Mountain Pygmies of Western New Guinea: A Morphological and Molecular Approach

The presence of pygmy or pygmoid groups among New Guinea populations has been the object of scientific interest since the end of the nineteenth century. Morphological and molecular data are used here to study western New Guinea population variability, focusing in particular on two pygmoid groups living in the eastern fringe highlands of Papua: the Una and the Ketengban. Various kinds of anthropometric data are examined, as well as height, weight, and body mass index, to carry out comparisons with nearby ethnic groups living in the highland and lowland regions. The Ketengban data were also compared with other data recorded 20 years before. The results of previous research on the sequencing of the mitochondrial DNA hypervariable segment 1 region and nuclear DNA nonrecombining Y-chromosome polymorphisms are presented. Both morphological and molecular studies involve adult subjects of both genders, representative of the same ethnic groups and/ or geographic regions. The pygmoid groups turn out to be significantly different from all other study groups, due to their small size, as confirmed by analysis of variance, although significant height and weight increments are observed with respect to those previously recorded. However, putative neutral genetic variation estimated from mitochondrial DNA and Y-chromosome markers support a recent shared common history between these pygmoid populations and the other central Papua groups (except for the Dani-Lani). These findings suggest that the short-stature phenotype is an independent secondary adaptation, possibly driven by an iodine-deficient environment, which leaves the potential for further investigations

A comprehensive collection of annotations to interpret sequence variation in human mitochondrial transfer RNAs

Background: The abundance of biological data characterizing the genomics era is contributing to a comprehensive understanding of human mitochondrial genetics. Nevertheless, many aspects are still unclear, specifically about the variability of the 22 human mitochondrial transfer RNA (tRNA) genes and their involvement in diseases. The complex enrichment and isolation of tRNAs in vitro leads to an incomplete knowledge of their post-transcriptional modifications and three-dimensional folding, essential for correct tRNA functioning. An accurate annotation of mitochondrial tRNA variants would be definitely useful and appreciated by mitochondrial researchers and clinicians since the most of bioinformatics tools for variant annotation and prioritization available so far cannot shed light on the functional role of tRNA variations. Results: To this aim, we updated our MToolBox pipeline for mitochondrial DNA analysis of high throughput and Sanger sequencing data by integrating tRNA variant annotations in order to identify and characterize relevant variants not only in protein coding regions, but also in tRNA genes. The annotation step in the pipeline now provides detailed information for variants mapping onto the 22 mitochondrial tRNAs. For each mt-tRNA position along the entire genome, the relative tRNA numbering, tRNA type, cloverleaf secondary domains (loops and stems), mature nucleotide and interactions in the three-dimensional folding were reported. Moreover, pathogenicity predictions for tRNA and rRNA variants were retrieved from the literature and integrated within the annotations provided by MToolBox, both in the stand-alone version and web-based tool at the Mitochondrial Disease Sequence Data Resource (MSeqDR) website. All the information available in the annotation step of MToolBox were exploited to generate custom tracks which can be displayed in the GBrowse instance at MSeqDR website. Conclusions: To the best of our knowledge, specific data regarding mitochondrial variants in tRNA genes were introduced for the first time in a tool for mitochondrial genome analysis, supporting the interpretation of genetic variants in specific genomic contexts

L’Afrofuturismo e la crisi dell’umanesimo: prospettive recenti, visioni attuali e linguaggi futuri in Kodwo Eshun, John Akomfrah e nella musica techno

The essay outlines the origins of Afrofuturism, comparing the philosophical and musical theories of one of its founders, Kodwo Eshun, with the languages that best express the aesthetics, the perspectives and the diasporic nature of Afrofuturism. First of all, the artistic work by director John Akomfrah, and secondarily the essential contribution of techno music as the emblem of hybridization between past and future through the black rhythms extrapolated from electronic machines in the deindustrialized city of Detroit at the end of the Nineties. Starting from the matrix it is possible to see through the significance of the afrofuturist mainstream wave of the recent years, taking into account the contemporary crisis of western humanism, which risks colonizing afrofuturism and to translate it into a new exoticism

Arrivederci a San Junipero. Estetiche metaseriali della paranoia, dalla theory-fiction alla funzione black mirror

The British TV series Black Mirror, with its enunciative (starting from the opening sequence) and marketing strategies (both online and offline), has triggered innovative spectatorial dynamics in audiovisual seriality. They operate in the interzone known as ‘the space of the black mirror’ and rely on a radical exploitation of media convergence. The series has a strong ‘meta-serial’ component which becomes even stronger from season to season, from episode to episode. Starting from the interactive film Bandersnacth (2018), as well as other relevant episodes, the present paper aims to analyse the contemporary and progressive loss of autonomy of human beings and the crisis of their individual unity. Therefore, this paper deals with the ineluctable nostalgia for and the importance of the human dimension, as well as the functions played by Black Mirror. In particular, we focus on the categories of humanism, the collapse of the space-time linearity, and the questionable notion of ‘future’ which is broadly applied to most scenarios. Videodrome (1982) is here proposed as the antecedent of Black Mirror in order to better understand the advent of the new flesh, an electronic flesh which innervates the so-called BlackDrome

Primates and mouse NumtS in the UCSC Genome Browser

<p>Abstract</p> <p>Background</p> <p>NumtS (Nuclear MiTochondrial Sequences) are mitochondrial DNA sequences that, after stress events involving the mitochondrion, colonized the nuclear genome. Accurate mapping of NumtS avoids contamination during mtDNA PCR amplification, thus supplying reliable bases for detecting false heteroplasmies. In addition, since they commonly populate mammalian genomes (especially primates) and are polymorphic, in terms of presence/absence and content of SNPs, they may be used as evolutionary markers in intra- and inter-species population analyses.</p> <p>Results</p> <p>The need for an exhaustive NumtS annotation led us to produce the Reference Human NumtS compilation, followed, as reported in this paper, by those for chimpanzee, rhesus macaque and mouse ones. Identification of NumtS inside the UCSC Genome Browser and their inter-species comparison required the design and the implementation of NumtS tracks, starting from the compilation data. NumtS retrieval through the UCSC Genome Browser, in the species examined, is now feasible at a glance.</p> <p>Conclusions</p> <p>Analyses involving NumtS tracks, together with other genome element tracks publicly available at the UCSC Genome Browser, can provide deep insight into genome evolution and comparative genomics, thus improving studies dealing with the mechanisms that drove the generation of NumtS. In addition, the NumtS tracks constitute a useful tool in the design of mitochondrial DNA primers.</p

RegExpBlasting (REB), a Regular Expression Blasting algorithm based on multiply aligned sequences

Background: One of the most frequent uses of bioinformatics tools concerns functional characterization of a newly produced nucleotide sequence (a query sequence) by applying Blast or FASTA against a set of sequences (the subject sequences). However, in some specific contexts, it is useful to compare the query sequence against a cluster such as a MultiAlignment (MA). We present here the RegExpBlasting (REB) algorithm, which compares an unclassified sequence with a dataset of patterns defined by application of Regular Expression rules to a given-as-input MA datasets. The REB algorithm workflow consists in i. the definition of a dataset of multialignments ii. the association of each MA to a pattern, defined by application of regular expression rules; iii. automatic characterization of a submitted biosequence according to the function of the sequences described by the pattern best matching the query sequence. Results: An application of this algorithm is used in the "characterize your sequence" tool available in the PPNEMA resource. PPNEMA is a resource of Ribosomal Cistron sequences from various species, grouped according to nematode genera. It allows the retrieval of plant nematode multialigned sequences or the classification of new nematode rDNA sequences by applying REB. The same algorithm also supports automatic updating of the PPNEMA database. The present paper gives examples of the use of REB within PPNEMA. Conclusion: The use of REB in PPNEMA updating, the PPNEMA "characterize your sequence" option clearly demonstrates the power of the method. Using REB can also rapidly solve any other bioinformatics problem, where the addition of a new sequence to a pre-existing cluster is required. The statistical tests carried out here show the powerful flexibility of the method

Lo statuto dell’immagine nel XXI Secolo

Abstract not availabl