Assessing the potential of nematode metabarcoding for benthic monitoring of offshore oil platforms.

Environmental DNA metabarcoding is gaining momentum as a time and cost-effective tool for biomonitoring and environmental impact assessment. Yet, its use as a replacement for the conventional marine benthic monitoring based on morphological analysis of macrofauna is still challenging. Here we propose to study the meiofauna, which is much better represented in sediment DNA samples. We focus on nematodes, which are the most numerous and diverse group of meiofauna. Our aim is to assess the potential of nematode metabarcoding to monitor impacts associated with offshore oil platform activities. To achieve this goal, we used nematode-optimized marker (18S V1V2-Nema) and universal eukaryotic marker (18S V9) region to analyse 252 sediment DNA samples collected near three offshore oil platforms in the North Sea. For both markers, we analysed changes in alpha and beta diversity in relation to distance from the platforms and environmental variables. We also defined three impact classes based on selected environmental variables that are associated with oil extraction activities and used random forest classifiers to compare the predictive performance of both datasets. Our results show that alpha- and beta-diversity of nematodes varies with the increasing distance from the platforms. The variables directly related to platform activity, such as Ba and THC, strongly influence the nematode community. The nematode metabarcoding data provide more robust predictive models than eukaryotic data. Furthermore, the nematode community appears more stable in time and space, as illustrated by the overlap of nematode datasets obtained from the same platform three years apart. A significative negative correlation between distance and Shannon diversity also advocates for higher performance of the V1V2-Nema over the V9. Overall, these results suggest that the sensitivity of nematodes is higher compared to the eukaryotic community. Hence, nematode metabarcoding has the potential to become an effective tool for benthic monitoring in marine environment.

Multifrequency nonlinear model of magnetic material with artificial intelligence optimization.

Magnetic rings are extensively used in power products where they often operate in high frequency and high current conditions, such as for mitigation of excessive voltages in high-power switchgear equipment. We provide a general model of a magnetic ring that reproduces both frequency and current dependencies with the use of artificial intelligence (AI) optimization methods. The model has a form of a lumped element equivalent circuit that is suitable for power system transient studies. A previously published conventional (non-AI) model, which we take as a starting point, gives a good fit of parameters but uneven characteristics as a function of current, which pose numerical instabilities in transient simulations. We first enforce the Langevin function relationship to obtain smooth characteristics of parameters, which reduces the number of parameters and ensures their even characteristics, however, compromises fit quality. We then use AI metaheuristic optimization methods that give a perfect fit for the model in the whole range of frequency up to 100 MHz and current up to saturation, with smooth characteristics of its parameters. Additionally, for such fitted parameters, we show that it is feasible to find a frequency dependence for the magnetic saturation parameter of the Jiles-Atherton (JA) model, thus enabling frequency-dependent JA.

Temperature induced giant shift of phonon energy in epitaxial boron nitride layers.

The recent progress in the growth of large-area boron nitride epilayers opens up new possibilities for future applications. However, it remains largely unclear how weakly attached two-dimensional BN layers interact with their substrate and how their properties are influenced by defects. In this work, we investigate hBN layers grown by metal organic vapor phase epitaxy using Fourier-transform infrared spectroscopy in the temperature range of 160-540 K. Our measurements reveal strong differences in the character of layer-substrate interaction for as-grown and delaminated epitaxial layers. A much weaker interaction of as-grown layers is explained by wrinkles formation that reduces strain at the layer-substrate interface, which for layers transferred to other substrates occurs only in a limited temperature range. The most striking result is the observation of a giant increase in theE1uphonon energy of up to ∼6 cm-1in a narrow temperature range. We show that the amplitude and temperature range of the anomaly is strongly modified by UV light illumination. The observed giant effect is explained in terms of strain generation resulting from charge redistribution between shallow traps and different defects, which can be interpreted as a result of strong electron-phonon coupling in hBN. The observed narrow temperature range of the anomaly indicates that the effect may be further enhanced for example by electrostrictive effects, expected for sp2boron nitride.

Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods.

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.

Assessing the ecological quality status of the highly polluted Bagnoli area (Tyrrhenian Sea, Italy) using foraminiferal eDNA metabarcoding.

Morphology-based benthic foraminifera indices are increasingly used worldwide for biomonitoring the ecological quality of marine sediments. The recent development of foraminiferal eDNA metabarcoding offers a reliable, time-, and cost-effective alternative to morphology-based foraminiferal biomonitoring. However, the practical applications of these new tools are still highly limited. In the present study, we evaluate the response of benthic foraminifera and define the ecological quality status (EcoQS) in the Bagnoli area (Tyrrhenian Sea, Italy) based on a traditional morphology-based approach and eDNA metabarcoding. The geochemical data show that several sites in front of the former industrial plant contain higher concentrations of potentially toxic elements than the effect range median and are characterized by the highest total organic carbon (TOC) content, whereas the distantly located sites can be considered relatively low- to unpolluted. Significant differences (i.e., diversity and assemblage composition) in both morphological and molecular datasets were found between the relatively low- to unpolluted and the most polluted areas. Similarly, the selected ecological indices of both morphological and molecular datasets strikingly and congruently resulted in a clear separation following the environmental stress gradient. The molecular indices (i.e., g-exp(H'bc), g-Foram AMBI, and g-Foram AMBI-MOTUs) reliably identified poor-to-bad EcoQS in the polluted area in front of the former industrial plant. On the other hand, the Foram-AMBI based on morphology well identified an overall trend but seemed to overestimate the EcoQS if the traditional class boundaries were considered. The congruent and complementary trends between morphological and metabarcoding data observed in the case of the Bagnoli site further support the application of foraminiferal metabarcoding in routine biomonitoring to assess the environmental impacts of heavily polluted marine areas.

Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring.

Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.

Towards apparent convergence in asymptotically safe quantum gravity.

The asymptotic safety scenario in gravity is accessed within the systematic vertex expansion scheme for functional renormalisation group flows put forward in Christiansen et al. (Phys Lett B 728:114, 2014), Christiansen et al. (Phy Rev D 93:044036, 2016), and implemented in Christiansen et al. (Phys Rev D 92:121501, 2015) for propagators and three-point functions. In the present work this expansion scheme is extended to the dynamical graviton four-point function. For the first time, this provides us with a closed flow equation for the graviton propagator: all vertices and propagators involved are computed from their own flows. In terms of a covariant operator expansion the current approximation gives access to Λ , R, R 2 as well as R µ ν 2 and higher derivative operators. We find a UV fixed point with three attractive and two repulsive directions, thus confirming previous studies on the relevance of the first three operators. In the infrared we find trajectories that correspond to classical general relativity and further show non-classical behaviour in some fluctuation couplings. We also find signatures for the apparent convergence of the systematic vertex expansion. This opens a promising path towards establishing asymptotically safe gravity in terms of apparent convergence.

Protist metabarcoding and environmental biomonitoring: Time for change.

High-throughput amplicon sequencing of environmental DNA and/or RNA proved to be a powerful tool to describe protist diversity. This new approach called also the metabarcoding has totally transformed our view of protist diversity, revealing a large number of novel lineages and expanding the range of protist phylogenetic diversity at almost every taxonomic level. However, until now the objectives of the vast majority of metabarcoding studies were purely academic. Practical applications of protist metabarcoding are surprisingly scarce, despite the fact that several groups of protists are commonly used as bioindicators of environmental impacts in freshwater or marine ecosystems. Here, we are reviewing studies that examine the ecological applications of metabarcoding for two groups of well-known protist bioindicators: diatoms and foraminifera. The results of these studies show that despite some biological and technical biases, molecular data quite faithfully reflect the morphology-based biotic indices and provide a similar assessment of ecosystem status. In view of these results, protist metabarcoding appears as a rapid and accurate tool for the evaluation of the quality of aquatic ecosystems. Hence, we plead for integration of protist metabarcoding in future biomonitoring projects as a complement of traditional methods and a source of new biosensors for environmental impact assessment.

Selective zircon accumulation in a new benthic foraminifer, Psammophaga zirconia, sp. nov.

Benthic foraminifera are single-celled eukaryotes that make a protective organic, agglutinated or calcareous test. Some agglutinated, single-chambered taxa, including Psammophaga Arnold, 1982, retain mineral particles in their cytoplasm, but the selective mechanism of accumulation is not clear. Here, we report the ability of a foraminiferal species to select and accumulate zircons and other heavy minerals in their cytoplasm. In particular, the use of Scanning Electron Microscope coupled with an Energy Dispersive X-ray microanalysis system (SEM-EDS) enabled a representative overview of the mineral diversity and showed that the analysed Psammophaga zirconia sp. nov. individuals contained dominantly crystals of zircon (51%), titanium oxides (27%), and ilmenite (11%) along with minor magnetite and other minerals. The studied specimens occur in the shallow central Adriatic Sea where the sediment has a content of zircon below 1% and of other heavy minerals below 4%. For that reason we hypothesize that: (i) P. zirconia may be able to chemically select minerals, specifically zircon and rutile; (ii) the chemical mechanism allowing the selection is based on electrostatic interaction, and it could work also for agglutinated foraminifera (whether for ingestion, like Xenophyophores, or incorporation in the test as in many other described taxa). In particular, this aptitude for high preferential uptake and differential ingestion or retention of zircon is reported here for the first time, together with the selection of other heavy minerals already described in members of the genus Psammophaga. They are generally counted among early foraminifera, constructing a morphologically simple test with a single chamber. Our molecular phylogenetic study confirms that P. zirconia is a new species, genetically distinctive from other Psammophaga, and occurs in the Adriatic as well as in the Black Sea.

Chiral fermions in asymptotically safe quantum gravity.

We study the consistency of dynamical fermionic matter with the asymptotic safety scenario of quantum gravity using the functional renormalisation group. Since this scenario suggests strongly coupled quantum gravity in the UV, one expects gravity-induced fermion self-interactions at energies of the Planck scale. These could lead to chiral symmetry breaking at very high energies and thus to large fermion masses in the IR. The present analysis which is based on the previous works (Christiansen et al., Phys Rev D 92:121501, 2015; Meibohm et al., Phys Rev D 93:084035, 2016), concludes that gravity-induced chiral symmetry breaking at the Planck scale is avoided for a general class of NJL-type models. We find strong evidence that this feature is independent of the number of fermion fields. This finding suggests that the phase diagram for these models is topologically stable under the influence of gravitational interactions.

Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding.

Assessing the environmental impact of salmon farms on benthic systems is traditionally undertaken using biotic indices derived from microscopic analyses of macrobenthic infaunal (MI) communities. In this study, we tested the applicability of using foraminiferal-specific high-throughput sequencing (HTS) metabarcoding for monitoring these habitats. Sediment samples and physico-chemical data were collected along an enrichment gradient radiating out from three Chinook salmon (Oncorhynchus tshawytscha) farms in New Zealand. HTS of environmental DNA and RNA (eDNA/eRNA) resulted in 1,875,300 sequences that clustered into 349 Operational Taxonomic Units. Strong correlations were observed among various biotic indices calculated from MI data and normalized fourth-root transformed HTS data. Correlations were stronger using eRNA compared to eDNA data. Quantile regression spline analyses identified 12 key foraminiferal taxa that have potential to be used as bioindicator species. This study demonstrates the huge potential for using this method for biomonitoring of fish-farming and other marine industrial activities.

Next-generation environmental diversity surveys of foraminifera: preparing the future.

Foraminifera are commonly defined as marine testate protists, and their diversity is mainly assessed on the basis of the morphology of their agglutinated or mineralized tests. Diversity surveys based on environmental DNA (eDNA) have dramatically changed this view by revealing an unexpected diversity of naked and organic-walled lineages as well as detecting foraminiferal lineages in soil and freshwater environments. Moreover, single-cell analyses have allowed discrimination among genetically distinctive types within almost every described morphospecies. In view of these studies, the foraminiferal diversity appeared to be largely underestimated, but its accurate estimation was impeded by the low speed and coverage of a cloning-based eDNA approach. With the advent of high-throughput sequencing (HTS) technologies, these limitations disappeared in favor of exhaustive descriptions of foraminiferal diversity in numerous samples. Yet, the biases and errors identified in early HTS studies raised some questions about the accuracy of HTS data and their biological interpretation. Among the most controversial issues affecting the reliability of HTS diversity estimates are (1) the impact of technical and biological biases, (2) the sensitivity and specificity of taxonomic sequence assignment, (3) the ability to distinguish rare species, and (4) the quantitative interpretation of HTS data. Here, we document the lessons learned from previous HTS surveys and present the current advances and applications focusing on foraminiferal eDNA. We discuss the problems associated with HTS approaches and predict the future trends and avenues that hold promises for surveying foraminiferal diversity accurately and efficiently.

Electron spin separation without magnetic field.

A nanodevice capable of separating spins of two electrons confined in a quantum dot formed in a gated semiconductor nanowire is proposed. Two electrons confined initially in a single quantum dot in the singlet state are transformed into the system of two electrons confined in two spatially separated quantum dots with opposite spins. In order to separate the electrons' spins we exploit transitions between the singlet and the triplet state, which are induced by resonantly oscillating Rashba spin-orbit coupling strength. The proposed device is all electrically controlled and the electron spin separation can be realized within tens of picoseconds. The results are supported by solving numerically the quasi-one-dimensional time-dependent Schroedinger equation for two electrons, where the electron-electron correlations are taken into account in the exact manner.

Ancient DNA sheds new light on the Svalbard foraminiferal fossil record of the last millennium.

Recent palaeogenetic studies have demonstrated the occurrence of preserved ancient DNA (aDNA) in various types of fossilised material. Environmental aDNA sequences assigned to modern species have been recovered from marine sediments dating to the Pleistocene. However, the match between the aDNA and the fossil record still needs to be evaluated for the environmental DNA approaches to be fully exploited. Here, we focus on foraminifera in sediments up to one thousand years old retrieved from the Hornsund fjord (Svalbard). We compared the diversity of foraminiferal microfossil assemblages with the diversity of aDNA sequenced from subsurface sediment samples using both cloning and high-throughput sequencing (HTS). Our study shows that 57% of the species archived in the fossil record were also detected in the aDNA data. However, the relative abundance of aDNA sequence reads and fossil specimens differed considerably. We also found a limited match between the stratigraphic occurrence of some fossil species and their aDNA sequences, especially in the case of rare taxa. The aDNA data comprised a high proportion of non-fossilised monothalamous species, which are known to dominate in modern foraminiferal communities of the Svalbard region. Our results confirm the relevance of HTS for studying past micro-eukaryotic diversity and provide insight into its ability to reflect fossil assemblages. Palaeogenetic studies including aDNA analyses of non-fossilised groups expand the range of palaeoceanographical proxies and therefore may increase the accuracy of palaeoenvironmental reconstructions.

Clinical factors affecting engraftment and transfusion needs in SCT: a single-center retrospective analysis.

Successful utilization of SCT modalities often requires utilization of both red cell and platelet transfusions. In this retrospective evaluation of clinical factors affecting transplant engraftment and transfusion utilization at a single transplant center in 505 patients from 2005 through 2009, we found that graft type, donor type and the conditioning regimen intensity significantly affected both the neutrophil engraftment time (P<0.001) and the platelet engraftment time (P<0.001). SCT patients required an average of 6.2 red cell units, and 7.9 platelet transfusions in the first 100 days with a wide s.d. Among auto-SCT patients, 5% required neither RBC nor platelet transfusions. Some reduced-intensity transplants were also associated with no transfusion need, and in allogeneic transplants, conditioning regimen intensity was positively correlated with platelet transfusion events as assessed by multivariate analysis. Other patient characteristics such as gender, graft type, donor type, underlying disease and use of TBI were all independently associated with transfusion needs in SCT patients. Further studies are required to understand the means to minimize transfusions and potential related complications in SCT patients.

Bipolar gene flow in deep-sea benthic foraminifera.

Despite its often featureless appearance, the deep-ocean floor includes some of the most diverse habitats on Earth. However, the accurate assessment of global deep-sea diversity is impeded by a paucity of data on the geographical ranges of bottom-dwelling species, particularly at the genetic level. Here, we present molecular evidence for exceptionally wide distribution of benthic foraminifera, which constitute the major part of deep-sea meiofauna. Our analyses of nuclear ribosomal RNA genes revealed high genetic similarity between Arctic and Antarctic populations of three common deep-sea foraminiferal species (Epistominella exigua, Cibicides wuellerstorfi and Oridorsalis umbonatus), separated by distances of up to 17, 000 km. Our results contrast with the substantial level of cryptic diversity usually revealed by molecular studies, of shallow-water benthic and planktonic marine organisms. The very broad ranges of the deep-sea foraminifera that we examined support the hypothesis of global distribution of small eukaryotes and suggest that deep-sea biodiversity may be more modest at global scales than present estimates suggest.

Mitochondrial genome of Savalia savaglia (Cnidaria, Hexacorallia) and early metazoan phylogeny.

Mitochondrial genomes have recently become widely used in animal phylogeny, mainly to infer the relationships between vertebrates and other bilaterians. However, only 11 of 723 complete mitochondrial genomes available in the public databases are of early metazoans, including cnidarians (Anthozoa, mainly Scleractinia) and sponges. Although some cnidarians (Medusozoa) are known to possess atypical linear mitochondrial DNA, the anthozoan mitochondrial genome is circular and its organization is similar to that of other metazoans. Because the phylogenetic relationships among Anthozoa as well as their relation to other early metazoans still need to be clarified, we tested whether sequencing the complete mitochondrial genome of Savalia savaglia, an anthozoan belonging to the order Zoantharia (=Zoanthidea), could be useful to infer such relationships. Compared to other anthozoans, S. savaglia's genome is unusually long (20,766 bp) due to the presence of several noncoding intergenic regions (3691 bp). The genome contains all 13 protein coding genes commonly found in metazoans, but like other Anthozoa it lacks most of the tRNAs. Phylogenetic analyses of S. savaglia mitochondrial sequences show Zoantharia branching closely to other Hexacorallia, either as a sister group to Actiniaria or as a sister group to Actiniaria and Scleractinia. The close relationships suggested between Zoantharia and Actiniaria are reinforced by strong similarities in their gene order and the presence of similar introns in the COI and ND5 genes. Our study suggests that mitochondrial genomes can be a source of potentially valuable information on the phylogeny of Hexacorallia and may provide new insights into the evolution of early metazoans.

Psychological distress in Brazilian caregivers of relatives with dementia.

The authors evaluated stress, anxiety, depression, and feelings of hopelessness in caregivers of relatives with dementia. One hundred and twenty-nine caregivers and 145 non-caregivers who lived in metropolitan Porto Alegre, Brazil completed Lipp's Inventory of Stress Symptoms for Adults, (ISSL), and Beck's Anxiety (BAI), Depression (BDI), and Hopelessness (BHS) scales. Caregivers showed higher levels of anxiety, depression, hopelessness, resistance/pre-exhaustion stress than controls. This study indicates that constant caregiving may significantly increase the risk of physical and mental health problems for caregivers in Brazil.

Constrictive bronchiolitis obliterans in patient with Castelman's disease.

A 37-year-old woman with hialin- vascular type Castelman's disease (CD) localised in the retroperitoneal region, incompletely resected, developed progressive dyspnoea. The chest radiograph taken 3 months before the operation was normal. The chest CT scan revealed diffused bronchiectases, hyperinflation and air trapping. Pulmonary function tests disclosed severe obstructive impairment with hyperinflation. The bronchoscopic examination of the bronchial tree was normal. Cultures of sputum, bronchial washing and blood were negative. No pemphigus antibodies were found. Mycoplasmal, chlamydial and viral infections were excluded. Histological examination of specimens obtained by open lung biopsy revealed bronchiolar inflammation, submucosal bronchial fibrosis with obliteration of bronchiolar lumen. Constrictive bronchiolitis obliterans (CBO) was diagnosed. Despite slight clinical and spirometric improvements that were achieved due to corticosteroid therapy, one year later she died as a result of respiratory failure. It is widely known that patients with CD develop CBO during the course of paraneoplastic pemphigus. However we present the case of CBO and CD but without any symptoms of this condition.