Highlights ► NGS has broadly opened the door to shotgun metagenomics. ► Read-based ‘and’ assembly-based approaches should be used for the most detailed analysis. ► Online resources are available for ...some analysis techniques. ► Computational resources are current bottlenecks for in-depth metagenome analysis. ► Current tools will not scale and novel metagenomic analysis algorithms are needed.
•A new approach for determining the settling velocity of microplastic particles.•Microplastic-fine sediment interaction through five settling velocity regions.•3D-numerical Modelling of microplastic ...transport in the tidal Weser river.•Higher probability of small microplastic to pass the estuary and reach the open sea.•Higher microplastic concentration in the estuarine turbidity zone.
Microplastic (MP) pollution is an important challenge for human life which has consequently affected the natural system of other organisms. Mismanagement and also careless handling of plastics in daily life has led to an accelerating contamination of air, water and soil compartments with MP. Under estuarine conditions, interactions with suspended particulate matter (SPM) like fine sediment in the water column play an important role on the fate of MP. Further studies to better understand the corresponding transport and accumulation mechanisms are required. This paper aims at providing a new modeling approach improving the MP settling velocity formulation based on higher suspended fine sediment concentrations, as i.e. existent in estuarine turbidity zones (ETZ). The capability of the suggested approach is examined through the modeling of released MP transport in water and their interactions with fine sediment (cohesive sediment/fluid mud). The model results suggest higher concentrations of MP in ETZ, both in the water column as well as the bed sediment, which is also supported by measurements. The key process in the modeling approach is the integration of small MP particles into estuarine fine sediment aggregates. This is realized by means of a threshold sediment concentration, above which the effective MP settling velocity increasingly approaches that of the sediment aggregates. The model results are in good agreement with measured MP mass concentrations. Moreover, the model results also show that lighter small MP particles can easier escape the ETZ towards the open sea.
We construct entanglement renormalization schemes that provably approximate the ground states of noninteracting-fermion nearest-neighbor hopping Hamiltonians on the one-dimensional discrete line and ...the two-dimensional square lattice. These schemes give hierarchical quantum circuits that build up the states from unentangled degrees of freedom. The circuits are based on pairs of discrete wavelet transforms, which are approximately related by a “half-shift”: translation by half a unit cell. The presence of the Fermi surface in the two-dimensional model requires a special kind of circuit architecture to properly capture the entanglement in the ground state. We show how the error in the approximation can be controlled without ever performing a variational optimization.
infection and high dietary salt intake are risk factors for the development of gastric adenocarcinoma. One possible mechanism by which a high-salt diet could influence gastric cancer risk is by ...modulating
gene expression. In this study, we utilized transcriptome sequencing (RNA-seq) methodology to compare the transcriptional profiles of
grown in media containing different concentrations of sodium chloride. We identified 118 differentially expressed genes (65 upregulated and 53 downregulated in response to high-salt conditions), including multiple members of 14 operons. Twenty-nine of the differentially expressed genes encode proteins previously shown to undergo salt-responsive changes in abundance, based on proteomic analyses. Real-time reverse transcription (RT)-PCR analyses validated differential expression of multiple genes encoding outer membrane proteins, including adhesins (SabA and HopQ) and proteins involved in iron acquisition (FecA2 and FecA3). Transcript levels of
,
, and
are increased under high-salt conditions, whereas transcript levels of
and
are decreased under high-salt conditions. Transcription of
,
,
, and
is derepressed in an
mutant strain, but salt-responsive transcription of these genes is not mediated by the ArsRS two-component system, and the CrdRS and FlgRS two-component systems do not have any detectable effects on transcription of these genes. In summary, these data provide a comprehensive view of
transcriptional alterations that occur in response to high-salt environmental conditions.
OP9 is a yet-uncultivated bacterial lineage found in geothermal systems, petroleum reservoirs, anaerobic digesters and wastewater treatment facilities. Here we use single-cell and metagenome ...sequencing to obtain two distinct, nearly complete OP9 genomes, one constructed from single cells sorted from hot spring sediments and the other derived from binned metagenomic contigs from an in situ-enriched cellulolytic, thermophilic community. Phylogenomic analyses support the designation of OP9 as a candidate phylum for which we propose the name 'Atribacteria'. Although a plurality of predicted proteins is most similar to those from Firmicutes, the presence of key genes suggests a diderm cell envelope. Metabolic reconstruction from the core genome suggests an anaerobic lifestyle based on sugar fermentation by Embden-Meyerhof glycolysis with production of hydrogen, acetate and ethanol. Putative glycohydrolases and an endoglucanase may enable catabolism of (hemi)cellulose in thermal environments. This study lays a foundation for understanding the physiology and ecological role of the 'Atribacteria'.
We show that the presence of an interaction in the quantum walk of two atoms leads to the formation of a stable compound, a molecular state. The wave function of the molecule decays exponentially in ...the relative position of the two atoms; hence it constitutes a true bound state. Furthermore, for a certain class of interactions, we develop an effective theory and find that the dynamics of the molecule is described by a quantum walk in its own right. We propose a setup for the experimental realization as well as sketch the possibility to observe quasi-particle effects in quantum many-body systems.
Jakarta Bay in Indonesia and its offshore island chain, the Thousand Islands, are facing extreme pollution. Surfactants and diesel-borne compounds from sewage and bilge water discharges are common ...pollutants. However, knowledge of their effects on reef fish physiology is scarce. This study investigated combined and single effects of a) the water accommodated fraction of diesel (WAF-D, determined by ƩEPA polycyclic aromatic hydrocarbons (PAHs)) and b) the surfactant linear alkylbenzene sulfonate (LAS) on metabolic performance of the coral reef fish Siganus guttatus. Responses to combinations of each pollutant with elevated temperature (+3°C) were determined. Short-term exposure to WAF-D led to a significant decrease in standard metabolic rates, while LAS led to an increase. During combined exposure, metabolic depression was observed. Effects of pollutants were not amplified by elevated temperature. This study highlights the need to reduce import of these pollutants and to avoid negative long-term effects on fish health.
•Surfactants and diesel-borne compounds were determined in Jakarta Bay and the Thousand Islands.•Exposure of Siganus guttatus to water accommodated fraction of diesel led to metabolic depression.•Exposure of Siganus guttatus to an anionic surfactant led to increased metabolic rates.•Combined exposure to both pollutants caused metabolic depression (interactive effect).•Effects of pollutants were not amplified by elevated temperature (no synergism).
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