The snails' tale in deep-sea habitats in the Gulf of Cadiz (NE Atlantic)

Bridging the Atlantic and Mediterranean continental margins, the South Iberian region has recently been the focus for geological and biological investigations. In this region, the Gulf of Cadiz (GoC) encompasses a great variety of deep-sea habitats that harbour highly diverse biological communities. In this study, we describe the composition of gastropod assemblages obtained from in situ colonization experiments and benthic sampling of deep-sea habitats in the GoC. Gastropod distributional patterns, such as bathymetric ranges, bathymetric turnover, affinity to substrate types and abundance-occupancy relationships, are analysed and interpreted in relation to their inferred dispersal capabilities and substrate availability. Overall, the GoC comprises a high diversity of gastropods (65 species), and distinct assemblages were found in typical sedimentary environments at mud volcanoes and in association with carbonate and coral samples or organic substrata. The number of taxa peaked at the Carbonate Province in the middle slope (600–1200 m depth), a highly heterogeneous area with numerous mud volcanoes, carbonate mounds and corals. Darwin (1100 m) and Captain Arutyunov (1300 m) mud volcanoes harboured the most species-rich and abundant gastropod assemblages, respectively. Colonization experiments with organic substrata (wood and alfalfa grass) also yielded diverse and abundant gastropod assemblages. These organic inputs allowed the recruitment of local species but mainly of wood specialist taxa that were not previously known from the GoC. Our results suggest that the distribution of gastropod assemblages may be primarily determined by the occurrence of suitable habitats, probably due to the effect of the substrate type on the structural complexity of the habitat and availability and diversity of adequate food sources. The type of larval development is apparently not a limiting factor for colonization of deep-sea habitats. However, the predominance of non-planktotrophy, and especially lecithotrophy, suggests that a trade-off between more limited dispersal capability and higher potential for self-recruitment may be a recurrent pattern in gastropod species inhabiting reducing environments and other patchily distributed deep-sea habitats. A network of suitable habitats that ensures effective population connectivity would explain the predominance and relatively wide distribution of short-distance dispersing non-planktotrophic species in the GoC deep-sea habitats and other geographical regions

nQuire: a statistical framework for ploidy estimation using next generation sequencing

BACKGROUND: Intraspecific variation in ploidy occurs in a wide range of species including pathogenic and nonpathogenic eukaryotes such as yeasts and oomycetes. Ploidy can be inferred indirectly - without measuring DNA content - from experiments using next-generation sequencing (NGS). We present nQuire, a statistical framework that distinguishes between diploids, triploids and tetraploids using NGS. The command-line tool models the distribution of base frequencies at variable sites using a Gaussian Mixture Model, and uses maximum likelihood to select the most plausible ploidy model. nQuire handles large genomes at high coverage efficiently and uses standard input file formats.  RESULTS: We demonstrate the utility of nQuire analyzing individual samples of the pathogenic oomycete Phytophthora infestans and the Baker's yeast Saccharomyces cerevisiae. Using these organisms we show the dependence between reliability of the ploidy assignment and sequencing depth. Additionally, we employ normalized maximized log- likelihoods generated by nQuire to ascertain ploidy level in a population of samples with ploidy heterogeneity. Using these normalized values we cluster samples in three dimensions using multivariate Gaussian mixtures. The cluster assignments retrieved from a S. cerevisiae population recovered the true ploidy level in over 96% of samples. Finally, we show that nQuire can be used regionally to identify chromosomal aneuploidies.  CONCLUSIONS: nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuire under the MIT license

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its Mexican center of origin was low, and one scenario held that a single strain, US-1, had dominated the global population for 150 years; this was later challenged based on DNA analysis of historical herbarium specimens. We have compared the genomes of 11 herbarium and 15 modern strains. We conclude that the nineteenth century epidemic was caused by a unique genotype, HERB-1, that persisted for over 50 years. HERB-1 is distinct from all examined modern strains, but it is a close relative of US-1, which replaced it outside of Mexico in the twentieth century. We propose that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species' center of diversity.Comment: To be published in eLIF

An overview of chemosynthetic symbioses in bivalves from the North Atlantic and Mediterranean Sea

Deep-sea bivalves found at hydrothermal vents, cold seeps and organic falls are sustained by chemosynthetic bacteria that ensure part or all of their carbon nutrition. These symbioses are of prime importance for the functioning of the ecosystems. Similar symbioses occur in other bivalve species living in shallow and coastal reduced habitats worldwide. In recent years, several deep-sea species have been investigated from continental margins around Europe, West Africa, eastern Americas, the Gulf of Mexico, and from hydrothermal vents on the Mid-Atlantic Ridge. In parallel, numerous, more easily accessible shallow marine species have been studied. Herein we provide a summary of the current knowledge available on chemosymbiotic bivalves in the area ranging west-to-east from the Gulf of Mexico to the Sea of Marmara, and north-to-south from the Arctic to the Gulf of Guinea. Characteristics of symbioses in 53 species from the area are summarized for each of the five bivalve families documented to harbor chemosynthetic symbionts (Mytilidae, Vesicomyidae, Solemyidae, Thyasiridae and Lucinidae). Comparisons are made between the families, with special emphasis on ecology, life cycle, and connectivity. Chemosynthetic symbioses are a major adaptation to ecosystems and habitats exposed to reducing conditions. However, relatively little is known regarding their diversity and functioning, apart from a few “model species” on which effort has focused over the last 30 yr. In the context of increasing concern about biodiversity and ecosystems, and increasing anthropogenic pressure on oceans, we advocate a better assessment of the diversity of bivalve symbioses in order to evaluate the capacities of these remarkable ecological and evolutionary units to withstand environmental change

First evidence of intersex condition in extensively reared mullets from Sardinian lagoons (central–western Mediterranean, Italy)

The term intersex describes alterations in gonadal development with the simultaneous presence of male and female reproductive stages in the same gonad of a gonochoristic species. In coastal and estuarine environments, euryhaline fish living in polluted waters such as Mugilidae can frequently show these sexual anomalies. In this work, we analysed adult specimens of three species of euryhaline mullets (Chelon labrosus, Liza aurata and Mugil cephalus) from two Sardinian lagoons (Marceddì and San Teodoro) devoted to extensive aquacultural practices, in order to identify putative alterations in gonads and in gamete development. Overall, 13 of the 158 mullets examined (8.2%) were affected by gonadal disorders: four subjects (one C. labrosus, two L. aurata and one M. cephalus) exhibiting an intersex condition were found in the Marceddì lagoon and the other nine (five C. labrosus, two L. aurata and two M. cephalus) in the San Teodoro lagoon. Twelve of these gonads were classified as testis-ova (TOs) and one, belonging to a C. labrosus specimen, was a mixed gonadal tissue (MGT). Intersex condition was evaluated using an intersex index and all the recorded values showed a mild Ovotestis Severity Index (OSI). However, our findings suggest that fish gonadal disorders may be underestimated in extensive reared fish species, particularly in coastal brackish environments polluted by intensive agriculture and animal husbandry activities

Oxygen consumption in bivalves

Os organismos vivos obtêm energia degradando moléculas orgânicas através da respiração celular. Esse processo pode ocorrer com ou sem consumo de oxigénio. Em muitos seres vivos com células complexas, a respiração celular ocorre com consumo de oxigénio pelo que se designa de respiração aeróbia. O consumo de oxigénio pode ser observado utilizando uma substância indicadora de presença/ausência de O2. O indicador utilizado neste experiencia foi o azul-de-metileno que muda de cor conforme está na forma reduzida ou na forma oxidada. Os resultados mostram que ocorreu a redução do azul-de-metileno, o que significa que o oxigénio foi consumido. O objetivo desta atividade é observar a mobilização de energia em bivalves (Scrobicularria plana) vulgarmente chamada de Lambujinha através do consumo de O2.Living organisms obtain energy by degrading organic molecules (cellular respiration). This process there is a consumption of oxygen which is known by aerobic respiration. Oxygen consumption can be observed busing substances that indicate the presence / absence of O2. The indicator that was used in this experiment is the methylene blue which changes colour as it is in its reduced form or oxidized. The results show a reduction of the methylene blue, which means that the oxygen has been consumed. The purpose of this activity is to observe the energy mobilization in bivalves (Scrobicularria plana) commonly called Lambujinha through the consumption of O2

State of the art in the use of bioceramics to elaborate 3D structures using robocasting

Robocasting, também conhecido como Direct Ink Writing, é uma técnica de fabricação aditiva (AM), que inclui extração direta de sistemas coloidais, que consiste na exposição de camadas e um controlador controlado por computador de uma mídia altamente concentrada nesta extrusão. Este artigo apresenta uma visão geral das contribuições e desafios no desenvolvimento de biomateriais cerâmicos tridimensionais (3D) por esse método de impressão. O estado da arte em diferentes biocerâmicas como alumina, zircônia, fosfato de vidro, vidro / vitrocerâmica e compostos é avaliado e discutido em relação a suas aplicações e comportamento biológico, em uma pesquisa que produziu desde uma produção de próteses dentárias personalizadas a biofabricantes 3D humanos tecidos.Embora o robocasting represente uma interrupção na fabricação de estruturas porosas, como os andaimes para a Engenharia de Tecidos (TE), muitas vantagens ainda são necessárias, mas ainda são divulgadas, essa técnica já está usando a utilização de peças densas. Assim, são necessárias estratégias para a fabricação de biocerâmica densificada, com o objetivo de ampliar as possibilidades dessa técnica de AM. As vantagens e desvantagens e também perspectivas futuras da aplicação do robocasting no processamento biocerâmico também são exploradas

DISTRIBUIÇÃO DE RENDA E CRESCIMENTO ECONÔMICO NO BRASIL: UMA ANÁLISE ECONOMÉTRICA DO PERÍODO 1976-2010

O modelo brasileiro de crescimento econômico predominante se caracteriza por baixas taxas de crescimento, grau reduzido de dinamismo e intensa desigualdade social. Esta pesquisa se norteia pela seguinte questão: de que forma e em que magnitude a distribuição de renda e o crescimento econômico brasileiro tem se inter-relacionado ao longo do período 1976-2012? O objetivo deste trabalho é estudar as relações de longo prazo entre a distribuição de renda e crescimento econômico no Brasil. Tanto a modelagem VEC quanto os modelos autorregressivos de defasagens distribuídas (ADLs) sugeriram a existência, no sentido de Granger, de bicausalidade da desigualdade para o crescimento e do crescimento para a desigualdade

Ocupação urbana e a impermeabilização do solo

A ocupação urbana acelerada e não planejada intensificou a degradação ambiental. Dentre as formas de degradação está a impermeabilização do solo que por sua vez, reduzem a infiltração de águas das chuvas, aumentando os riscos de erosão, compactação e deslizamentos dos solos, bem como inundações de córregos e ruas. Em vista disso o objetivo desse estudo é analisar a ocupação do solo urbano sem planejamento, o mesmo apresenta consequências catastróficas, impactos ambientais negativos a sobrecarga no sistema de drenagem urbana por meio do aumento da impermeabilização do solo e da diminuição da infiltração, a perda da cobertura vegetal. Para minimizar tais impactos, as engenharias propõem alternativas de contenção dos escoamentos superficiais, que permitem uma maior infiltração e a percolação da água no sistema de drenagem urbana e que podem ser adotados nas unidades individuais assim como a criação de reservatórios ou bacias para armazenamento temporário da água escoada nas proximidades. Dessa forma é viável a conservação da natureza, e que os grandes centros urbanos contem com as áreas vegetadas, tais como jardins, pomares, passeios, praças, parques, entre outros, meios que visa diminuir os processos impermeabilização