Clustering of classical swine fever virus isolates by codon pair bias

<p>Abstract</p> <p>Background</p> <p>The genetic code consists of non-random usage of synonymous codons for the same amino acids, termed codon bias or codon usage. Codon juxtaposition is also non-random, referred to as codon context bias or codon pair bias. The codon and codon pair bias vary among different organisms, as well as with viruses. Reasons for these differences are not completely understood. For classical swine fever virus (CSFV), it was suggested that the synonymous codon usage does not significantly influence virulence, but the relationship between variations in codon pair usage and CSFV virulence is unknown. Virulence can be related to the fitness of a virus: Differences in codon pair usage influence genome translation efficiency, which may in turn relate to the fitness of a virus. Accordingly, the potential of the codon pair bias for clustering CSFV isolates into classes of different virulence was investigated.</p> <p>Results</p> <p>The complete genomic sequences encoding the viral polyprotein of 52 different CSFV isolates were analyzed. This included 49 sequences from the GenBank database (NCBI) and three newly sequenced genomes. The codon usage did not differ among isolates of different virulence or genotype. In contrast, a clustering of isolates based on their codon pair bias was observed, clearly discriminating highly virulent isolates and vaccine strains on one side from moderately virulent strains on the other side. However, phylogenetic trees based on the codon pair bias and on the primary nucleotide sequence resulted in a very similar genotype distribution.</p> <p>Conclusion</p> <p>Clustering of CSFV genomes based on their codon pair bias correlate with the genotype rather than with the virulence of the isolates.</p

Creativity beyond innovation: Musical performance and craft

While creativity has been defined in a multiplicity of ways across disciplines, scholars generally agree that it involves the generation of ideas or products that are novel, of value, and appropriate to the field. Yet by too readily connecting creativity in musical performance to innovation, does this model neglect the more inconspicuous and unrecognised, but no less valuable, dimensions of creativity in score-based performance? This article offers a characterisation of musical performance situated within a framework of craft, by tracing rehearsal strategies employed in two new performance projects: the rehearsals for, and first performance of Four Duets for clarinet and piano (2012) by Edmund Finnis, written for Mark Simpson and Víkingur Ólafsson; and a recording made by Antony Pay of Alexander Goehr’s Paraphrase for solo clarinet Op. 28 (1969). My argument draws attention to “everyday” aspects of music-making, in which musicians make decisions in engaging with their work which are less explicit than the conventional “moments of revelation” that are prevalent in the literature, but which are nonetheless significant. Acknowledging these attributes of musicians’ performance practices can serve to develop a more nuanced understanding of creativity based on processes rather than outcomes, in order to move beyond a paradigm that opposes notated permanence to improvised transience

Complete mitochondrial genome of Asian longhorned tick, Haemaphysalis longicornis, Neumann, 1901 (Acari: Ixodida: Ixodidae) identified in the United States

Haemaphysalis longicornis (Ixodida: Ixodidae), the Asian longhorned tick, which is native to temperate East Asia, has been recently detected in the northeastern region of the United States, drawing concerns about its potential impact on the US animal and public health sectors. Knowledge about the genetic features of H. longicornis found in the US is limited. Therefore, we sequenced the complete mitochondrial genome (mt-genome) from two H. longicornis ticks recently collected in the State of New York, USA, in 2020. These ticks were morphologically identified and tested for tick-borne pathogens at the Connecticut Veterinary Medical Diagnostic Laboratory (Storrs, CT). The mt-genome was 14,694 bp in length and encoded 37 genes, including 13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs. Phylogenetic analysis showed that the mt-genome clustered with those of other H. longicornis identified in China. The mt-genome sequence was 99.7% identical to a H. longicornis mt-genome (GenBank: MK439888) collected in China. The cox1 gene haplotype in these ticks belonged to the H1 type, which is the dominant haplotype present in central NJ and Staten Island, NY. The complete mt-genome data are needed to provide insights into genetic changes and phylogenetic studies of H. longicornis ticks

Reflections on craft research for and through design

As design practice has become more integrated in HCI research, there are on-going discussions around the role of design in research. Design research may take different forms, among which 'Research for Design' and 'Research through Design'. While, by definition, these two differ in their focus and result- The first informs the creation of a design artefact and the second aims for a contribution to knowledge-this paper presents a case study of design research in which Research for and through Design were used iteratively to gain insight into hybrid craft-an integrated physical-digital craft form. Based on our own reflections, this paper discusses what different roles these two strategies may play depending on the research topic under study; the phase in the design process; and the level of abstraction of the research activity and knowledge gained. It thus argues that using Research for and through Design together is a powerful strategy. Copyright is held by the owner/author(s)

Teaching digital craft

At the overlap of maker culture, ubiquitous computing, critical making, and novel interfaces, digital craft emerges as a new research and teaching domain. It offers new opportunities in interaction design but it also poses particular challenges to academic curricula. This paper first discusses the value and challenges connected to digital craft. Then, based on our experience with exploring digital craft in a research university\u27s teaching environment, we highlight viable approaches and teaching practices in this new field. It closes with a discussion of the prototype results achieved in those classes. Copyright © ACM