Phylogeny of genes for secretion NTPases: Identification of the widespread tadA subfamily and development of a diagnostic key for gene classification

Macromolecular transport systems in bacteria currently are classified by function and sequence comparisons into five basic types. In this classification system, type II and type IV secretion systems both possess members of a superfamily of genes for putative NTP hydrolase (NTPase) proteins that are strikingly similar in structure, function, and sequence. These include VirB11, TrbB, TraG, GspE, PilB, PilT, and ComG1. The predicted protein product of tadA, a recently discovered gene required for tenacious adherence of Actinobacillus actinomycetemcomitans, also has significant sequence similarity to members of this superfamily and to several unclassified and uncharacterized gene products of both Archaea and Bacteria. To understand the relationship of tadA and tadA-like genes to those encoding the putative NTPases of type II/IV secretion, we used a phylogenetic approach to obtain a genealogy of 148 NTPase genes and reconstruct a scenario of gene superfamily evolution. In this phylogeny, clear distinctions can be made between type II and type IV families and their constituent subfamilies. In addition, the subgroup containing tadA constitutes a novel and extremely widespread subfamily of the family encompassing all putative NTPases of type IV secretion systems. We report diagnostic amino acid residue positions for each major monophyletic family and subfamily in the phylogenetic tree, and we propose an easy method for precisely classifying and naming putative NTPase genes based on phylogeny. This molecular key-based method can be applied to other gene superfamilies and represents a valuable tool for genome analysis.

The biotic crisis and the future of evolution

The biotic crisis overtaking our planet is likely to precipitate a major extinction of species. That much is well known. Not so well known but probably more significant in the long term is that the crisis will surely disrupt and deplete certain basic processes of evolution, with consequences likely to persist for millions of years. Distinctive features of future evolution could include a homogenization of biotas, a proliferation of opportunistic species, a pest-and-weed ecology, an outburst of speciation among taxa that prosper in human-dominated ecosystems, a decline of biodisparity, an end to the speciation of large vertebrates, the depletion of “evolutionary powerhouses” in the tropics, and unpredictable emergent novelties. Despite this likelihood, we have only a rudimentary understanding of how we are altering the evolutionary future. As a result of our ignorance, conservation policies fail to reflect long-term evolutionary aspects of biodiversity loss.

The current biodiversity extinction event: Scenarios for mitigation and recovery

The current massive degradation of habitat and extinction of species is taking place on a catastrophically short timescale, and their effects will fundamentally reset the future evolution of the planet's biota. The fossil record suggests that recovery of global ecosystems has required millions or even tens of millions of years. Thus, intervention by humans, the very agents of the current environmental crisis, is required for any possibility of short-term recovery or maintenance of the biota. Many current recovery efforts have deficiencies, including insufficient information on the diversity and distribution of species, ecological processes, and magnitude and interaction of threats to biodiversity (pollution, overharvesting, climate change, disruption of biogeochemical cycles, introduced or invasive species, habitat loss and fragmentation through land use, disruption of community structure in habitats, and others). A much greater and more urgently applied investment to address these deficiencies is obviously warranted. Conservation and restoration in human-dominated ecosystems must strengthen connections between human activities, such as agricultural or harvesting practices, and relevant research generated in the biological, earth, and atmospheric sciences. Certain threats to biodiversity require intensive international cooperation and input from the scientific community to mitigate their harmful effects, including climate change and alteration of global biogeochemical cycles. In a world already transformed by human activity, the connection between humans and the ecosystems they depend on must frame any strategy for the recovery of the biota.

Toward a plant genomics initiative: Thoughts on the value of cross-species and cross-genera comparisons in the grasses

Comparative genomics offers unparalleled opportunities to integrate historically distinct disciplines, to link disparate biological kingdoms, and to bridge basic and applied science. Cross-species, cross-genera, and cross-kingdom comparisons are proving key to understanding how genes are structured, how gene structure relates to gene function, and how changes in DNA have given rise to the biological diversity on the planet. The application of genomics to the study of crop species offers special opportunities for innovative approaches for combining sequence information with the vast reservoirs of historical information associated with crops and their evolution. The grasses provide a particularly well developed system for the development of tools to facilitate comparative genetic interpretation among members of a diverse and evolutionarily successful family. Rice provides advantages for genomic sequencing because of its small genome and its diploid nature, whereas each of the other grasses provides complementary genetic information that will help extract meaning from the sequence data. Because of the importance of the cereals to the human food chain, developments in this area can lead directly to opportunities for improving the health and productivity of our food systems and for promoting the sustainable use of natural resources.

Extrasolar planets

The first known extrasolar planet in orbit around a Sun-like star was discovered in 1995. This object, as well as over two dozen subsequently detected extrasolar planets, were all identified by observing periodic variations of the Doppler shift of light emitted by the stars to which they are bound. All of these extrasolar planets are more massive than Saturn is, and most are more massive than Jupiter. All orbit closer to their stars than do the giant planets in our Solar System, and most of those that do not orbit closer to their star than Mercury is to the Sun travel on highly elliptical paths. Prevailing theories of star and planet formation, which are based on observations of the Solar System and of young stars and their environments, predict that planets should form in orbit about most single stars. However, these models require some modifications to explain the properties of the observed extrasolar planetary systems.

Mantle dynamics and seismic tomography

Three-dimensional imaging of the Earth's interior, called seismic tomography, has achieved breakthrough advances in the last two decades, revealing fundamental geodynamical processes throughout the Earth's mantle and core. Convective circulation of the entire mantle is taking place, with subducted oceanic lithosphere sinking into the lower mantle, overcoming the resistance to penetration provided by the phase boundary near 650-km depth that separates the upper and lower mantle. The boundary layer at the base of the mantle has been revealed to have complex structure, involving local stratification, extensive structural anisotropy, and massive regions of partial melt. The Earth's high Rayleigh number convective regime now is recognized to be much more interesting and complex than suggested by textbook cartoons, and continued advances in seismic tomography, geodynamical modeling, and high-pressure–high-temperature mineral physics will be needed to fully quantify the complex dynamics of our planet's interior.

Solution to Darwin's dilemma: Discovery of the missing Precambrian record of life

In 1859, in On the Origin of Species, Darwin broached what he regarded to be the most vexing problem facing his theory of evolution—the lack of a rich fossil record predating the rise of shelly invertebrates that marks the beginning of the Cambrian Period of geologic time (≈550 million years ago), an “inexplicable” absence that could be “truly urged as a valid argument” against his all embracing synthesis. For more than 100 years, the “missing Precambrian history of life” stood out as one of the greatest unsolved mysteries in natural science. But in recent decades, understanding of life's history has changed markedly as the documented fossil record has been extended seven-fold to some 3,500 million years ago, an age more than three-quarters that of the planet itself. This long-sought solution to Darwin's dilemma was set in motion by a small vanguard of workers who blazed the trail in the 1950s and 1960s, just as their course was charted by a few pioneering pathfinders of the previous century, a history of bold pronouncements, dashed dreams, search, and final discovery.

Hypothalamic integration of body fluid regulation.

The progression of animal life from the paleozoic ocean to rivers and diverse econiches on the planet's surface, as well as the subsequent reinvasion of the ocean, involved many different stresses on ionic pattern, osmotic pressure, and volume of the extracellular fluid bathing body cells. The relatively constant ionic pattern of vertebrates reflects a genetic "set" of many regulatory mechanisms--particularly renal regulation. Renal regulation of ionic pattern when loss of fluid from the body is disproportionate relative to the extracellular fluid composition (e.g., gastric juice with vomiting and pancreatic secretion with diarrhea) makes manifest that a mechanism to produce a biologically relatively inactive extracellular anion HCO3- exists, whereas no comparable mechanism to produce a biologically inactive cation has evolved. Life in the ocean, which has three times the sodium concentration of extracellular fluid, involves quite different osmoregulatory stress to that in freshwater. Terrestrial life involves risk of desiccation and, in large areas of the planet, salt deficiency. Mechanisms integrated in the hypothalamus (the evolutionary ancient midbrain) control water retention and facilitate excretion of sodium, and also control the secretion of renin by the kidney. Over and above the multifactorial processes of excretion, hypothalamic sensors reacting to sodium concentration, as well as circumventricular organs sensors reacting to osmotic pressure and angiotensin II, subserve genesis of sodium hunger and thirst. These behaviors spectacularly augment the adaptive capacities of animals. Instinct (genotypic memory) and learning (phenotypic memory) are melded to give specific behavior apt to the metabolic status of the animal. The sensations, compelling emotions, and intentions generated by these vegetative systems focus the issue of the phylogenetic emergence of consciousness and whether primal awareness initially came from the interoreceptors and vegetative systems rather than the distance receptors.

Trans-Pacific migrations of the loggerhead turtle (Caretta caretta) demonstrated with mitochondrial DNA markers.

Juvenile loggerhead turtles (Caretta caretta) have recently been documented in the vicinity of Baja California and thousands of these animals have been captured in oceanic fisheries of the North Pacific. The presence of loggerhead turtles in the central and eastern North Pacific is a prominent enigma in marine turtle distribution because the nearest documented nesting concentrations for this species are in Australia and Japan, over 10,000 km from Baja California. To determine the origin of the Baja California feeding aggregate and North Pacific fishery mortalities, samples from nesting areas and pelagic feeding aggregates were compared with genetic markers derived from mtDNA control region sequences. Overall, 57 of 60 pelagic samples (95%) match haplotypes seen only in Japanese nesting areas, implicating Japan as the primary source of turtles in the North Pacific Current and around Baja California. Australian nesting colonies may contribute the remaining 5% of these pelagic feeding aggregates. Juvenile loggerhead turtles apparently traverse the entire Pacific Ocean, approximately one-third of the planet, in the course of developmental migrations, but mortality in high-seas fisheries raises concern over the future of this migratory population.

Desigualdade social entre as crianças menores de 5 anos em diferentes regiões mundiais

Introdução: A Organização Mundial da Saúde indica que a prevalência do déficit de altura tem diminuído no planeta nas últimas décadas, pouco se sabe ainda sobre os fatores associados a este declínio ou sua associação com a desigualdade social. Objetivo: Descrever a evolução do déficit de altura e da desigualdade socioeconômica em diferentes regiões do mundo. Métodos: A pesquisa foi baseada em dados secundários provenientes do programa Demografic Health Surveys DHS de 6 sub-regiões do mundo representando 24 países em um total de 48 pesquisas na década de 90 e na primeira década do século 21 com 377.151 crianças menores de 5 anos. Foi considerada como variável de interesse o Déficit de altura para idade considerado como a ocorrência deste índice inferior a -2 escore Z da distribuição de referência WHO-2006. Foram imputados através de modelo de regressão os valores faltantes das variáveis água para beber, esgoto sanitário e escolaridade materna. Foi estimado o Índice de Concentração para as variáveis déficit de altura, educação materna deficiente, água para beber insegura, esgoto domiciliar deficiente e ocorrência de doenças, tendo como variável de ranqueamento o Índice de Riqueza. Dados do poder de paridade de compra fornecidos pelo Banco Mundial foram utilizados para verificar as diferenças na evolução da desnutrição. Resultados: Nessa análise acerca da evolução da desigualdade socioeconômica do déficit de altura para idade em países em desenvolvimento constatou-se que: a) a prevalência do déficit de altura para idade decresceu em 87 por cento dos países; b) apenas 8 países (33 por cento ) aumentaram a diferença entre prevalência do déficit de altura nos quintos extremos c) quatorze países (58 por cento ) evoluíram com diminuição do déficit de altura e aumento do índice de concentração; d) Dois países que diminuíram a o déficit de altura e a desigualdade tinham os menores valores de escolaridade materna deficiente; e) 13 países (93 por cento ) daqueles que diminuíram déficit mas aumentaram a desigualdade possuíam indicadores de vulnerabilidade infantil deficientes. Conclusões: Os países em desenvolvimento apresentam redução no déficit de altura em crianças menores de 5 anos. A diminuição da desigualdade na riqueza e na escolaridade materna deficiente explicaram maior parte da melhoria da desigualdade do déficit de altura para idade.

DUst around NEarby Stars. The survey observational results

Context. Debris discs are a consequence of the planet formation process and constitute the fingerprints of planetesimal systems. Their solar system counterparts are the asteroid and Edgeworth-Kuiper belts. Aims. The DUNES survey aims at detecting extra-solar analogues to the Edgeworth-Kuiper belt around solar-type stars, putting in this way the solar system into context. The survey allows us to address some questions related to the prevalence and properties of planetesimal systems. Methods. We used Herschel/PACS to observe a sample of nearby FGK stars. Data at 100 and 160 μm were obtained, complemented in some cases with observations at 70 μm, and at 250, 350 and 500 μm using SPIRE. The observing strategy was to integrate as deep as possible at 100 μm to detect the stellar photosphere. Results. Debris discs have been detected at a fractional luminosity level down to several times that of the Edgeworth-Kuiper belt. The incidence rate of discs around the DUNES stars is increased from a rate of ~12.1% ± 5% before Herschel to ~20.2% ± 2%. A significant fraction (~52%) of the discs are resolved, which represents an enormous step ahead from the previously known resolved discs. Some stars are associated with faint far-IR excesses attributed to a new class of cold discs. Although it cannot be excluded that these excesses are produced by coincidental alignment of background galaxies, statistical arguments suggest that at least some of them are true debris discs. Some discs display peculiar SEDs with spectral indexes in the 70–160 μm range steeper than the Rayleigh-Jeans one. An analysis of the debris disc parameters suggests that a decrease might exist of the mean black body radius from the F-type to the K-type stars. In addition, a weak trend is suggested for a correlation of disc sizes and an anticorrelation of disc temperatures with the stellar age.

Competitividade da cadeia produtiva do Arapaima gigas, o pirarucu da Amazônia brasileira

Com um quinto da água doce do planeta, o sistema fluvial da Amazônia apresenta um enorme potencial para piscicultura. De acordo com a FAO, em função das suas condições geográficas, o Brasil é um dos poucos países que tem condições de atender à crescente demanda mundial, podendo tornar-se um dos maiores produtores de peixes do mundo. A observação desse potencial amazônico motivou o desenvolvimento desta pesquisa que se debruça sobre a questão da competitividade da cadeia produtiva de Arapaima gigas, o pirarucu da Amazônia brasileira. As pesquisas de campo levaram ao mapeamento de duas cadeias: a cadeia extrativista e a piscicultura. A abordagem sistêmica permitiu a verificação das características dos atores e as bases sob as quais as transações se estabelecem. À luz da teoria das restrições foram identificados os gargalos que impedem a competitividade do sistema, inclusive alertando para os recursos com restrição de capacidade. Comprovou-se que a falta de uma cadeia produtiva devidamente organizada pode provocar graves prejuízos a determinados elos, enquanto outros membros aproveitam-se de ações oportunistas para ampliar suas margens de lucro. Da mesma forma, a ausência de uma cadeia produtiva completa impede a fixação do valor gerado na região de origem das matérias-primas. No entanto, também foi possível comprovar que há possibilidade de desenvolver o extrativismo atribuindo valor econômico aos recursos naturais e gerando renda para a comunidade local. Além de apresentar o panorama do setor na região delimitada, este estudo culminou em reflexões capazes de orientar políticas públicas para o desenvolvimento de cadeias produtivas completas na região da Amazônia brasileira.

EChO. Exoplanet characterisation observatory

A dedicated mission to investigate exoplanetary atmospheres represents a major milestone in our quest to understand our place in the universe by placing our Solar System in context and by addressing the suitability of planets for the presence of life. EChO—the Exoplanet Characterisation Observatory—is a mission concept specifically geared for this purpose. EChO will provide simultaneous, multi-wavelength spectroscopic observations on a stable platform that will allow very long exposures. The use of passive cooling, few moving parts and well established technology gives a low-risk and potentially long-lived mission. EChO will build on observations by Hubble, Spitzer and ground-based telescopes, which discovered the first molecules and atoms in exoplanetary atmospheres. However, EChO’s configuration and specifications are designed to study a number of systems in a consistent manner that will eliminate the ambiguities affecting prior observations. EChO will simultaneously observe a broad enough spectral region—from the visible to the mid-infrared—to constrain from one single spectrum the temperature structure of the atmosphere, the abundances of the major carbon and oxygen bearing species, the expected photochemically-produced species and magnetospheric signatures. The spectral range and resolution are tailored to separate bands belonging to up to 30 molecules and retrieve the composition and temperature structure of planetary atmospheres. The target list for EChO includes planets ranging from Jupiter-sized with equilibrium temperatures T_ eq up to 2,000 K, to those of a few Earth masses, with T _eq \u223c 300 K. The list will include planets with no Solar System analog, such as the recently discovered planets GJ1214b, whose density lies between that of terrestrial and gaseous planets, or the rocky-iron planet 55 Cnc e, with day-side temperature close to 3,000 K. As the number of detected exoplanets is growing rapidly each year, and the mass and radius of those detected steadily decreases, the target list will be constantly adjusted to include the most interesting systems. We have baselined a dispersive spectrograph design covering continuously the 0.4–16 μm spectral range in 6 channels (1 in the visible, 5 in the InfraRed), which allows the spectral resolution to be adapted from several tens to several hundreds, depending on the target brightness. The instrument will be mounted behind a 1.5 m class telescope, passively cooled to 50 K, with the instrument structure and optics passively cooled to \u223c45 K. EChO will be placed in a grand halo orbit around L2. This orbit, in combination with an optimised thermal shield design, provides a highly stable thermal environment and a high degree of visibility of the sky to observe repeatedly several tens of targets over the year. Both the baseline and alternative designs have been evaluated and no critical items with Technology Readiness Level (TRL) less than 4–5 have been identified. We have also undertaken a first-order cost and development plan analysis and find that EChO is easily compatible with the ESA M-class mission framework.

Chromospheric activity and rotation of FGK stars in the solar vicinity. An estimation of the radial velocity jitter

Context. Chromospheric activity produces both photometric and spectroscopic variations that can be mistaken as planets. Large spots crossing the stellar disc can produce planet-like periodic variations in the light curve of a star. These spots clearly affect the spectral line profiles, and their perturbations alter the line centroids creating a radial velocity jitter that might “contaminate” the variations induced by a planet. Precise chromospheric activity measurements are needed to estimate the activity-induced noise that should be expected for a given star. Aims. We obtain precise chromospheric activity measurements and projected rotational velocities for nearby (d ≤ 25 pc) cool (spectral types F to K) stars, to estimate their expected activity-related jitter. As a complementary objective, we attempt to obtain relationships between fluxes in different activity indicator lines, that permit a transformation of traditional activity indicators, i.e., Ca II H & K lines, to others that hold noteworthy advantages. Methods. We used high resolution (~50 000) echelle optical spectra. Standard data reduction was performed using the IRAF ECHELLE package. To determine the chromospheric emission of the stars in the sample, we used the spectral subtraction technique. We measured the equivalent widths of the chromospheric emission lines in the subtracted spectrum and transformed them into fluxes by applying empirical equivalent width and flux relationships. Rotational velocities were determined using the cross-correlation technique. To infer activity-related radial velocity (RV) jitter, we used empirical relationships between this jitter and the R’_HK index. Results. We measured chromospheric activity, as given by different indicators throughout the optical spectra, and projected rotational velocities for 371 nearby cool stars. We have built empirical relationships among the most important chromospheric emission lines. Finally, we used the measured chromospheric activity to estimate the expected RV jitter for the active stars in the sample.

Percepções sociais sobre o futuro da humanidade no planeta: um estudo na cidade de Piracicaba, SP

A pesquisa sobre as percepções de residentes da região de Piracicaba em relação às questões ambientais e ao futuro da humanidade no planeta foi desenvolvida com base em um questionário semi-estruturado. As questões buscaram levantar dados autoavaliativos sobre perfil, comportamentos, estado de humor, qualidade de vida, condição econômica e hábitos de consumo, práticas para destinação de resíduos, iniciativas de exercício de cidadania em prol da sustentabilidade socioambiental, para enfim, indagar sobre percepções de futuro e avaliações sobre o contexto socioambiental dos participantes da pesquisa. A aplicação dos questionários foi feita de forma aleatória estratificada nos bairros das cinco regiões da cidade de Piracicaba: Norte, Sul, Leste, Oeste e Centro. Por meio dessas aplicações, foram obtidos 655 questionários, que foram sistematizados, tabulados e analisados estatisticamente, utilizando-se gráficos de frequência, o Teste de Kruskal Wallis, os Testes de Correlação de Spearman e Kendall, o Teste de Qui-Quadrado e o Teste Exato de Fisher. Foram também criadas nuvens de palavras, desenvolvidas no software online \"Wordle\" (FEINBERG, 2014). Os resultados obtidos com essa pesquisa e as análises desenvolvidas indicam que 227 pessoas, isto é, aproximadamente 35% dos respondentes, possui uma percepção pessimista sobre o futuro da humanidade no planeta. Porém, 493 pessoas, o equivalente a aproximadamente 75% do total de respondentes, considerou que, dentre as alternativas apresentadas no questionário (Desenvolvimento de tecnologias; Controle de natalidade; Educação e mudanças culturais; Cobrança de impostos com base nos impactos ambientais; Intervenção do Estado), a educação e mudanças culturais são fundamentais no processo de transformação social e de superação das problemáticas ambientais. Observou-se também que a crise hídrica vivenciada na época em que os questionários foram aplicados também influenciou na percepção social dos respondentes, uma vez que a palavra \"água\" foi citada 380 vezes. Por meio do trabalho, foi também possível analisar o comportamento ambiental dos pesquisados, notando-se que ainda há a necessidade de promoção de atividades educacionais e comunicacionais que possam estimular a adoção de hábitos e comportamentos mais comprometidos com ideias de sustentabilidade e que levem a mudanças mais efetivas nos padrões de relacionamento entre sociedade e meio ambiente.