied PERMANOVA, non-metric multidimensional scaling, and source-sink analysis to characterize BC composition. Overall, BCs were different among habitats with the littoral showing the highest variability and the hypolimnion the highest stability. The BC of rainy 2014 was distinct from the BCs of other years irrespective of the habitats considered. Seasonal differences in BCs were limited to spring, probably linked to melt-water inflow and mixing. Thus, temporal effects related to year and season were linked to the hydrological gradient of habitats. We suggest that despite potential within-lake dispersal of bacterioplankton by water flow and mixing, local environmental conditions played a major role in Lake Tovel, fostering distinct BCs in the three habitats
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
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
Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars‐like conditions outside the space station
Full text linkDespite the increasing interest in using microbial‐based technologies to support human space exploration, many unknowns remain not only on bioprocesses but also on microbial survivability and genetic stability under non‐Earth conditions. Here the desert cyanobacterium Chroococcidiopsis sp. CCMEE 029 was investigated for robustness of the repair capability of DNA lesions accumulated under Mars‐like conditions (UV radiation and atmosphere) simulated in low Earth orbit using the EXPOSE‐R2 facility installed outside the International Space Station. Genomic alterations were determined in
a space‐derivate of Chroococcidiopsis sp. CCMEE 029 obtained upon reactivation on Earth of the space‐exposed cells. Comparative analysis of whole‐genome sequences showed no increased variant numbers in the space‐derivate compared to triplicates of the reference strain maintained on the ground. This result advanced cyanobacteria‐based technologies to support human space exploration
Efficient and 'clean' CRISPR/CAS9 editing for fire blight resistance in apple
Full text linkFire blight, caused by the bacterium Erwinia amylovora (E.a.), is one of the most
economically important and invasive diseases affecting apple (Malus x domestica).
Nowadays, the E.a.-apple interaction is widely described and the main molecular
mechanisms underlying both plant host resistance and E.a. pathogenesis are elucidated.
Nevertheless, the management of the disease remains still ardous in apple orchard.
Indeed, the use of genetically modified plants is forbidden by the current GMO legislation
and the application of antibiotic-based pesticides is prohibited due to their effects on
human health and environment. Therefore, one of the hardest challenges for plant
biotechnology is to provide apple varieties that are simultaneously disease-resistant and
public-acceptable. In this study, conducted on two Malus x domestica susceptible
varieties, ‘Royal Gala’ and ‘Golden Delicious’, a genome editing approach based on
CRISPR/Cas9 via Agrobacterium tumefaciens (A.t.) was applied to produce the knock-
out of MdDIPM4. In apple, evidences show that MdDIPM4 protein interacts specifically
with the DspE effector, mandatory for the pathogenesis of Erwinia amylovora. About sixty
transgenic lines were analyzed using an high throughput screening approach on the
Illumina MiSeq platform in order to verify the CRISPR/Cas9-induced mutations. The
eighty percent of the plants showed mutations, especially translation-terminated deletions
resulting in MdDIPM4 knock-out. Moreover, with the aim of producing public-acceptale
engineered apple plants, our strategy allowed to remove the entire exogenous T-DNA in
those lines selected for the desired mutation. This mechanism relies on the heat schock-
inducible expression of the Flp gene which induces a site-specific recombination at the
two FRT sites flanking the A.t. left and right borders. Some genome edited lines were
heat-treated and the removal of a 10.5 kb T-DNA cassette was proved. Currently, the
selected genome edited and T-DNA-free apple plants are under in vivo investigation to
test their resistance to Erwinia amylovora
Shotgun metagenomic sequencing for conservation genomics: rock ptarmigan as a case study
Full text linkThe rock ptarmigan (Lagopus muta) inhabits alpine and arctic tundra throughout the northern hemisphere with its current distribution mainly determined by the last glacial maximum. In southern Europe this species is only found in fragmented populations on the main mountain ranges, where numbers are decreasing due to habitat loss, degradation and fragmentation, climate warming and human disturbance. This decline could be mitigated through conservation measures, but these require fundamental information on the evolutionary ecology, distribution and genetic diversity. Such data is difficult to collect in a species which is particularly elusive and living in extreme environments. Thanks to the technological and computational advances of recent years, understanding of species’ biology has been greatly enhanced by analyzing fecal samples, collected non-invasively in the field, using shotgun metagenomics sequencing. Although this approach is still poorly tested in wild species, ongoing studies highlight its potential for conservation and biomonitoring that should be further explored. In the present study, this approach was applied to 30 rock ptarmigan from three different areas of the Paneveggio-Pale di San Martino Natural Park, characterized by contrasting rocky substrates. The shotgun metagenomic sequencing method does not require the enrichment or targeted amplification of specific molecular markers, thus allowing both qualitative and quantitative evaluation of data on different aspects related to the species. In particular, the ongoing analyses aimed to determine: i) the genomic relationships between individuals and population, ii) the fundamental resources for the species through the study of the diet, iii) the health status of individuals through the analysis of gut microbiota and parasites. First results confirmed the utility of shotgun metagenomic sequencing for conservation purposes and provides fundamental data for improving conservation strategies for this species
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