1,720,985 research outputs found
Genome organization and X-Y chromosome aneuploidy in river buffalo (Bubalus bubalis L.) spermatozoa by multicolor fluorescence in situ hybridization (FISH) and chromosome microdissection.
No full textHigh-Throughput De Novo Sequencing of Laser Microdissected Y Chromosome in the Mediterranean River Buffalo (2n = 50,XY)
No full textThe sequencing and correct assembly of the Y chromosome sequences is still a challenge in mammals. In fact, apart from the pseudoautosomal regions (PARs), the Y chromosome lacks a homologous counterpart in the X chromosome. Therefore, in males, the use of genomic DNA as a template for NGS allows isolating the specific Y sequences only as a difference from the X sequences, with many potential gaps and assembly errors for the contemporary presence of X and Y. To overcome this problem, we present a high-throughput sequencing approach based on the direct isolation of Y-chromosomes by laser microdissection in the Mediterranean river buffalo.
Peripheral blood lymphocytes from 10 buffalo bulls were cultured in vitro for normal cultures. Fixed lymphocytes were spread on a polyethylene naphthalate membrane (PEN), which was attached to a 24 × 60 glass slide and treated for GTG-banding. Ten copies of the Y-chromosome from each bull were laser microdissected and collected in individual PCR tubes for DOP-PCR amplification and labeling. FISH confirmed the specific hybridization of each Y-probe on lymphocyte metaphases before NGS. Library preparation was performed with the NEB Next Ultra II DNA Library Prep Kit for Illumina. High-throughput sequencing was performed by Illumina technology with the NovaSeq 6000 S4 Reagent Kit v1.5 (300 cycles). Raw data were processed by TrimGalore (v0.6.7), and de novo assembly was accomplished by SPAdes genome assembler v3.15.5. Gene sequences were predicted by AUGUSTUS (v3.5.0).
We generated about 40 Gb (90×) of Illumina short reads. Total assembly length was 2,260,027 bp, with an average GC% of 48.11%. A total of 861 genes were predicted, and 807 of them have a hit-to-reference, 210 are uncharacterized, and around 30 are without description. The total number of microsatellites identified was 552. Variant calling was conducted using the GATK4 pipeline, specifically employing the HaplotypeCaller tool for each sample separately and also in a multi-sample version. The total number of variants across all samples was 25,100.
Our approach yielded valuable insights into the genomic characteristics of the Y chromosome, and our results represent a milestone for the river buffalo
Karyotype, centric fusion polymorphism and chromosomal aberrations in captive-born mountain reedbuck (Redunca fulvorufula).
No full textChromosomes of fourteen captive-born mountain reedbucks (Redunca fulvorufula) have been investigated. The diploid chromosome number was 2n = 56 (FN = 60). The mountain reedbuck karyotype consists of 26 acrocentric and two biarmed chromosome pairs resulting from two centric fusions involving chromosomes 2 and 25, and 6 and 10, respectively. In some animals, 57 chromosomes were detected. Variation in the diploid number was found to be due to polymorphism for the centric fusion 6;10. Both X and Y chromosomes are large and acrocentric. The entire Y chromosome and the proximal part of the X chromosome consist of heterochromatin. The chromosomes X, 9 and 14 appeared to be of caprine type. Chromosome aberrations have been detected in two of the 14 animals investigated. A de novo formed Robertsonian translocation rob(6;13) was found in one female heterozygous for the fusion 6;10. CBG-banding revealed one block of centromeric heterochromatin in the de novo formed translocation rob(6;13) and also in the evolutionarily fixed centric fusions 6;10 and 2;25. One examined male homozygous for fusion 6;10, had a mosaic 56,XY/57,XYY karyotype, with 11% of analyzed cells containing two Y chromosomes. The findings were confirmed by cross-species fluorescence in situ hybridization (FISH) with bovine (Bos taurus L.) chromosome painting probes. The study demonstrates the relevance of cytogenetic screening in captive animals from zoological gardens
Isolation and physical localization of new chromosome-specific centromeric repeats in farm animals
No full textGoing Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Recent developments on genetic information among river type buffaloes by chromosome microdissection and cloning
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Variations on the Author
Get PDF“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
Get PDFWe 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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