Modelling estuarine biogeochemical dynamics: from the local to the global scale

Estuaries act as strong carbon and nutrient filters and are relevant contributors to the atmospheric CO2 budget. They thus play an important, yet poorly constrained, role for global biogeochemical cycles and climate. This manuscript reviews recent developments in the modelling of estuarine biogeochemical dynamics. The first part provides an overview of the dominant physical and biogeochemical processes that control the transformations and fluxes of carbon and nutrients along the estuarine gradient. It highlights the tight links between estuarine geometry, hydrodynamics and scalar transport, as well as the role of transient and nonlinear dynamics. The most important biogeochemical processes are then discussed in the context of key biogeochemical indicators such as the net ecosystem metabolism (NEM), air–water CO2 fluxes, nutrient-filtering capacities and element budgets. In the second part of the paper, we illustrate, on the basis of local estuarine modelling studies, the power of reaction-transport models (RTMs) in understanding and quantifying estuarine biogeochemical dynamics. We show how a combination of RTM and high-resolution data can help disentangle the complex process interplay, which underlies the estuarine NEM, carbon and nutrient fluxes, and how such approaches can provide integrated assessments of the air–water CO2 fluxes along river–estuary–coastal zone continua. In addition, trends in estuarine biogeochemical dynamics across estuarine geometries and environmental scenario are explored, and the results are discussed in the context of improving the modelling of estuarine carbon and CO2 dynamics at regional and global scales

Asymmetries in symmetric quantum walks on two-dimensional networks

We study numerically the behavior of continuous-time quantum walks over networks which are topologically equivalent to square lattices. On short time scales, when placing the initial excitation at a corner of the network, we observe a fast, directed transport through the network to the opposite corner. This transport is not ballistic in nature, but rather produced by quantum mechanical interference. In the long time limit, certain walks show an asymmetric limiting probability distribution; this feature depends on the starting site and, remarkably, on the precise size of the network. The limiting probability distributions show patterns which are correlated with the initial condition. This might have consequences for the application of continuous time quantum walk algorithms.Comment: 9 pages, 12 figures, revtex

Quantum transport on two-dimensional regular graphs

We study the quantum-mechanical transport on two-dimensional graphs by means of continuous-time quantum walks and analyse the effect of different boundary conditions (BCs). For periodic BCs in both directions, i.e., for tori, the problem can be treated in a large measure analytically. Some of these results carry over to graphs which obey open boundary conditions (OBCs), such as cylinders or rectangles. Under OBCs the long time transition probabilities (LPs) also display asymmetries for certain graphs, as a function of their particular sizes. Interestingly, these effects do not show up in the marginal distributions, obtained by summing the LPs along one direction.Comment: 22 pages, 11 figure, acceted for publication in J.Phys.

Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood

notes: PMCID: PMC3446315© 2012 Davies et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Dynamic changes to the epigenome play a critical role in establishing and maintaining cellular phenotype during differentiation, but little is known about the normal methylomic differences that occur between functionally distinct areas of the brain. We characterized intra- and inter-individual methylomic variation across whole blood and multiple regions of the brain from multiple donors

The greatest air quality experiment ever: Policy suggestions from the COVID-19 lockdown in twelve European cities

COVID-19 (Coronavirus disease 2019) hit Europe in January 2020. By March, Europe was the active centre of the pandemic. As a result, widespread "lockdown" measures were enforced across the various European countries, even if to a different extent. Such actions caused a dramatic reduction, especially in road traffic. This event can be considered the most significant experiment ever conducted in Europe to assess the impact of a massive switch-off of atmospheric pollutant sources. In this study, we focus on in situ concentration data of the main atmospheric pollutants measured in twelve European cities, characterized by different climatology, emission sources, and strengths. We propose a methodology for the fair comparison of the impact of lockdown measures considering the non-stationarity of meteorological conditions and emissions, which are progressively declining due to the adoption of stricter air quality measures. The analysis of these unmatched circumstances allowed us to estimate the impact of a nearly zero-emission urban transport scenario on air quality in 12 European cities. The clearest result, common to all the cities, is that a dramatic traffic reduction effectively reduces NO2 concentrations. In contrast, each city’s PM and ozone concentrations can respond differently to the same type of emission reduction measure. From the policy point of view, these findings suggest that measures targeting urban traffic alone may not be the only effective option for improving air quality in cities

Tissue-specific patterns of allelically-skewed DNA methylation

While DNA methylation is usually thought to be symmetrical across both alleles, there are some notable exceptions. Genomic imprinting and X chromosome inactivation are two well-studied sources of allele-specific methylation (ASM), but recent research has indicated a more complex pattern in which genotypic variation can be associated with allelically-skewed DNA methylation in cis. Given the known heterogeneity of DNA methylation across tissues and cell types we explored inter- and intra-individual variation in ASM across several regions of the human brain and whole blood from multiple individuals. Consistent with previous studies, we find widespread ASM with >4% of the ~220,000 loci interrogated showing evidence of allelically-skewed DNA methylation. We identify ASM flanking known imprinted regions, and show that ASM sites are enriched in DNase I hypersensitivity sites and often located in an extended genomic context of intermediate DNA methylation. We also detect examples of genotype-driven ASM, some of which are also tissue-specific. These findings contribute to our understanding about the nature of differential DNA methylation across tissues and have important implications for genetic studies of complex disease. As a resource to the community, ASM patterns across each of the tissues studied are available in a searchable online database: http://epigenetics.essex.ac.uk/ASMBrainBlood

Double-weak decays of 124Xe and 136Xe in the XENON1T and XENONnT experiments

We present results on the search for two-neutrino double-electron capture (2νECEC) of 124Xe and neutrinoless double-β decay (0νββ) of 136Xe in XENON1T. We consider captures from the K shell up to the N shell in the 2νECEC signal model and measure a total half-life of T2νECEC1/2=(1.1±0.2stat±0.1sys)×1022yr with a 0.87kgyr isotope exposure. The statistical significance of the signal is 7.0σ. We use XENON1T data with 36.16kgyr of 136Xe exposure to search for 0νββ. We find no evidence of a signal and set a lower limit on the half-life of T0νββ1/2>1.2×1024yrat90%CL. This is the best result from a dark matter detector without an enriched target to date. We also report projections on the sensitivity of XENONnT to 0νββ. Assuming a 275kgyr 136Xe exposure, the expected sensitivity is T0νββ1/2>2.1×1025yrat90%CL, corresponding to an effective Majorana mass range of ⟨mββ⟩<(0.19–0.59)eV/c2

Application of CRISPR/Cas9 editing and digital droplet PCR in human iPSCs to generate novel knock-in reporter lines to visualize dopaminergic neurons

Human induced pluripotent stem cells (hiPSCs) have become indispensable for disease modelling. They are an important resource to access patient cells harbouring disease-causing mutations. Derivation of midbrain dopaminergic (DAergic) neurons from hiPSCs of PD patients represents the only option to model physiological processes in a cell type that is not otherwise accessible from human patients. However, differentiation does not produce a homogenous population of DA neurons and contaminant cell types may interfere with the readout of the in vitro system. Here, we use CRISPR/Cas9 to generate novel knock-in reporter lines for DA neurons, engineered with an endogenous fluorescent tyrosine hydroxylase \u2013 enhanced green fluorescent protein (TH-eGFP) reporter. We present a reproducible knock-in strategy combined with a highly specific homologous directed repair (HDR) screening approach using digital droplet PCR (ddPCR). The knock-in cell lines that we created show a functioning fluorescent reporter system for DA neurons that are identifiable by flow cytometry