Mutational analysis of the active centre of coronavirus 3C-like proteases.

Formation of the coronavirus replication-transcription complex involves the synthesis of large polyprotein precursors that are extensively processed by virus-encoded cysteine proteases. In this study, the coding sequence of the feline infectious peritonitis virus (FIPV) main protease, 3CL(pro), was determined. Comparative sequence analyses revealed that FIPV 3CL(pro) and other coronavirus main proteases are related most closely to the 3C-like proteases of potyviruses. The predicted active centre of the coronavirus enzymes has accepted unique replacements that were probed by extensive mutational analysis. The wild-type FIPV 3CL(pro) domain and 25 mutants were expressed in Escherichia coli and tested for proteolytic activity in a peptide-based assay. The data strongly suggest that, first, the FIPV 3CL(pro) catalytic system employs His(41) and Cys(144) as the principal catalytic residues. Second, the amino acids Tyr(160) and His(162), which are part of the conserved sequence signature Tyr(160)-Met(161)-His(162) and are believed to be involved in substrate recognition, were found to be indispensable for proteolytic activity. Third, replacements of Gly(83) and Asn(64), which were candidates to occupy the position spatially equivalent to that of the catalytic Asp residue of chymotrypsin-like proteases, resulted in proteolytically active proteins. Surprisingly, some of the Asn(64) mutants even exhibited strongly increased activities. Similar results were obtained for human coronavirus (HCoV) 3CL(pro) mutants in which the equivalent Asn residue (HCoV 3CL(pro) Asn(64)) was substituted. These data lead us to conclude that both the catalytic systems and substrate-binding pockets of coronavirus main proteases differ from those of other RNA virus 3C and 3C-like proteases.

The thermohaline expressway: the Southern Ocean as a centre of origin for deep-sea octopuses

Understanding how environmental forcing has generated and maintained large-scale patterns of biodiversity is a key goal of evolutionary research and critical to predicting the impacts of global climate change. We suggest that the initiation of the global thermohaline circulation provided a mechanism for the radiation of Southern Ocean fauna into the deep sea. We test this hypothesis using a relaxed phylogenetic approach to coestimate phylogeny and divergence times for a lineage of octopuses with Antarctic and deep-sea representatives. We show that the deep-sea lineage had their evolutionary origins in Antarctica, and estimate that this lineage diverged around 33?million years ago (Ma) and subsequently radiated at 15?Ma. Both of these dates are critical in development of the thermohaline circulation and we suggest that this has acted as an evolutionary driver enabling the Southern Ocean to become a centre of origin for deep-sea fauna. This is the first unequivocal molecular evidence that deep-sea fauna from other ocean basins originated from Southern Ocean taxa and this is the first evidence to be dated.

Informalilty in the Social and Culture Life in the City Centre of Nairobi

We live in a world of advanced technology, stiff global competition and rapid transformation of all facets of life and as a result architecture has not been spared. These transformations affect the social relations, cultural consumption and political economy that have influenced the manner in which people perform in and out of space in the city centres. The residents have adopted strategies for negotiating through the spaces sanitized by authorities and other agents. The public spaces provide the background materials for informal urban practices that are sometimes deemed illegal yet are necessary for animating the city spaces. Cities market themselves ecstatically beyond the baroque with a more visible presence of the contending parties through trademarks, public relations invasively advertised in streets, monuments (signature buildings or projects), and language. This paper comes out of a research carried out in Nairobi in February and March 2007. It examined how the notions of globalisation are reflected in the life in the city centre; the impacts on the quality of life of users of the city centre and how informal urbanism has developed as copying strategy to deal with the transformations due to liberalization and globalization.

Judging where a ball will go: the case of curved free kicks in football

This study examined whether adding spin to a ball in the free kick situation in football affects a professional footballer's perception of the ball's future arrival position. Using a virtual reality set-up, participants observed the flight paths of aerodynamically realistic free kicks with (+/- 600 rpm) and without sidespin. With the viewpoint being fixed in the centre of the goal, participants had to judge whether the ball would have ended up in the goal or not. Results show that trajectories influenced by the Magnus force caused by sidespin gave rise to a significant shift in the percentage of goal responses. The resulting acceleration that causes the ball to continually change its heading direction as the trajectory unfolds does not seem to be taken into account by the participants when making goal judgments. We conclude that the visual system is not attuned to such accelerated motion, which may explain why goalkeepers appear to misjudge the future arrival point of such curved free kicks.

rbcL sequences reveal multiple cryptic introductions of the Japanese red alga Polysiphonia harveyi.

In Europe, the last 20 years have seen a spectacular increase in accidental introductions of marine species, but it has recently been suggested that both the actual number of invaders and their impacts have been seriously underestimated because of the prevalence of sibling species in marine habitats. The red alga Polysiphoniaharveyi is regarded as an alien in the British Isles and Atlantic Europe, having appeared in various locations there during the past 170 years. Similar or conspecific populations are known from Atlantic North America and Japan. To choose between three competing hypotheses concerning the origin of P. harveyi in Europe, we employed rbcL sequence analysis in conjunction with karyological and interbreeding data for samples and isolates of P. harveyi and various congeners from the Pacific and North Atlantic Oceans. All cultured isolates of P. harveyi were completely interfertile, and there was no evidence of polyploidy or aneuploidy. Thus, this biological species is both morphologically and genetically variable: intraspecific rbcL divergences of up to 2.1% are high even for red algae. Seven rbcL haplotypes were identified. The four most divergent haplotypes were observed in Japanese samples from Hokkaido and south-central Honshu, which are linked by hypothetical 'missing' haplotypes that may be located in northern Honshu. These data are consistent with Japan being the centre of diversity and origin for P. harveyi. Two non-Japanese lineages were linked to Hokkaido and Honshu, respectively. A single haplotype was found in all North Atlantic and Mediterranean accessions, except for North Carolina, where the haplotype found was the same as that invading in New Zealand and California. The introduction of P. harveyi into New Zealand has gone unnoticed because P. strictissima is a morphologically indistinguishable native sibling species. The sequence divergence between them is 4–5%, greater than between some morphologically distinct red algal species. Two different types of cryptic invasions of P. harveyi have therefore occurred. In addition to its introduction as a cryptic sibling species in New Zealand, P. harveyi has been introduced at least twice into the North Atlantic from presumed different source populations. These two introductions are genetically and probably also physiologically divergent but completely interfertile.

Mentally disordered offenders and the European Court of Human Rights

This article presents the findings from a study of cases taken to the European Court of Human Rights by mentally disordered offenders. The issues raised include the problems raised by indeterminate sentences, the use of detention for preventive purposes, and debates about treatment. The countries represented are Belgium, Norway, Poland, the Netherlands, Russia and the United Kingdom.

Spatial structures of plasma parameters in a magnetic neutral loop discharge

Spatial structures of plasma parameters in a radio-frequency inductively coupled magnetic neutral loop discharge are investigated under various parameter variations using spatially resolved Langmuir probe measurements. A strong coupling between the plasma production region, in the neutral loop (NL) plane, and the axially remote substrate region is observed. The two regions are connected through the separatrices and therefore, spatial profiles in the substrate region are strongly influenced by the plasma production region and the structure of the separatrices. The electron temperature in the plasma production region peaks in the centre of the NL while the maximum in electron density is shifted radially inwards due to diffusion. Details of the structures in both regions, the production region and the substrate region, are determined through the position of the NL and the gradient of the inhomogeneous magnetic field around the NL confinement region. Parameter combinations are found providing higher plasma densities and better uniformity than in common inductively coupled plasmas without applying an additional magnetic field. The uniformity can be further improved using temporal variations of the magnetic field structure.

Patterns of cytoplasmic variation in Arabidopsis thaliana (Brassicaceae) revealed by polymorphic chloroplast microsatellites

Despite being the model organism for plant molecular genetic studies, little is known about the origins and evolutionary history of extant natural populations of Arabidopsis thaliana. We have analysed phylogenetic relationships between worldwide populations of Arabidopsis using polymorphic chloroplast microsatellites. These highly variable markers have revealed previously undetected levels of cytoplasmic variation and confirm previous hypotheses of a recent and rapid expansion of the species from its centre of origin. Furthermore, the results seem to verify previous nuclear analyses that call into question the true origin of several individual Arabidopsis ecotypes.

The masses of the cataclysmic variables AC Cancri and V363 Aurigae

We present time-resolved spectroscopy and photometry of the double-lined eclipsing cataclysmic variables AC Cnc and V363 Aur (=Lanning 10). There is evidence of irradiation on the inner hemisphere of the secondary star in both systems, which we correct for using a model that reproduces the observations remarkably well. We find the radial velocity of the secondary star in AC Cnc to be K-R=176+/-3 km s(-1) and its rotational velocity to be v sin i=135+/-3 km s(-1). From these parameters we obtain masses of M-1=0.76+/-0.03 M-circle dot for the white-dwarf primary and M-2=0.77+/-0.05 M-circle dot for the K2+/-1 V secondary star, giving a mass ratio of q=1.02+/-0.04. We measure the radial and rotational velocities of the G7+/-2V secondary star in V363 Aur to be K-R=168+/-5 km s(-1) and v sin i=143+/-5 km s(-1), respectively. The component masses of V363 Aur are M-1=0.90+/-0.06M(circle dot) and M-2=1.06+/-0.11 M-circle dot giving a mass ratio of q=1.17+/-0.07. The mass ratios for AC Cnc and V363 Aur fall within the theoretical limits for dynamically and thermally stable mass transfer. Both systems are similar to the SW Sex stars, exhibiting single-peaked emission lines with transient absorption features, high-velocity S-wave components and phase-offsets in their radial-velocity curves. The Balmer lines in V363 Aur show a rapid increase in flux around phase 0 followed by a rapid decrease, which we attribute to the eclipse of an optically thick region at the centre of the disc. This model could also account for the behaviour of other SW Sex stars where the Balmer lines show only a shallow eclipse compared to the continuum.

First record of minimum Irish hare (Lepus timidus hibernicus Bell 1837) longevity in the wild.

Average longevity of the mountain hare (Lepus timidus L., 1758) has been estimated at nine years in the wild (Macdonald D. and Barrett, P. 1993 Mammals of Britain and Europe. Harper Collins Publishers, London) with a maximum recorded age of 18 years for one marked animal (Angerbjörn, A. and Flux, J. E. C. 1995 Lepus timidus. Mammalian Species 495: 1–11). However, the longevity of the Irish hare (L. t. hibernicus Bell 1837) is entirely unknown. A total of 14 Irish hares was trapped and tagged at Belfast International Airport, Co. Antrim from February to April 2005. The sex, age (juvenile or adult) and weight of each animal were recorded. Adults were taken as those individuals >8-10 months old defined by the fusing of the notch between the apophysis and diaphysis of the tibia and humerus (Flux, J. E. C. 1970 Journal of Zoology 161: 75-123). Individual identification was made by a system of colourcoded ear tags (Roxan iD Ltd. Selkirk, Scotland) being inserted in the centre of the pinna of each ear. Each ear tag (6 × 34 mm) and puncture site was disinfected with 70 per cent ethanol prior to insertion. An adult male, #001/002 ‘Blue/Blue’, was tagged on 3 March 2005 weighing 3.8 kg and was sighted during a return site visit on 4 April 2007. An adult female, #026/003 ‘Green/Yellow’, was tagged on 15 April 2005 weighing 4.0 kg and was sighted during return visits on 25 March 2010 and 19 October 2010. The latest possible date of birth for both individuals was spring/summer 2004. Consequently, they were at least 3 years and 6.5 years old, respectively. This is the first record of minimum Irish hare longevity in the wild. These observations suggest that ear tagging does not compromise animal welfare and is an effective means of long-term monitoring. Future research may utilize capture-mark-recapture methods.