1,720,975 research outputs found
Honey as a source of environmental DNA for the detection and monitoring of honey bee pathogens and parasites
Full text linkEnvironmental DNA (eDNA) has been proposed as a powerful tool to detect and monitor cryptic, elusive, or invasive organisms. We recently demonstrated that honey constitutes an easily accessible source of eDNA. In this study, we extracted DNA from 102 honey samples (74 from Italy and 28 from 17 other countries of all continents) and tested the presence of DNA of nine honey bee pathogens and parasites (Paenibacillus larvae, Melissococcus plutonius, Nosema apis, Nosema ceranae, Ascosphaera apis, Lotmaria passim, Acarapis woodi, Varroa destructor, and Tropilaelaps spp.) using qualitative PCR assays. All honey samples contained DNA from V. destructor, confirming the widespread diffusion of this mite. None of the samples gave positive amplifications for N. apis, A. woodi, and Tropilaelaps spp. M. plutonius was detected in 87% of the samples, whereas the other pathogens were detected in 43% to 57% of all samples. The frequency of Italian samples positive for P. larvae was significantly lower (49%) than in all other countries (79%). The co-occurrence of positive samples for L. passim and A. apis with N. ceranae was significant. This study demonstrated that honey eDNA can be useful to establish monitoring tools to evaluate the sanitary status of honey bee populations
Entomological authentication of honey based on a DNA method that distinguishes Apis mellifera mitochondrial C mitotypes: Application to honey produced by A. m. ligustica and A. m. carnica
Full text linkHoney contains DNA of all organisms that directly or indirectly have been involved in its production, including the DNA of the honey bees. Therefore, using DNA extracted from honey, it is possible to analyse DNA markers useful to authenticate its entomological origin. In this study we developed an assay that can distinguish two mitotypes within the mitochondrial C lineage of Apis mellifera: the C1 mitotype, mainly carried by A. m. ligustica subspecies; the C2 mitotype, that is highly specific for the A. m. carnica subspecies. This method is based on Sanger sequencing of an informative regions of the honey bee mitochondrial DNA. A total of 255 honey samples were analysed. These samples included 157 commercial honey samples produced in three Italian regions of the North of Italy, in which A. m. ligustica is widely spread and 15 honey samples directly obtained from honeycombs. Fifteen of these commercial samples and all samples from honeycombs were known to be produced by A. m. ligustica. Other commercial honey samples, produced in Slovenia (n 38), Croatia (n. 22) and Serbia (n. 23), derived from A. m. carnica. All honey samples produced by A. m. ligustica had only the C1 mitotype whereas all honey samples produced by A. m. carnica had the C2 mitotype. C1 was the most frequent mitotype in Emilia-Romagna region (Italy). This assay can be used to identify honey produced by these two subspecies and for population genetic studies in A. mellifera using the honey as source of DNA
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
Known loci in the KIT and TYR genes do not explain the depigmented white coat colour of Austro-Hungarian Baroque donkey
Full text linkThe Italian Asinara donkey and the White Austro-Hungarian Baroque donkey share an identical coat colour phenotype which is characterised by unpigmented skin, white hair, white hooves and blue eyes. Whereas for the Asinara donkey the white coat colour phenotype was assigned to a recessive inherited missense mutation in the Tyrosinase gene (TYR), the underlying genetic background in the White Austro-Hungarian Baroque donkey has not been studied yet. Historical documents derived by the presence of Austro-Hungarian prisoners in the Asinara Island during the First World War might suggest a possible common origin of the same coat colour phenotype in the two breeds. Genotyping of this mutation in the TYR gene and the loci in the KIT gene associated with Dominant White and White Spotting phenotype, revealed, that none of the mutated alleles segregated in the White Austro-Hungarian Baroque Donkey breed. Also sequencing analysis of the TYR gene did not result in the detection of further candidate variants. Therefore, the TYR gene can be excluded as a possible candidate gene for this specific coat colour in the White Austro-Hungarian Baroque donkey. This result excludes a common genetic origin of the white coat colour of the Asinara and White Austro-Hungarian Baroque donkeys that historical documents could have suggested.Highlights Historical information indicated that the white (albino) Asinara donkey breed and the White Austro-Hungarian Baroque donkey breed could be genetically related. The TYR mutation identified in Asinara donkeys and known polymorphic sites in the KIT gene associated with depigmented white coat colour in donkeys do not segregate in the White Austro-Hungarian Baroque Donkey. Due to different underlying genetic background of one identical phenotype in two populations, no common ancestors can be assumed between Asinara donkey and White Austro-Hungarian Baroque donkey throughout the last century
A comprehensive atlas of nuclear sequences of mitochondrial origin (NUMT) inserted into the pig genome
Full text linkBackground: The integration of nuclear mitochondrial DNA (mtDNA) into the mammalian genomes is an ongoing, yet rare evolutionary process that produces nuclear sequences of mitochondrial origin (NUMT). In this study, we identified and analysed NUMT inserted into the pig (Sus scrofa) genome and in the genomes of a few other Suinae species. First, we constructed a comparative distribution map of NUMT in the Sscrofa11.1 reference genome and in 22 other assembled S. scrofa genomes (from Asian and European pig breeds and populations), as well as the assembled genomes of the Visayan warty pig (Sus cebifrons) and warthog (Phacochoerus africanus). We then analysed a total of 485 whole genome sequencing datasets, from different breeds, populations, or Sus species, to discover polymorphic NUMT (inserted/deleted in the pig genome). The insertion age was inferred based on the presence or absence of orthologous NUMT in the genomes of different species, taking into account their evolutionary divergence. Additionally, the age of the NUMT was calculated based on sequence degradation compared to the authentic mtDNA sequence. We also validated a selected set of representative NUMT via PCR amplification. Results: We have constructed an atlas of 418 NUMT regions, 70 of which were not present in any assembled genomes. We identified ancient NUMT regions (older than 55 million years ago, Mya) and NUMT that appeared at different time points along the Suinae evolutionary lineage. We identified very recent polymorphic NUMT (private to S. scrofa, with < 1 Mya), and more ancient polymorphic NUMT (3.5–10 Mya) present in various Sus species. These latest polymorphic NUMT regions, which segregate in European and Asian pig breeds and populations, are likely the results of interspecies admixture within the Sus genus. Conclusions: This study provided a first comprehensive analysis of NUMT present in the Sus scrofa genome, comparing them to NUMT found in other species within the order Cetartiodactyla. The NUMT-based evolutionary window that we reconstructed from NUMT integration ages could be useful to better understand the micro-evolutionary events that shaped the modern pig genome and enriched the genetic diversity of this species
Analysis of honey environmental DNA indicates that the honey bee (Apis mellifera L.) trypanosome parasite Lotmaria passim is widespread in the apiaries of the North of Italy
Full text linkLotmaria passim is a trypanosomatid that infects honey bees. In this study, we established an axenic culture of L. passim from Italian isolates and then used its DNA as a control in subsequent analyses that investigated environmental DNA (eDNA) to detect this trypasonosomatid. The source of eDNA was honey, which has been already demonstrated to be useful to detect honey bee parasites. DNA from a total of 164 honey samples collected in the North of Italy was amplified with three L. passim specific PCR primers and 78% of the analysed samples gave positive results. These results indicated a high prevalence rate of this trypanosomatid in the North of Italy, where it might be considered another threat to honey bee health
Application of next generation semiconductor-based sequencing for the identification of apis mellifera complementary sex determiner (Csd) alleles from honey dna
Full text linkThe complementary sex determiner (csd) gene plays an essential role in the sex determination of Apis mellifera L. Females develop only if fertilized eggs have functional heterozygous genotypes at this gene whereas males, being haploids, are hemizygous. Two identical csd alleles produce non vital males. In light of the recent decline in honey bee populations, it is therefore important to monitor the allele variability at this gene. In this study, we tested the application of next generation semiconductor-based sequencing technology (Ion Torrent) coupled with environmental honey DNA as a source of honey bee genome information to retrieve massive sequencing data for the analysis of variability at the hypervariable region (HVR) of the csd gene. DNA was extracted from 12 honey samples collected from honeycombs directly retrieved from 12 different colonies. A specifically designed bioinformatic pipeline, applied to analyze a total of about 1.5 million reads, identified a total of 160 different csd alleles, 55% of which were novel. The average number of alleles per sample was compatible with the number of expected patrilines per colony, according to the mating behavior of the queens. Allele diversity at the csd could also provide information useful to reconstruct the history of the honey
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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