Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing

Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructing de novo the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotgun metagenomics on wide scale projects is the high cost associated with the approach. We set out to determine if it is possible to use shallow shotgun metagenomics to characterize complex biological matrices while reducing costs. We measured the variation of several summary statistics simulating a decrease in sequencing depth by randomly subsampling a number of reads. The main statistics that were compared are alpha diversity estimates, species abundance, and ability of reconstructing de novo the metagenome in terms of length and completeness. Our results show that diversity indices of complex prokaryotic, eukaryotic and viral communities can be accurately estimated with 500,000 reads or less, although particularly complex samples may require 1,000,000 reads. On the contrary, any task involving the reconstruction of the metagenome performed poorly, even with the largest simulated subsample (1,000,000 reads). The length of the reconstructed assembly was smaller than the length obtained with the full dataset, and the proportion of conserved genes that were identified in the meta-genome was drastically reduced compared to the full sample. Shallow shotgun metagenomics can be a useful tool to describe the structure of complex matrices, but it is not adequate to reconstruct—even partially—the metagenome

Tectono-metamorphic history of the ophiolitic Lento unit (northern Corsica): evidences for the complexity of accretion-exhumation processes in a fossil subduction system

The Alpine Corsica (Corsica Island, France) is characterized by a stack of continent- and ocean-derived tectonic units, known as Schistes Lustres complex. This complex is affected by deformation and metamorphic imprint achieved during Late Cretaceous – Early Tertiary subduction- related processes connected with the closure of the Ligure-Piemontese oceanic basin and subsequent continental collision. In the Schistes Lustres complex, the Lento oceanic unit is characterized by four deformation phases, from D1 to D4 phase. The D1 phase, characterized by blueschist metamorphism, is regarded as related to coherent underplating in a subduction zone at a depth of about 25-30 km. The subsequent deformation phases can be referred to exhumation history, as suggested by the continuous decrease of metamorphic conditions. The transition from accretion to exhumation is represented by the D2 phase, achieved during the development of a duplex structure of accreted units. The D3 phase is in turn achieved by a further horizo..

Designing a diving protocol for thermocline identification using dive computers in marine citizen science

Dive computers have an important potential for citizen science projects where recreational SCUBA divers can upload the depth temperature profile and the geolocation of the dive to a central database which may provide useful information about the subsurface temperature of the oceans. However, their accuracy may not be adequate and needs to be evaluated. The aim of this study is to assess the accuracy and precision of dive computers and provide guidelines in order to enable their contribution to citizen science projects. Twenty-two dive computers were evaluated during real ocean dives for consistency and scatter in the first phase. In the second phase, the dive computers were immersed in sufficient depth to initiate the dive record inside a precisely controlled sea aquarium while using a calibrated device as a reference. Results indicate that the dive computers do not have the accuracy required for monitoring temperature changes in the oceans, however, they can be used to detect thermoclines if the users follow a specific protocol with specific dive computers. This study enabled the authors to define this protocol based on the results of immersion in two different sea aquarium tanks set to two different temperatures in order to simulate the conditions of a thermocline

Physiological and RNA sequencing data of white lupin plants grown under Fe and P deficiency

This DIB article provides details about transcriptional and physiological response of Fe- and P-deficient white lupin roots, an extensive and complete description of plant response is shown in the research article \u201cPhysiological and transcriptomic data highlight common features between iron and phosphorus acquisition mechanisms in white lupin roots\u201d Venuti et al. [1]. White lupin plants were grown under hydroponic system and three different nutritional regimes: Fe deficiency (-Fe), P deficiency (-P), or Fe and P sufficiency (+P + Fe). Depending on nutritional treatment, white lupin plants showed changes in the fresh weights, in root external acidification and FeIII-reductase activity. Moreover, the transcriptomic changes occurring in apices and clusters of Fe-deficient lupin roots were investigated and compared with differences of gene expression occurring in P-deficient plants (-P) and in Fe- and P-sufficient plants (+P + Fe). Transcriptomic data are available in the public repository Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under the series entry (GSE112220). The annotation, mapping and enrichment analyses of differentially modulated transcripts were assessed

The Intra-Pontide ophiolites in Northern Turkey revisited: From birth to death of a Neotethyan oceanic domain

The Anatolian peninsula is a key location to study the central portion of the Neotethys Ocean(s) and to understand how its western and eastern branches were connected. One of the lesser known branches of the Mesozoic ocean(s) is preserved in the northern ophiolite suture zone exposed in Turkey, namely, the Intra-Pontide suture zone. It is located between the Sakarya terrane and the Eurasian margin (i.e., Istanbul-Zonguldak terrane) and consists of several metamorphic and non-metamorphic units containing ophiolites produced in supra-subduction settings from the Late Triassic to the Early Cretaceous. Ophiolites preserved in the metamorphic units recorded pervasive deformations and peak metamorphic conditions ranging from blueschist to eclogite facies. In the non-metamorphic units, the complete oceanic crust sequence is preserved in tectonic units or as olistoliths in sedimentary mélanges. Geochemical, structural, metamorphic and geochronological investigations performed on ophiolite-bearing units allowed the formulation of a new geodynamic model of the entire "life" of the Intra-Pontide oceanic basin(s). The reconstruction starts with the opening of the Intra-Pontide oceanic basins during the Late Triassic between the Sakarya and Istanbul-Zonguldak continental microplates and ends with its closure caused by two different subductions events that occurred during the upper Early Jurassic and Middle Jurassic. The continental collision between the Sakarya continental microplate and the Eurasian margin developed from the upper Early Cretaceous to the Palaeocene. The presented reconstruction is an alternative model to explain the complex and articulate geodynamic evolution that characterizes the southern margin of Eurasia during the Mesozoic era. Keywords: Intra-Pontide suture zone, Central Pontides, Northern Turkey, Ophiolites, Neotethys Ocean, Geodynamic

Intelligence as a Dynamic Capacity to Generate Competitive Advantage

Intelligence is a process of scanning the environment, that enhances the capacity for adaptation and organizational anticipation, being a source of competitive advantage and a necessary factor for the business\u27 sustainability. Research indicates the need to develop an internal capacity of the organization to the environmental scanning to be established, opening an innovative way of investigation in terms of association of intelligence and organizational capacities - among which dynamic capacities. Thus, with the objective of verifying the association of Intelligence as a Dynamic Capability, and its contribution to the generation of sustainable competitive advantage, a model with an application is proposed - through a model of structural equations - to demonstrate the potential relationship between Intelligence, Dynamic Capabilities and Advantage Competitive. The results indicate a high correlation between Intelligence and Dynamic Capabilities, and through these, the Competitive Advantage. La inteligencia es un proceso de exploración del entorno, que potencia la capacidad de adaptación y anticipación organizacional, siendo fuente de ventaja competitiva y factor necesario para la sustentabilidad del negocio. La investigación indica la necesidad de desarrollar una capacidad interna de la organización para el escaneo ambiental a establecerse, abriendo una vía innovadora de investigación en términos de asociación de inteligencia y capacidades organizacionales, entre las que se encuentran las capacidades dinámicas. Así, con el objetivo de verificar la asociación de la Inteligencia como Capacidad Dinámica, y su contribución a la generación de ventaja competitiva sustentable, se propone un modelo con una aplicación, a través de un modelo de ecuaciones estructurales, para demostrar la relación potencial entre Inteligencia, Capacidades dinámicas y ventaja competitiva. Los resultados indican una alta correlación entre la Inteligencia y las Capacidades Dinámicas y, a través de ellas, la Ventaja Competitiva. A inteligência é um processo de monitoramento do ambiente que potencializa a capacidade de adaptação e antecipação organizacional, sendo fonte de vantagem competitiva e fator necessário para a sustentabilidade do negócio. Pesquisas indicam a necessidade de desenvolvimento de uma capacidade interna da organização para que o monitoramento do ambiente se estabeleça, abrindo uma via inovadora de investigação em termos de associação da inteligência e de capacidades organizacionais, dentre as quais as capacidades dinâmicas. Assim, com o objetivo de verificar a associação da Inteligência como uma Capacidades Dinâmica, e sua contribuição para a geração da vantagem competitiva sustentável, propõe-se um modelo com aplicação via modelagem de equações estruturais para demonstrar a potencial relação entre Inteligência, Capacidades Dinâmicas e Vantagem Competitiva. Os resultados indicam alta correlação entre Inteligência e Capacidades Dinâmicas, e destas com a Vantagem Competitiva

The Arkot Dağ Mélange Central Turkey: evidences for the geodynamic evolution of the Intra-Pontide suture zone.

The geological setting of Turkey can be described as an assemblage of continental terranes separated by ophiolite-bearing suture zones that mark the areas where the PaleoTethyan and NeoTehyan oceanic basins were destroyed. In northern Turkey, one of the most important suture zones is represented by the Intra-Pontide one consisting of an east-west trending belt of deformed and/or metamorphic units located at the boundary between the Istanbul-Zonguldak terrane to the north and the Sakarya terrane to the south. These units can be regarded as issued from the Intra-Pontide domain, whose geodynamic history is still a matter of debate. Along the Akpinar-Araç-Bayramoren geotraverse, located in central Turkey, an ophiolite-bearing mélange, known as the Arkot Dağ Mélange, is well-exposed along the Intra-Pontide suture zone. The Arkot Dağ Mélange can be described as an Upper Santonian chaotic sedimentary deposit consisting of an up to 1000-m-thick succession of slide-blocks of different sizes and lithologies enclosed in a sedimentary matrix consisting of shales, coarse-grained arenites, pebbly mudstones and pebbly sandstones. The slide-blocks, from a few meters to hectometers in size, are represented by metamorphic rocks (mainly micaschists and gneisses), by ophiolites (peridotites, gabbros, IAT and BAB basalts and cherts) and by sedimentary rocks (cherts, neritic and pelagic limestone, marly limestone and ophiolite-bearing turbidites). The youngest age among the slide- blocks has been provided by the ophiolite-bearing turbidites where a late Coniacian nannofossil assemblage has been found. The cherts have provided a wide range of ages from the Middle Triassic to Late Cretaceous, whereas the fossils found in the limestone indicate Late Jurassic to Early Cretaceous ages. The matrix of the Arkot Dağ Mélange, even if unaffected by metamorphism, shows deformations represented by multiple meters-thick cataclastic shear zones at the boundaries of the mélange slices or inside them. According to its features, the source area of the Arkot Dağ Mélange was most likely a stack of continental and oceanic thrust sheets emplaced in the Late Cretaceous onto a continental margin. The data collected from the different slide-blocks suggest that the Intra-Pontide domain was characterised by an oceanic basin that opened at the latest in the Early Jurassic. The opening of the Intra-Pontide oceanic basin was followed by the development of a subduction zone with a subsequent opening of suprasubduction oceanic basin in the Middle Jurassic – Early Cretaceous. The convergence in this suprasubduction oceanic basin started at the Early/Late Cretaceous boundary by an obduction process, whereas its final closure can be regarded as Late Paleocene

the intra pontide suture zone in the tosya kastamonu area northern turkey

ABSTRACTWe present the first detailed geological map of the tectonic units documented in the easternmost branch of the Intra-Pontide suture (IPS) zone in the Tosya-Kastamonu area (Northern Turkey). The Main Map is at 1:50,000 scale and covers an area of about 350 km2. It derived from 1:25,000 scale classic field mapping and represents a detailed overview of the complexities documented in the IPS zone, a tectonic nappe stack originating from the closure of the Intra-Pontide Oceanic basin and the subsequent collision between the Istanbul-Zonguldak terrane and the Sakarya composite terrane. The map shows the orientations of superposed foliations, fold axes and mineral lineations on the basis of geometric cross-cutting relationships documented within the five tectonic units of the IPS zone and provides information on its present-day architecture resulting from activity of the North Anatolian Fault