1,720,965 research outputs found
An over-time distribution map of the main Apis mellifera mitochondrial DNA lineage using honey as source of eDNA.
No full textAn extensive multi-approaches distribution map of Apis mellifera mitochondrial DNA lineages in Italy
No full textThe conservation of the genetic integrity of honey bee subspecies is a matter of concern in Europe. Specific mitochondrial DNA (mtDNA) lineages characterize several Apis mellifera subspecies. In this study we produced a distribution map of the main A. mellifera mtDNA lineages in Italy by combining two approaches: (1) mtDNA analyses of individual honey bees; (2) mtDNA analyses from honey environmental DNA. This second approach was also applied to obtain a distribution map of mtDNA lineages over four years in the North of Italy. DNA was extracted from ~800 worker bees collected in 2020 and 730 pupae collected in 2021 from different colonies. DNA was also extracted from about 1,600 honey samples produced in the North of Italy over four years (2018-2021) and additional 400 honey samples produced in 2018 in the Central and South of Italy and in the two main Italian islands (Sardinia and Sicily). PCR amplified fragments were sequenced or separated using a size-based assay. Both approaches showed that the C lineages were the most frequent mitotypes all over Italy except in Sicily, where the A lineage was highly represented. Individual bee analyses showed that the C1 mitotype, which mainly characterizes the A. m. ligustica subspecies, was the most frequent mtDNA haplotype in the investigated cohorts. Nevertheless, mtDNA haplotypes associated with non-endemic subspecies (A and M lineages) were present in almost all Italian regions and constantly represented over years. The obtained information can be useful to design conservation strategies of A. mellifera genetic resources in Italy
Developing genomic information for Holothuria polii (Echinodermata: Holothuroidea), a novel potential aquaculture species
No full textSea cucumbers (Holothuroidea) are ecologically important organisms for their bioturbation and alkalinization activities of the seabed. They are also important as luxury food and for the production of bioactive compounds and for these reasons they are extensively fished. A few initiatives are also evaluating sea cucumbers as novel species for cultivation in aquaculture systems. In this study we generated sequence information for Holothuria polii, a common sea cucumber species of the Mediterranean Sea, for which no detailed genomic studies have been carried out so far. Whole genome sequence information was produced from an individual whose species identity was obtained by scanning electron microscope analysis of sclerites, which are anatomical features that can discriminate closely related species of the genus Holothuria. Illumina paired end sequencing produced a total of ~210 millions of reads for a about 21 Gbp. Generated data was analyzed against the genome sequence of other echinoderms to characterize several nuclear genes. In addition, the complete mitochondrial genome was assembled and used to evaluate the phylogenetic relationship of H. polii against the other few Holothuroidea species for which the whole mitochondrial DNA (mtDNA) was available. The 15,907 bp H. polii mtDNA sequence has the same gene order already reported for H. scabra, H. forskali and other species of the same family. Cox1 gene sequences were informative for species identification across the genus and could be used for the authentication of commercialized Holothuria spp. These first genomic data we produced for H. polii may constitute starting information to obtain an assembled genome and analyze variability in the Mediterranean populations of this species
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
A genomic-based approach to redefine herd book information in two local cattle breeds.
No full textReggiana and Modenese are autochthonous cattle breeds of the North of Italy. Their milk is mainly used to produce breed branded Protected Designation of Origin Parmigiano-Reggiano cheeses. As in most local breeds, pedigree records in Reggiana and Modenese herd books are not always complete. In this study, we applied a few approaches to verify and complete pedigree information: opposing homozygotes (OH) that identifies parentage inconsistencies in candidate parent offspring pairs; methods that apply Identity by Descent (IBD). Pedigree information was evaluated on a total of 3400 Reggiana and 630 Modenese cattle (which represent about 3/4th and 2/3rd of the respective breed populations), using genotyping data obtained from the GGP Bovine 150k single nucleotide polymorphism array. PLINK, and KING software and ad hoc scripts provided pairwise comparisons of the genotyped cattle. By comparing OH and IBD approaches and estimating the genotyping error rate, a threshold of inconsistent OH SNPs to correct a record and to infer up to 2nd or 3rd relationship degree was defined. These methods made it possible to correct and complete Herd Book information in the two breeds. These approaches will improve conservation strategies in Reggiana and Modenese breeds.Acknowledgements: Funded by the Programma di Sviluppo Rurale Nazionale (PSRN) Dual Breeding 2, co-funded by the European Agricultural Fund for Rural Development of the European Union and by the MASAF
Development and application of genomic approaches to identify Apis mellifera subspecies
No full textA growing concern across Europe is emerging to preserve the genetic integrity of Apis mellifera populations and subspecies that might be adapted to local environmental conditions and climates. Subspecies integrity is also important for the beekeeping sector i) that in many countries or regions requires certified queens of authorized subspecies, according to local regulations, or ii) that needs different genetic resources to design selection and crossbreeding programs. In this study we developed and applied DNA based approaches to identify the honey bee subspecies, combining information at the mitochondrial DNA and nuclear genome levels. These methods were applied both indirectly, using environmental DNA (eDNA) present in the honey, and directly, using DNA extracted from honey bee workers of different colonies to obtain genetic information on the A. mellifera populations of the whole Italian peninsula, Sardinia and Sicily. In addition, results obtained with the traditional morphometric method, usually applied to identify honey bee subspecies, have been compared with results obtained from genomic analyses. Genomic data revealed a broad genetic diversity in the Italian honey bee populations. Genomic approaches resulted much more informative than morphometric analyses. We also demonstrated that eDNA from honey can be exploited to design a cost-effective population genetic study in honey bees. The obtained results can be useful to design conservation strategies of A. mellifera genetic resources in Italy
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
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