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The European eel, a catadromous endangered species, displays plasticity in phenotypic traits and in trophic behaviour, features that can eventually affect growth. The aim of this study was to compare variation in carbon (?13C) and nitrogen (?15N) stable isotopes in muscle tissue of the adult eel life stages (i.e. yellow and silver eel), as function of growth. Eel samples were obtained from nine sites across the Mediterranean region, that included seven coastal lagoons of different size and ecological structure, and two freshwater habitats corresponding to one river and one lake. A large variability was found in both ?13C and ?15N values, suggesting that eels fed over a broad range of potential food sources. Eels from each location showed specific range values of ?13C, in most sites irrespective of stage, reflecting lagoon- or freshwater-specific carbon sources. A positive correlation was found between individual ?15N values and annual growth rates, suggesting that eels generally seem to feed on prey of higher ?15N values among the trophic resources available in each foraging habitat. This allows individuals to grow faster and to attain earlier the pre-spawning phase (i.e. the silver stage). A better understanding of eel trophic ecology across different life stages and different habitats is one of the prerequisites for the effective management of local stocks.

Mgaloblishvili, a Vitis vinifera cultivar, exhibits unique resistance traits against Plasmopara viticola, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pinot noir (a V. vinifera susceptible cultivar), and Bianca (a resistant hybrid) leaves, inoculated and non-inoculated with the pathogen, were used to identify P. viticola effector-encoding genes and plant susceptibility/resistance genes. Multiple effector-encoding genes were identified in P. viticola transcriptome, with remarkable expression differences in relation to the inoculated grapevine cultivar. Intriguingly, five apoplastic effectors specifically associated with resistance in V. vinifera. Gene coexpression network analysis identified specific modules and metabolic changes occurring during infection in the three grapevine cultivars. Analysis of these data allowed, for the first time, the detection in V. vinifera of a putative P. viticola susceptibility gene, encoding a LOB domain-containing protein. Finally, the de novo assembly of Mgaloblishvili, Pinot noir, and Bianca transcriptomes and their comparison highlighted novel candidate genes that might be at the basis of the resistant phenotype. These results open the way to functional analysis studies and to new perspectives in molecular breeding of grapevine for resistance to P. viticola.

In recent years, the advent of NGS technology has made genome sequencing much cheaper than in the past; the high parallelization capability and the possibility to sequence more than one organism at once have opened the door to processing whole symbiotic consortia. However, this approach needs the development of specific bioinformatics tools able to analyze these data. In this work, we describe SeqDex, a tool that starts from a preliminary assembly obtained from sequencing a mixture of DNA from different organisms, to identify the contigs coming from one organism of interest. SeqDex is a fully automated machine learning–based tool exploiting partial taxonomic affiliations and compositional analysis to predict the taxonomic affiliations of contigs in an assembly. In literature, there are few methods able to deconvolve host–symbiont datasets, and most of them heavily rely on user curation and are therefore time consuming. The problem has strong similarities with metagenomic studies, where mixed samples are sequenced and the bioinformatics challenge is trying to separate contigs on the basis of their source organism; however, in symbiotic systems, additional information can be exploited to improve the output. To assess the ability of SeqDex to deconvolve host–symbiont datasets, we compared it to state-of-the-art methods for metagenomic binning and for host–symbiont deconvolution on three study cases. The results point out the good performances of the presented tool that, in addition to the ease of use and customization potential, make SeqDex a useful tool for rapid identification of endosymbiont sequences.

Grotta Romanelli, located on the Adriatic coast of southern Apulia (Italy), is considered a key site for the Mediterranean Pleistocene for its archaeological and palaeontological contents. The site, discovered in 1874, was re-evaluated only in 1900, when P. E. Stasi realised that it contained the first evidence of the Palaeolithic in Italy. Starting in 1914, G.A. Blanc led a pioneering excavation campaign, for the first-time using scientific methods applied to systematic paleontological and stratigraphical studies. Blanc proposed a stratigraphic framework for the cave. Different dating methods (C14 and U/Th) were used to temporally constrain the deposits. The extensive studies of the cave and its contents were mostly published in journals with limited distribution and access, until the end of the 1970s, when the site became forgotten. In 2015, with the permission of the authorities, a new excavation campaign began, led by a team from Sapienza University of Rome in collaboration with IGAG CNR and other research institutions. The research team had to deal with the consequences of more than 40 years of inactivity in the field and the combined effect of erosion and legal, as well as illegal, excavations. In this paper, we provide a database of all the information published during the first 70 years of excavations and highlight the outstanding problems and contradictions between the chronological and geomorphological evidence, the features of the faunal assemblages and the limestone artefacts., Rivista Italiana di Paleontologia e Stratigrafia (Research In Paleontology and Stratigraphy), V. 124, N. 2 (2018)

Travertine sequences from petrified channels used in antiquity as water supply canals in the city of Hierapolis (Denizli, Turkey) for irrigation and domestic use were sampled and analyzed for stable isotopes composition. Data records from two channels show composite quasi-periodic variations. Radium-226 activity was measured to calculate temporal constrains; one of the channels, 182cm thick, deposited in 790±71 years, whereas the other, 644cm thick, in 995±71 years. Isotope data, studied through spectral and cross-spectral analysis, indicate that the different oscillation frequencies may be related to surface temperature and rainfall pulses.

Alabastro listato or fiorito of Hierapolis in Phrygia was a prestigious coloured marble widely used in Roman architecture and decoration. This stone is generally identified in artefacts on autoptic examination, but it may sometimes be confused with alabasters of different provenances. This study describes a simple, but effective, scientific method to contribute to the determination of Hierapolis alabaster. Due to its unique genetic context, it is characterized by a distinctive carbon isotope signature. A comparison between the stable carbon isotope data from this paper and from the literature confirms the uniqueness of the isotopic character of Hierapolis alabaster. Carbon isotopes can ensure a reliably provenance attribution of the alabaster artefacts along with visual recognition by an expert eye.

Peptidoglycan is the predominant stress-bearing structure in the cell envelope of most bacteria, and also a potent stimulator of the eukaryotic immune system. Obligate intracellular bacteria replicate exclusively within the interior of living cells, an osmotically protected niche. Under these conditions peptidoglycan is not necessarily needed to maintain the integrity of the bacterial cell. Moreover, the presence of peptidoglycan puts bacteria at risk of detection and destruction by host peptidoglycan recognition factors and downstream effectors. This has resulted in a selective pressure and opportunity to reduce the levels of peptidoglycan. In this review we have analysed the occurrence of genes involved in peptidoglycan metabolism across the major obligate intracellular bacterial species. From this comparative analysis, we have identified a group of predicted "peptidoglycan-intermediate" organisms that includes the Chlamydiae, Orientia tsutsugamushi, Wolbachia and Anaplasma marginale. This grouping is likely to reflect biological differences in their infection cycle compared with peptidoglycan-negative obligate intracellular bacteria such as Ehrlichia and Anaplasma phagocytophilum, as well as obligate intracellular bacteria with classical peptidoglycan such as Coxiella, Buchnera and members of the Rickettsia genus. The signature gene set of the peptidoglycan-intermediate group reveals insights into minimal enzymatic requirements for building a peptidoglycan-like sacculus and/or division septum. This article is protected by copyright. All rights reserved.

L'area di Cottanello si inserisce nel settore occidentale dei Monti Sabini, una catena montuosa allungata in direzione nord-sud e caratterizzata da un morfologia aspra con cime aguzze, pareti ripide e profonde incisioni torrentizie. L'elevazione è modesta, con i settori di cresta che raggiungono i m 1200 di quota. La dorsale montuosa è delimitata a nord e nord-ovest dalla piana di Terni, a sud e sud-ovest dalla valle del Tevere ed a est dalla piana di Rieti.

The Ipanema alkaline-carbonatitic complex is part of the Meso-Cenozoic alkaline magmatism located within the southeastern part of the Brazilian Platform. Drill-core and field sampling have indicated the occurrence of glimmerites, with subordinate shonkinites (mela-syenites), clinopyroxene-bearing glimmerites, diorites and syenites. The glimmerites are cross-cut by lamprophyric dykes and calciocarbonatites. Fenitization has deeply affected the country rocks, originating dioritic and syenitic rocks. The Ipanema rocks show a distinct potassic affinity. The initial Sr-Nd- isotopic composition of the Ipanema rocks ( 87Sr/ 86Sr = 0.70661-0.70754 and 143Nd/ 144Nd = 0.51169-0.51181) is similar to that of tholeiitic and potassium-rich-alkaline rocks of the Eastern Paraguay. Stable isotope data for the Ipanema calciocarbonatite suggest interaction with fluids at temperatures typical of hydrothermal stages, as hypothesized for other carbonatite complexes from southeastern Brazil. The chemical differences between the lamprophyre, glimmerites, carbonatites, apatitites and magnetitites, and the absence of marked REE enrichment in the evolved lithologies, all indicate that fractional crystallization and accumulus of liquidus phases in a magma reservoir, likely coupled with liquid immiscibility processes, may have played an important role in the genesis of the Ipanema rocks.

This paper reports an infrared spectroscopic study of a set of sodalite-group minerals. The specimens have been identified using a combination of X-ray diffraction and microchemical analysis. As expected, the Si/Al ratio is ~1; the extra framework cation content is characterized by a well-defined Na > (Ca+K) substitution. The lattice parameters of the studied samples range from sodalite (sample LM11) with a = 8.889(2) Å , to haüyne (sample HR3S) with a = 9.1265(2) Å . The specimens, having the SO42- group as a dominant anion, show a clear correlation between the a cell edge and the K content. Singlecrystal FTIR spectroscopy shows that haüyne and nosean typically contain enclathrated CO2 molecules, inadditionto H2O and minor carbonate, while sodalite is virtually CO2-free. Detailed microspectrometric mappings show a non-homogeneous distribution of volatile constituents across the crystals, which may be related to the presence of fractures in the crystals. Because of such zoning, a relatively wide variation is observed when calibrating extinction coefficients on the basis of a bulk analytical method such as CHN elemental analysis.

The sodalite-group include: sodalite s.s. Na8[Al6Si6O24]Cl2, noseane Na8[Al6Si6O24]SO4•H2O, haüyne, Na6Ca2[Al6Si6O24](SO4)2, and lazurite Na6Ca2[[Al6Si6O24]S2. These minerals occur almost exclusively in alkali-rich, silica-deficient igneous rocks, and occasionally in metasomatized limestones. The structure of the sodalite-group minerals is cubic P 3n and is characterized by an ordered framework of AlO4 and SiO4 tetrahedra, with an Al:Si ratio = 1:1. These tetrahedra are linked such as to form six-membered rings stacked following an ABCABC... sequence, and are arranged such as to form continuous channels parallel to [111] that offer diffusion paths for intra-framework ions (Barrer and Vaughan, 1971). The overall linkage between the rings gives rise to cubo-octahedral “sodalite” cages, also known as $IMM_COM_0005 cages (Pauling, 1930); these may host a large variety of cations (e.g. Na+, Ca2+, K+), anions (e.g. OH-, Cl-, SO42-, S2-) and neutral molecules (H2O), but also noble gases (e.g. Xe, Ar). The cage has a diameter of  4 Å hence sodalite-group minerals can be considered as microporous materials (Rouquerol et al. 1994). We relate here the recent developments of our micro-FTIR studies on a series of sodalite-group minerals from different localities and geological occurrences. Spectra were collected on doubly-polished slabs using a NicPlan microscope with a nitrogen-cooled MCT detector attached to a Nicolet Magna 760 spectrometer with a KBr beamsplitter and a Globar as IR source. Microspectrometric mappings were acquired with a Hyperion 3000 Bruker microscope equipped with a computer-controlled motorized stage. HT spectra in situ were collected using a Linkam FTIR600 heating stage (single-crystals); annealing experiment were done using an HT device. Single-crystal FTIR spectra show that the different species in the group, and different samples of the same species, have different degrees of hydration; H is present in various forms, including OH, H2O, H3O+ and H3O2- groups. Carbon occurs as CO2, CO32- and possibly as HCO3-. Carbonate and hydrogencarbonate arrangements are detected in several haüyne and sodalites s.s. specimens, while CO2 is observed, in decreasing amount, in noesane, lazurites and haüynes; CO2 has been so far observed only in one sample of sodalites s.s. HT-FTIR measurements show, in all samples, a continuous and linear release of H2O up to the structure collapse at ~ 900° C. On heating, the CO2 absorption increasingly broadens, as already observed for beryl and codierite (Aines and Rossman 1984), and recovers its initial shape for decreasing T. However, release of CO2 from the sample occurs only for T > 900°C. Microspectrometry mappings shows typically a non-homogeneous distributions of hydrogen and carbon across the samples. Using the molar absorption coefficients available in the literature for glasses with similar compositions, H contents in the range 400 to 800 ppm and CO2 contents in the range 200 to 800 ppm are calculated. References Aines R.D., Rossman G.R. (1984) Am. Mineral., 69, 319-327. Barrer, R.M., Vaughan D.E.W. (1971) J. Phys. Chem. Solids 32, 731-743. Pauling, L. (1930) Z. Kristallogr., 74, 213-225. Rouquerolt T., Avnir D., Fairbridge C.W., Everett D.H., Haynes J.H., Pernicone N., Ramsay J.D.F., Sing K.S.W., Unger K.K. (1994) Pure and Appl. Chem., 66, 1739-1758.

Structural investigations, integrated with X-ray diffraction, fluid inclusion microthermometry and oxygen-stable isotope analyses are used to reconstruct the deformation history and the palaeo-fluid circulation during formation of the low-grade, turbidite-dominated Early Palaeozoic Robertson Bay accretionary complex of north Victoria Land (Antarctica). Evidence for progressive deformation is elucidated by analysing the textural fabric of chronologically distinct, thrust-related quartz vein generations, incrementally developed during progressive shortening and thickening of the Robertson Bay accretionary complex. Our data attest that orogenic deformation was mainly controlled by dissolution–precipitation creep, modulated by stress- and strain-rate-dependent fluid pressure cycling, associated with local and regional permeability variations induced by the distribution and evolution of the fracture network during regional thrusting. Fracture-related fluid pathways constituted efficient conduits for episodic fluid flow. The dominant migrating fluid was pre-to-syn-folding and associated with the migration of warm (160–200 C) nitrogen- and carbonic (CO2 and CH4)-bearing fluids. Both fluid advection and diffusive mass transfer are recognized as operative mechanisms for fluid–rock interaction and vein formation during continuous shortening. In particular, fluid–rock interaction was the consequence of dissolution–precipitation creep assisted by tectonically driven cooling fluids moving through the rock section as a result of seismic pumping. The most likely source of the migrating fluids would be the frontal part of the growing accretionary complex, where fluids from the deep levels in the hinterland are driven trough channelization operated by the thrust-related fracture (fault) systems.

This paper describes the fluids circulating in the extensive thrust-related quartz-bearing vein systems developed within the low-grade turbidite-dominated Early Paleozoic Robertson Bay Terrane of north Victoria Land, Antarctica. It provides a well-preserved example of fossil accretionary complex, developed during the Paleozoic subdution-related accretionary process at the paleo-Pacifica margin of Gondwana. Fluid inclusions are analysed in quartz crystals hosted within distinct generations of veins, which are interpreted to record the incremental deformation history during shortening and accretionary complex formation. Our data provides clues to the tectono-thermal history associated with orogenic complex formation, also providing inferences on the fluid storage and recycling through time.

Sinorhizobium meliloti is a soil bacterium that invades the root nodules it induces on Medicago sativa, whereupon it undergoes an alteration of its cell cycle and differentiates into nitrogen-fixing, elongated and polyploid bacteroid with higher membrane permeability. In Caulobacter crescentus, a related alphaproteobacterium, the principal cell cycle regulator, CtrA, is inhibited by the phosphorylated response regulator DivK. The phosphorylation of DivK depends on the histidine kinase DivJ, while PleC is the principal phosphatase for DivK. Despite the importance of the DivJ in C. crescentus, the mechanistic role of this kinase has never been elucidated in other Alphaproteobacteria. We show here that the histidine kinases DivJ together with CbrA and PleC participate in a complex phosphorylation system of the essential response regulator DivK in S. meliloti. In particular, DivJ and CbrA are involved in DivK phosphorylation and in turn CtrA inactivation, thereby controlling correct cell cycle progression and the integrity of the cell envelope. In contrast, the essential PleC presumably acts as a phosphatase of DivK. Interestingly, we found that a DivJ mutant is able to elicit nodules and enter plant cells, but fails to establish an effective symbiosis suggesting that proper envelope and/or low CtrA levels are required for symbiosis., National Institutes of Health (U.S.) (Grant GM31010)

Background Cansiliella servadeii (Coleoptera) is an endemic troglobite living in deep carbonate caves in North-Eastern Italy. The beetle constantly moves and browses in its preferred habitat (consisting in flowing water and moonmilk, a soft speleothem colonized by microorganisms) self-preens to convey material from elytra, legs, and antennae towards the mouth. We investigated its inner and outer microbiota using microscopy and DNA-based approaches. Results Abundant microbial cell masses were observed on the external appendages. Cansiliella’s midgut is fully colonized by live microbes and culture-independent analyses yielded nearly 30 different 16S phylotypes that have no overlap with the community composition of the moonmilk. Many of the lineages, dominated by Gram positive groups, share very low similarity to database sequences. However for most cases, notwithstanding their very limited relatedness with existing records, phylotypes could be assigned to bacterial clades that had been retrieved from insect or other animals’ digestive traits. Conclusions Results suggest a history of remote separation from a common ancestor that harboured a set of gut-specific bacteria whose functions are supposedly critical for host physiology. The phylogenetic and coevolutionary implications of the parallel occurrences of these prokaryotic guilds appear to apply throughout a broad spectrum of animal diversity. Their persistence and conservation underlies a possibly critical role of precise bacterial assemblages in animal-bacteria interactions.