Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene

Abstract Background The genus Orbivirus includes several species that infect livestock – including Bluetongue virus (BTV) and African horse sickness virus (AHSV). These viruses have linear dsRNA genomes divided into ten segments, all of which have previously been assumed to be monocistronic. Results Bioinformatic evidence is presented for a short overlapping coding sequence (CDS) in the Orbivirus genome segment 9, overlapping the VP6 cistron in the +1 reading frame. In BTV, a 77–79 codon AUG-initiated open reading frame (hereafter ORFX) is present in all 48 segment 9 sequences analysed. The pattern of base variations across the 48-sequence alignment indicates that ORFX is subject to functional constraints at the amino acid level (even when the constraints due to coding in the overlapping VP6 reading frame are taken into account; MLOGD software). In fact the translated ORFX shows greater amino acid conservation than the overlapping region of VP6. The ORFX AUG codon has a strong Kozak context in all 48 sequences. Each has only one or two upstream AUG codons, always in the VP6 reading frame, and (with a single exception) always with weak or medium Kozak context. Thus, in BTV, ORFX may be translated via leaky scanning. A long (83–169 codon) ORF is present in a corresponding location and reading frame in all other Orbivirus species analysed except Saint Croix River virus (SCRV; the most divergent). Again, the pattern of base variations across sequence alignments indicates multiple coding in the VP6 and ORFX reading frames. Conclusion At ~9.5 kDa, the putative ORFX product in BTV is too small to appear on most published protein gels. Nonetheless, a review of past literature reveals a number of possible detections. We hope that presentation of this bioinformatic analysis will stimulate an attempt to experimentally verify the expression and functional role of ORFX, and hence lead to a greater understanding of the molecular biology of these important pathogens.</p

Reliability and Validity of the Star Excursion Balance Test for Patients with Chronic Patellar Instability

The Star Excursion Balance Test (SEBT) is an eight-direction, maximal-reach balance test whose measurement properties are unknown in participants with chronic patellar instability. We designed an observational study with repeated measures to evaluate the test-retest reliability, cross-sectional and longitudinal construct validity, sensitivity to change and responsiveness of the SEBT in this population. Fifteen patients completed the SEBT and reported outcomes at baseline and two weeks and four patients completed testing three months later at the Fowler Kennedy Sports Medicine Clinic. Intra-class correlation coefficients (ICC) for the SEBT were fair to good, ranging from 0.66-0.84. The SEBT demonstrates good cross-sectional construct validity and we are unable to comment with certainty on longitudinal construct validity; correlations between SEBT reach distance and patient-reported outcomes showed agreement with our hypotheses in 93 of 126 (74%) and 46 of 108 (43%) directions. These are preliminary results of a larger continuing study; therefore definitive conclusions cannot be made

The selection of auditor firms by companies in the new issue market

The paper provides some empirical evidence on the question of product differentiation in the market for audits. Using agency cost and signalling frameworks we posit that there will be a demand for varying levels of audit quality. Because audit quality is not directly observable to investors we postulate that quality will be proxied by the auditor's brand name reputation. Big Eight auditors are categorised as being high quality producers. Using data on companies newly listing on the New Zealand Stock Exchange we test the derived models of auditor choice. Auditor choice is a dummy variable (0,1) partitioned on the basis of non Big Eight and Big Eight accounting firms. The results provide support for the idea of product differentiation in the market for audits

Robotopias: mapping Utopian perspectives on new industrial technology

Purpose This paper maps utopian theories of technological change. The focus is on debates surrounding emerging industrial technologies which contribute to making the relationship between humans and machines more symbiotic and entangled, such as robotics, automation and artificial intelligence. The aim is to provide a map to navigate complex debates on the potential for technology to be used for emancipatory purposes and to plot the grounds for tactical engagements. Design/methodology/approach The paper proposes a two-way axis to map theories into to a six-category typology. Axis one contains the parameters humanist–assemblage. Humanists draw on the idea of a human essence of creative labour-power, and treat machines as alienated and exploitative form of this essence. Assemblage theorists draw on posthumanism and poststructuralism, maintaining that humans always exist within assemblages which also contain non-human forces. Axis two contains the parameters utopian/optimist; tactical/processual; and dystopian/pessimist, depending on the construed potential for using new technologies for empowering ends. Findings The growing social role of robots portends unknown, and maybe radical, changes, but there is no single human perspective from which this shift is conceived. Approaches cluster in six distinct sets, each with different paradigmatic assumptions. Practical implications Mapping the categories is useful pedagogically, and makes other political interventions possible, for example interventions between groups and social movements whose practice-based ontologies differ vastly. Originality/value Bringing different approaches into contact and mapping differences in ways which make them more comparable, can help to identify the points of disagreement and the empirical or axiomatic grounds for these. It might facilitate the future identification of criteria to choose among the approaches

Life-cycle assessment of a 100% solar fraction thermal supply to a European apartment building using water-based sensible heat storage

Providing 100% of a building’s heating and hot water using a solar thermal system in a European climate has been shown to be both practically feasible and functionally successful for a new apartment building in Switzerland. The research conducted a life cycle assessment of the solar thermal system and compared the results with an air-source heat-pump, ground-source heat pump, natural gas furnace, oil furnace and a wood-pellet furnace. Using a range of lifetime scenarios it was found that the solar thermal system displays potentially significant advantages over all other systems in terms of reductions for purchased primary energy (from 84 to 93%) and reductions in GHG emissions (from 59 to 97%). However, due to the heavy industrial processes and the particular metals used in manufacturing, the solar thermal system was shown to have a higher demand for resources which, in relation to the natural gas system, can be by a factor of almost 38. Potential impacts on ecosystem quality were marginally worse than for the heat-pump and fossil fuel systems due to resource use impacts whilst potential human health impacts were similar to the heat pump systems but better than the fossil and biomass fuelled systems

A case for a CUG-initiated coding sequence overlapping torovirus ORF1a and encoding a novel 30 kDa product

The genus Torovirus (order Nidovirales) includes a number of species that infect livestock. These viruses have a linear positive-sense ssRNA genome of ~25-30 kb, encoding a large polyprotein that is expressed from the genomic RNA, and several additional proteins expressed from a nested set of 3'-coterminal subgenomic RNAs. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF that overlaps the 5' end of the polyprotein coding sequence, ORF1a, in the +2 reading frame. The new ORF has a strong coding signature and, in fact, is more conserved at the amino acid level than the overlapping region of ORF1a. We propose that the new ORF utilizes a non-AUG initiation codon - namely a conserved CUG codon in a strong Kozak context - upstream of the ORF1a AUG initiation codon, resulting in a novel 258 amino acid protein, dubbed '30K'

A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting

Japanese encephalitis, West Nile, Usutu and Murray Valley encephalitis viruses form a tight subgroup within the larger Flavivirus genus. These viruses utilize a single-polyprotein expression strategy, resulting in ~10 mature proteins. Plotting the conservation at synonymous sites along the polyprotein coding sequence reveals strong conservation peaks at the very 5' end of the coding sequence, and also at the 5' end of the sequence encoding the NS2A protein. Such peaks are generally indicative of functionally important non-coding sequence elements. The second peak corresponds to a predicted stable pseudoknot structure whose biological importance is supported by compensatory mutations that preserve the structure. The pseudoknot is preceded by a conserved slippery heptanucleotide (Y CCU UUU), thus forming a classical stimulatory motif for -1 ribosomal frameshifting. We hypothesize, therefore, that the functional importance of the pseudoknot is to stimulate a portion of ribosomes to shift -1 nt into a short (45 codon), conserved, overlapping open reading frame, termed foo. Since cleavage at the NS1-NS2A boundary is known to require synthesis of NS2A in cis, the resulting transframe fusion protein is predicted to be NS1-NS2AN-term-FOO. We hypothesize that this may explain the origin of the previously identified NS1 'extension' protein in JEV-group flaviviruses, known as NS1'

Detecting overlapping coding sequences in virus genomes

BACKGROUND: Detecting new coding sequences (CDSs) in viral genomes can be difficult for several reasons. The typically compact genomes often contain a number of overlapping coding and non-coding functional elements, which can result in unusual patterns of codon usage; conservation between related sequences can be difficult to interpret – especially within overlapping genes; and viruses often employ non-canonical translational mechanisms – e.g. frameshifting, stop codon read-through, leaky-scanning and internal ribosome entry sites – which can conceal potentially coding open reading frames (ORFs). RESULTS: In a previous paper we introduced a new statistic – MLOGD (Maximum Likelihood Overlapping Gene Detector) – for detecting and analysing overlapping CDSs. Here we present (a) an improved MLOGD statistic, (b) a greatly extended suite of software using MLOGD, (c) a database of results for 640 virus sequence alignments, and (d) a web-interface to the software and database. Tests show that, from an alignment with just 20 mutations, MLOGD can discriminate non-overlapping CDSs from non-coding ORFs with a typical accuracy of up to 98%, and can detect CDSs overlapping known CDSs with a typical accuracy of 90%. In addition, the software produces a variety of statistics and graphics, useful for analysing an input multiple sequence alignment. CONCLUSION: MLOGD is an easy-to-use tool for virus genome annotation, detecting new CDSs – in particular overlapping or short CDSs – and for analysing overlapping CDSs following frameshift sites. The software, web-server, database and supplementary material are available at

Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping gene

Members of the genus Cypovirus (family Reoviridae) are common pathogens of insects. These viruses have linear dsRNA genomes divided into 10–11 segments, which have generally been assumed to be monocistronic. Here, bioinformatic evidence is presented for a short overlapping coding sequence (CDS) in the cypovirus genome segment encoding the major core capsid protein VP1, overlapping the 5'-terminal region of the VP1 ORF in the +1 reading frame. In Cypovirus type 1 (CPV-1), a 62-codon AUG-initiated open reading frame (hereafter ORFX) is present in all four available segment 1 sequences. The pattern of base variations across the sequence alignment indicates that ORFX is subject to functional constraints at the amino acid level (even when the constraints due to coding in the overlapping VP1 reading frame are taken into account; MLOGD software). In fact the translated ORFX shows greater amino acid conservation than the overlapping region of VP1. The genomic location of ORFX is consistent with translation via leaky scanning. A 62–64 codon AUG-initiated ORF is present in a corresponding location and reading frame in other available cypovirus sequences (2 CPV-14, 1 CPV-15) and an 87-codon ORFX homologue may also be present in Aedes pseudoscutellaris reovirus. The ORFX amino acid sequences are hydrophilic and basic, with between 12 and 16 Arg/Lys residues in each though, at 7.5–10.2 kDa, the putative ORFX product is too small to appear on typical published protein gels