Mercury dynamics in a San Francisco estuary tidal wetland : assessing dynamics using in situ measurements

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Estuaries and Coasts 35 (2012): 1036-1048, doi:10.1007/s12237-012-9501-3.We used high-resolution in situ measurements of turbidity and fluorescent dissolved organic matter (FDOM) to quantitatively estimate the tidally driven exchange of mercury (Hg) between the waters of the San Francisco estuary and Browns Island, a tidal wetland. Turbidity and FDOM—representative of particle-associated and filter-passing Hg, respectively—together predicted 94 % of the observed variability in measured total mercury concentration in unfiltered water samples (UTHg) collected during a single tidal cycle in spring, fall, and winter, 2005–2006. Continuous in situ turbidity and FDOM data spanning at least a full spring-neap period were used to generate UTHg concentration time series using this relationship, and then combined with water discharge measurements to calculate Hg fluxes in each season. Wetlands are generally considered to be sinks for sediment and associated mercury. However, during the three periods of monitoring, Browns Island wetland did not appreciably accumulate Hg. Instead, gradual tidally driven export of UTHg from the wetland offset the large episodic on-island fluxes associated with high wind events. Exports were highest during large spring tides, when ebbing waters relatively enriched in FDOM, dissolved organic carbon (DOC), and filter-passing mercury drained from the marsh into the open waters of the estuary. On-island flux of UTHg, which was largely particle-associated, was highest during strong winds coincident with flood tides. Our results demonstrate that processes driving UTHg fluxes in tidal wetlands encompass both the dissolved and particulate phases and multiple timescales, necessitating longer term monitoring to adequately quantify fluxes.This work was supported by funding from the California Bay Delta Authority Ecosystem Restoration and Drinking Water Programs (grant ERP-00- G01) and matching funds from the United States Geological Survey Cooperative Research Program

Stochastic flowering phenology in Dactylis Glomerata populations described by Markov chain modelling

Understanding the relationship between flowering patterns and pollen dispersal is important in climate change modelling, pollen forecasting, forestry and agriculture. Enhanced understanding of this connection can be gained through detailed spatial and temporal flowering observations on a population level, combined with modelling simulating the dynamics. Species with large distribution ranges, long flowering seasons, high pollen production and naturally large populations can be used to illustrate these dynamics. Revealing and simulating species-specific demographic and stochastic elements in the flowering process will likely be important in determining when pollen release is likely to happen in flowering plants. Spatial and temporal dynamics of eight populations of Dactylis glomerata were collected over the course of two years to determine high-resolution demographic elements. Stochastic elements were accounted for using Markov Chain approaches in order to evaluate tiller-specific contribution to overall population dynamics. Tiller-specific developmental dynamics were evaluated using three different RV matrix correlation coefficients. We found that the demographic patterns in population development were the same for all populations with key phenological events differing only by a few days over the course of the seasons. Many tillers transitioned very quickly from non-flowering to full flowering, a process that can be replicated with Markov Chain modelling. Our novel approach demonstrates the identification and quantification of stochastic elements in the flowering process of D. glomerata, an element likely to be found in many flowering plants. The stochastic modelling approach can be used to develop detailed pollen release models for Dactylis, other grass species and probably other flowering plants

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Isotope Fractionation from in Vivo Methylmercury Detoxification in Waterbirds

The robust application of stable mercury (Hg) isotopes for mercury source apportionment and risk assessment necessitates the understanding of mass-dependent fractionation (MDF) as a result of internal transformations within organisms. Here, we used high energy-resolution X-ray absorption near edge structure spectroscopy and isotope ratios of total mercury (δ202THg) and methylmercury (δ202MeHg) to elucidate the chemical speciation of Hg and the resultant MDF as a result of internal MeHg demethylation in waterbirds. In three waterbirds (Clark's grebe, Forster's tern, and south polar skua), between 17 and 86% of MeHg was demethylated to inorganic mercury (iHg) species primarily in the liver and kidneys as Hg-tetraselenolate [Hg(Sec)4] and minor Hg-dithiolate [Hg(SR)2] complexes. Tissular differences between δ202THg and δ202MeHg correlated linearly with %iHg [Hg(Sec)4 + Hg(SR)2] and were interpreted to reflect a kinetic isotope effect during in vivo MeHg demethylation. The product-reactant isotopic enrichment factor (ϵp/r) for the demethylation of MeHg → Hg(Sec)4 was -2.2 ± 0.1‰. δ202MeHg values were unvarying within each bird, regardless of Hg(Sec)4 abundance, indicating fast internal cycling or replenishment of MeHg relative to demethylation. Our findings document a universal selenium-dependent demethylation reaction in birds, provide new insights on the internal transformations and cycling of MeHg and Hg(Sec)4, and allow for mathematical correction of δ202THg values as a result of the MeHg → Hg(Sec)4 reaction

The role of hepatocyte growth factor and its receptor c-met in interactions between lymphocytes and stromal cells in secondary human lymphoid organs

Secondary lymphoid tissue consists of two major populations of cells: lymphoid cells and stromal cells. It is generally accepted that these two cell populations influence each other however, factors mediating these processes are poorly understood. In this paper we characterize one of the possible means of communication between stroma and lymphocytes namely through hepatocyte growth factor/c-met receptor interactions. Hepatocyte growth factor (HGF) is a pleiotropic factor that is mainly produced by mesenchymal cells and acts on cells of epithelial origin which express the HGF receptor c-met. Here we demonstrate that biologically active HGF is constitutively produced by fibroblast-like stromal cells from human lymphoid tissues. HGF secretion from stromal cells was increased by direct contact with activated T cells. This increase was abrogated when activated T cells were separated physically from stromal cells. Using neutralizing antibody or cytokine inhibitors we provide evidence that enhancement of HGF production was due to additive effects of T-cell membrane-associated interleukin-1 (IL-1) and CD40 ligand. Finally, we also show that B lymphocytes activated with CD40L/anti-µ or phorbol 12-myristate 13-acetate (PMA) express c-met receptor. Co-culture of activated B cells with stromal cells from spleen leads to enhanced production of immunoglobulins. This can be partially inhibited by introduction of anti-HGF neutralizing antibodies to the culture system. Substitution of stromal cells with recombinant HGF did not produce enhancement of immunoglobulin secretion. On the other hand stimulation of c-met receptor with HGF leads to enhanced integrin-mediated adhesion of activated B cells to vascular cell adhesion molecule (VCAM-1) and fibronectin. On the basis of the above experiments we conclude that HGF production by fibroblast-like stromal cells can be modulated by activated T cells, thus providing signals for the regulation of adhesion of c-met expressing B cells to extracellular matrix proteins. In this way HGF may indirectly influence immunoglobulin secretion by B cells