Respiration in the open ocean

A key question when trying to understand the global carbon cycle is whether the oceans are net sources or sinks of carbon. This will depend on the production of organic matter relative to the decomposition due to biological respiration. Estimates of respiration are available for the top layers, the mesopelagic layer, and the abyssal waters and sediments of various ocean regions. Although the total open ocean respiration is uncertain, it is probably substantially greater than most current estimates of particulate organic matter production. Nevertheless, whether the biota act as a net source or sink of carbon remains an open question.     

Behaviourally driven gene expression reveals song nuclei in hummingbird brain

Hummingbirds have developed a wealth of intriguing features, such as backwards flight, ultraviolet vision, extremely high metabolic rates, nocturnal hibernation, high brain-to-body size ratio and a remarkable species-specific diversity of vocalizations. Like humans, they have also developed the rare trait of vocal learning, this being the ability to acquire vocalizations through imitation rather than instinct. Here we show, using behaviourally driven gene expression in freely ranging tropical animals, that the forebrain of hummingbirds contains seven discrete structures that are active during singing, providing the first anatomical and functional demonstration of vocal nuclei in hummingbirds. These structures are strikingly similar to seven forebrain regions that are involved in vocal learning and production in songbirds and parrots--the only other avian orders known to be vocal learners. This similarity is surprising, as songbirds, parrots and hummingbirds are thought to have evolved vocal learning and associated brain structures independently, and it indicates that strong constraints may influence the evolution of forebrain vocal nuclei.     

Experimental determination of entanglement with a single measurement

Nearly all protocols requiring shared quantum information--such as quantum teleportation or key distribution--rely on entanglement between distant parties. However, entanglement is difficult to characterize experimentally. All existing techniques for doing so, including entanglement witnesses or Bell inequalities, disclose the entanglement of some quantum states but fail for other states; therefore, they cannot provide satisfactory results in general. Such methods are fundamentally different from entanglement measures that, by definition, quantify the amount of entanglement in any state. However, these measures suffer from the severe disadvantage that they typically are not directly accessible in laboratory experiments. Here we report a linear optics experiment in which we directly observe a pure-state entanglement measure, namely concurrence. Our measurement set-up includes two copies of a quantum state: these 'twin' states are prepared in the polarization and momentum degrees of freedom of two photons, and concurrence is measured with a single, local measurement on just one of the photons.     

Computational redesign of endonuclease DNA binding and cleavage specificity

The reprogramming of DNA-binding specificity is an important challenge for computational protein design that tests current understanding of protein-DNA recognition, and has considerable practical relevance for biotechnology and medicine. Here we describe the computational redesign of the cleavage specificity of the intron-encoded homing endonuclease I-MsoI using a physically realistic atomic-level forcefield. Using an in silico screen, we identified single base-pair substitutions predicted to disrupt binding by the wild-type enzyme, and then optimized the identities and conformations of clusters of amino acids around each of these unfavourable substitutions using Monte Carlo sampling. A redesigned enzyme that was predicted to display altered target site specificity, while maintaining wild-type binding affinity, was experimentally characterized. The redesigned enzyme binds and cleaves the redesigned recognition site approximately 10,000 times more effectively than does the wild-type enzyme, with a level of target discrimination comparable to the original endonuclease. Determination of the structure of the redesigned nuclease-recognition site complex by X-ray crystallography confirms the accuracy of the computationally predicted interface. These results suggest that computational protein design methods can have an important role in the creation of novel highly specific endonucleases for gene therapy and other applications.     

New occurrences and host records for two species of parasitic isopods (Isopoda,Cymothoida, Bopyridae) associated with caridean shrimps (Decapoda,Caridea) from Brazil

ABSTRACT

Two species of bopyrid isopods of the Bopyrinae subfamily are recorded from new localities and hosts in northeastern Brazil. Parabopyrella lata (Nierstrasz and Brender à Brandis, 1929) was recorded from the state of Ceará, found for the first time parasitising the caridean shrimp Alpheus packardii Kingsley, 1880. In addition, Probopyrus cf. pandalicola (Packard, 1879) is recorded from the state of Bahia, parasitising the palaemonid shrimp Palaemon northropi (Rankin, 1898). Taxonomic comments are provided for each species.     

The bounded heavens: defining the limits of astrological practice in the Iberian indices

ABSTRACT

This paper explores the rules for the expurgation of texts of astrology in the Iberian Indices of forbidden books. It addresses the prohibitions put forward in Rule IX of the Index of Trent and the bull Coeli et terrae of Sixtus V, and studies its impact on the rules and their interpretation in the Spanish and Portuguese Indices, in particular, those published in the first decades of the seventeenth century: the Spanish Index librorum prohibitorum et expurgatorum of 1612 and the Portuguese Index auctorum damnatae memoriae of 1624. It shows how these indices offer a more meticulous examination of the prohibitions providing not only more detail regarding the different practices of astrology, but also explicitly accept the doctrine of inclinations of Thomas Aquinas as a central rule to deal with astrological judgments on human behaviour. It also highlights some specific details of the practice of censorship of astrological books by examining case studies of censored Portuguese and Spanish astrological publications. These provide new dimensions and highlight significant differences between the theoretical rules, practical guidelines, and actual restriction of astrological content.     

Thermal ecology,activity pattern,habitat, and microhabitats used by the skink Mabuya arajara (Squamata: Scincidae) in the Araripe Plateau,northeastern Brazil

ABSTRACT

We evaluated the activity period, thermal ecology, habitats, and preference for microhabitats of the skink Mabuya arajara in a humid forest environment on the slope of the Araripe Plateau, Brazil. A total of 283 lizards were observed. The lizards were found to be diurnally active (unimodal type pattern), with peak activity during the hottest hours of the day (1100 to 1200). About habitat use, the majority of individuals (73.8% N = 209) were recorded in the narrow transitional area, in the edges of the forest; while 26.4% of individuals were observed in open areas and no observations were made in dense forest. Seven different types of microhabitats were used, with fallen palm leaves (Arecaceae) being the preferred (47.7% N = 135). Considering all lizards, microhabitat niche breadth was 3.27. Males and females presented a high overlap (0.95) in microhabitat use. The average T_c recorded for M. arajara was 32.06 ± 2.72°C. Body size (SVL) did not influence body temperature (F = 0.51, P = > 0.05). Most of the animals were observed with their bodies completely exposed (67.84%, N = 192), 18.37% (N = 52) were semi-exposed and 13.79% (N = 39) were in shelters. Among animals with some degree of sunlight exposure, 57.59% (N = 163) were in shadows, 25.10% (N = 71) were under sunlight filtered by vegetation, and 17.31% (N = 49) were under direct sunlight.A review of the ecology of Mabuya spp. shows that several features appear to be conserved among members of the genus.     

Pervasive alteration of tree communities in undisturbed Amazonian forests

Amazonian rainforests are some of the most species-rich tree communities on earth. Here we show that, over the past two decades, forests in a central Amazonian landscape have experienced highly nonrandom changes in dynamics and composition. Our analyses are based on a network of 18 permanent plots unaffected by any detectable disturbance. Within these plots, rates of tree mortality, recruitment and growth have increased over time. Of 115 relatively abundant tree genera, 27 changed significantly in population density or basal area--a value nearly 14 times greater than that expected by chance. An independent, eight-year study in nearby forests corroborates these shifts in composition. Contrary to recent predictions, we observed no increase in pioneer trees. However, genera of faster-growing trees, including many canopy and emergent species, are increasing in dominance or density, whereas genera of slower-growing trees, including many subcanopy species, are declining. Rising atmospheric CO2 concentrations may explain these changes, although the effects of this and other large-scale environmental alterations remain uncertain. These compositional changes could have important impacts on the carbon storage, dynamics and biota of Amazonian forests.     

Such small hands: the roles of centrins/caltractins in the centriole and in genome maintenance

Centrins are small, highly conserved members of the EF-hand superfamily of calcium-binding proteins that are found throughout eukaryotes. They play a major role in ensuring the duplication and appropriate functioning of the ciliary basal bodies in ciliated cells. They have also been localised to the centrosome, which is the major microtubule organising centre in animal somatic cells. We describe the identification, cloning and characterisation of centrins in multiple eukaryotic species. Although centrins have been implicated in centriole biogenesis, recent results have indicated that centrosome duplication can, in fact, occur in the absence of centrins. We discuss these data and the non-centrosomal functions that are emerging for the centrins. In particular, we discuss the involvement of centrins in nucleotide excision repair, a process that repairs the DNA lesions that are induced primarily by ultraviolet irradiation. We discuss how centrin may be involved in these diverse processes and contribute to nuclear and cytoplasmic events.