Identifying Web Tables - Supporting a Neglected Type of Content on the Web

The abundance of the data in the Internet facilitates the improvement of extraction and processing tools. The trend in the open data publishing encourages the adoption of structured formats like CSV and RDF. However, there is still a plethora of unstructured data on the Web which we assume contain semantics. For this reason, we propose an approach to derive semantics from web tables which are still the most popular publishing tool on the Web. The paper also discusses methods and services of unstructured data extraction and processing as well as machine learning techniques to enhance such a workflow. The eventual result is a framework to process, publish and visualize linked open data. The software enables tables extraction from various open data sources in the HTML format and an automatic export to the RDF format making the data linked. The paper also gives the evaluation of machine learning techniques in conjunction with string similarity functions to be applied in a tables recognition task.Comment: 9 pages, 4 figure

A nonmitochondrial hydrogen production in Naegleria gruberi

Naegleria gruberi is a free-living heterotrophic aerobic amoeba well known for its ability to transform from an amoeba to a flagellate form. The genome of N. gruberi has been recently published, and in silico predictions demonstrated that Naegleria has the capacity for both aerobic respiration and anaerobic biochemistry to produce molecular hydrogen in its mitochondria. This finding was considered to have fundamental implications on the evolution of mitochondrial metabolism and of the last eukaryotic common ancestor. However, no actual experimental data have been shown to support this hypothesis. For this reason, we have decided to investigate the anaerobic metabolism of the mitochondrion of N. gruberi. Using in vivo biochemical assays, we have demonstrated that N. gruberi has indeed a functional [FeFe]-hydrogenase, an enzyme that is attributed to anaerobic organisms. Surprisingly, in contrast to the published predictions, we have demonstrated that hydrogenase is localized exclusively in the cytosol, while no hydrogenase activity was associated with mitochondria of the organism. In addition, cytosolic localization displayed for HydE, a marker component of hydrogenase maturases. Naegleria gruberi, an obligate aerobic organism and one of the earliest eukaryotes, is producing hydrogen, a function that raises questions on the purpose of this pathway for the lifestyle of the organism and potentially on the evolution of eukaryotes

Phylogenetic Diversity of NTT Nucleotide Transport Proteins in Free-Living and Parasitic Bacteria and Eukaryotes

Plasma membrane-located nucleotide transport proteins (NTTs) underpin the lifestyle of important obligate intracellular bacterial and eukaryotic pathogens by importing energy and nucleotides from infected host cells that the pathogens can no longer make for themselves. As such their presence is often seen as a hallmark of an intracellular lifestyle associated with reductive genome evolution and loss of primary biosynthetic pathways. Here, we investigate the phylogenetic distribution of NTT sequences across the domains of cellular life. Our analysis reveals an unexpectedly broad distribution of NTT genes in both host-associated and free-living prokaryotes and eukaryotes. We also identify cases of within-bacteria and bacteria-to-eukaryote horizontal NTT transfer, including into the base of the oomycetes, a major clade of parasitic eukaryotes. In addition to identifying sequences that retain the canonical NTT structure, we detected NTT gene fusions with HEAT-repeat and cyclic nucleotide binding domains in Cyanobacteria, pathogenic Chlamydiae and Oomycetes. Our results suggest that NTTs are versatile functional modules with a much wider distribution and a broader range of potential roles than has previously been appreciated

Morphology and phylogeny of a new species of anaerobic ciliate, Trimyema finlayi n. sp., with endosymbiotic methanogens

Many anaerobic ciliated protozoa contain organelles of mitochondrial ancestry called hydrogenosomes. These organelles generate molecular hydrogen that is consumed by methanogenic Archaea, living in endosymbiosis within many of these ciliates. Here we describe a new species of anaerobic ciliate, Trimyema finlayi n. sp., by using silver impregnation and microscopy to conduct a detailed morphometric analysis. Comparisons with previously published morphological data for this species, as well as the closely related species, Trimyema compressum, demonstrated that despite them being similar, both the mean cell size and the mean number of somatic kineties are lower for T. finlayi than for T. compressum, which suggests that they are distinct species. This was also supported by analysis of the 18S rRNA genes from these ciliates, the sequences of which are 97.5% identical, (6 substitutions, 1479 compared bases), and in phylogenetic analyses these sequences grouped with other 18S rRNA genes sequenced from previous isolates of the same respective species. Together these data provide strong evidence that T. finlayi is a novel species of Trimyema, within the class Plagiopylea. Various microscopic techniques demonstrated that Trimyema finlayi n. sp. contains polymorphic endosymbiotic methanogens, and analysis of the endosymbionts 16S rRNA gene showed that they belong to the genus Methanocorpusculum, which was confirmed using fluorescence in situ hybridisation with specific probes. Despite the degree of similarity and close relationship between these ciliates, T. compressum contains endosymbiotic methanogens from a different genus, Methanobrevibacter. In phylogenetic analyses of 16S rRNA genes, the Methanocorpusculum endosymbiont of T. finlayi n. sp. grouped with sequences from Methanomicrobia, including the endosymbiont of an earlier isolate of the same species, ‘Trimyema sp.’, which was sampled approximately 22 years earlier, at a distant (~400 km) geographical location. Identification of the same endosymbiont species in the two separate isolates of T. finlayi n. sp. provides evidence for spatial and temporal stability of the Methanocorpusculum-T. finlayi n. sp. endosymbiosis. T. finlayi n. sp. and T. compressum provide an example of two closely related anaerobic ciliates that have endosymbionts from different methanogen genera, suggesting that the endosymbionts have not co-speciated with their hosts

Venting of a separate CO2-rich gas phase from submarine arc volcanoes: Examples from the Mariana and Tonga-Kermadec arcs

Submersible dives on 22 active submarine volcanoes on the Mariana and Tonga-Kermadec arcs have discovered systems on six of these volcanoes that, in addition to discharging hot vent fluid, are also venting a separate CO2-rich phase either in the form of gas bubbles or liquid CO2 droplets. One of the most impressive is the Champagne vent site on NW Eifuku in the northern Mariana Arc, which is discharging cold droplets of liquid CO2 at an estimated rate of 23 mol CO2/s, about 0.1% of the global mid-ocean ridge (MOR) carbon flux. Three other Mariana Arc submarine volcanoes (NW Rota-1, Nikko, and Daikoku), and two volcanoes on the Tonga-Kermadec Arc (Giggenbach and Volcano-1) also have vent fields discharging CO2-rich gas bubbles. The vent fluids at these volcanoes have very high CO2 concentrations and elevated C/3He and δ 13C (CO2) ratios compared to MOR systems, indicating a contribution to the carbon flux from subducted marine carbonates and organic material. Analysis of the CO2 concentrations shows that most of the fluids are undersaturated with CO2. This deviation from equilibrium would not be expected for pressure release degassing of an ascending fluid saturated with CO2. Mechanisms to produce a separate CO2-rich gas phase at the seafloor require direct injection of magmatic CO2-rich gas. The ascending CO2-rich gas could then partially dissolve into seawater circulating within the volcano edifice without reaching equilibrium. Alternatively, an ascending high-temperature, CO2-rich aqueous fluid could boil to produce a CO2-rich gas phase and a CO2-depleted liquid. These findings indicate that carbon fluxes from submarine arcs may be higher than previously estimated, and that experiments to estimate carbon fluxes at submarine arc volcanoes are merited. Hydrothermal sites such as these with a separate gas phase are valuable natural laboratories for studying the effects of high CO2 concentrations on marine ecosystems

Plastid establishment did not require a chlamydial partner

Primary plastids descend from the cyanobacterial endosymbiont of an ancient eukaryotic host, but the initial selective drivers that stabilized the association between these two cells are still unclear. One hypothesis that has achieved recent prominence suggests that the first role of the cyanobiont was in energy provision for a host cell whose reserves were being depleted by an intracellular chlamydial pathogen. A pivotal claim is that it was chlamydial proteins themselves that converted otherwise unusable cyanobacterial metabolites into host energy stores. We test this hypothesis by investigating the origins of the key enzymes using sophisticated phylogenetics. Here we show a mosaic origin for the relevant pathway combining genes with host, cyanobacterial or bacterial ancestry, but we detect no strong case for Chlamydiae to host transfer under the best-fitting models. Our conclusion is that there is no compelling evidence from gene trees that Chlamydiae played any role in establishing the primary plastid endosymbiosis

Smart biomimetic construction materials for next generation infrastructure

The resilience of building and civil engineering structures is typically associated with the design of individual elements such that they have sufficient capacity or potential to react in an appropriate manner to adverse events. Traditionally this has been achieved by using ‘robust’ design procedures that focus on defining safety factors for individual adverse events and providing redundancy. As such, construction materials are designed to meet a prescribed specification; material degradation is viewed as inevitable and mitigation necessitates expensive maintenance regimes; ~£40 billion/year is spent in the UK on repair and maintenance of existing, mainly concrete, structures. More recently, based on a better understanding and knowledge of microbiological systems, materials that have the ability to adapt and respond to their environment have been developed. This fundamental change has the potential to facilitate the creation of a wide range of ‘smart’ materials and intelligent structures, including both autogenous and autonomic self‐healing materials and adaptable, self‐sensing and self‐repairing structures, which can transform our infrastructure by embedding resilience in the materials and components of these structures so that rather than being defined by individual events, they can evolve over their lifespan. We therefore advocate that next generation infrastructure will include next generation infrastructure materials based on smart biomimetic construction materials. This paper presents details of the national consortium that is leading international efforts in the development of those next generation infrastructure materials. It presents details of the work done to date, over the past three years, as part of the EPSRC funded project Materials for Life and the plans for work to be done over the next five years as part of a follow-on Programme grant: Resilient Materials for Life

Waning magmatic activity along the Southern Explorer Ridge revealed through fault restoration of rift topography

International audienceWe combine high-resolution bathymetry acquired using the Autonomous Underwater Vehicle ABE with digital seafloor imagery collected using the remotely operated vehicle ROPOS across the axial valley of the Southern Explorer Ridge (SER) to infer the recent volcanic and tectonic processes. The SER is an intermediate spreading ridge located in the northeast Pacific. It hosts the Magic Mountain hydrothermal vent. We reconstruct the unfaulted seafloor terrain at SER based on calculations of the vertical displacement field and fault parameters. The vertical changes between the initial and the restored topographies reflect the integrated effects of volcanism and tectonism on relief-forming processes over the last 11,000-14,000 years. The restored topography indicates that the axial morphology evolved from a smooth constructional dome >500 m in diameter, to a fault-bounded graben, ~500 m wide and 30-70 m deep. This evolution has been accompanied by changes in eruptive rate, with deposition of voluminous lobate and sheet flows when the SER had a domed morphology, and limited-extent low-effusion rate pillow eruptions during graben development. Most of the faults shaping the present axial valley postdate the construction of the dome. Our study supports a model of cyclic volcanism at the SER with periods of effusive eruptions flooding the axial rift, centered on the broad plateau at the summit of the ridge, followed by a decrease in eruptive activity and a subsequent dominance of tectonic processes, with minor low-effusion rate eruptions confined to the axial graben. The asymmetric shape of the axial graben supports an increasing role of extensional processes, with a component of simple shear in the spreading processes