Zebrafish cardiovascular cDNA microarrays : expression profiling and gene discovery in embryos exposed to 2,3,7,8-Tetrachlorodibenzo-ρ-dioxin

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 20032,3,7,8-Tetrachlorodibenzo-ρ-dioxin (TCDD) is a potent teratogen that impacts the developing cardiovascular system. Hallmarks of embryonic exposure include cardiac malformation, impaired circulation, loss of erythrocytes, pericardial and yolk sac edema, and early life stage mortality. However, the mechanism of TCDD cardiovascular embryotoxicity is poorly understood. The primary goal of this thesis was to identify TCDD-responsive genes likely to be involved in processes of toxicity. We constructed microarrays using cDNA libraries derived from zebrafish embryonic and adult heart tissue. Embryonic heart arrays were used for protocol development. The resulting workflow was employed in the production of adult heart microarrays containing ~2800 unique cardiovascular genes. These arrays were used to establish gene expression profiles of zebrafish embryos exposed to 1.84±0.42 or 10.74±0.38 ng TCDD/g embryo. Alterations in cardiovascular gene expression were limited; 44 genes or ESTs were significantly differentially expressed ≥1.8-fold (p-values ≤5x10-4), and only CYP1A and CYP1B1 were induced >4- fold. Transcriptional responses to TCDD were highly dose-dependent, and adaptive responses were a prevalent feature of TCDD-modulated gene expression. Microarray analyses indicated induction of genes in three major functional classes - xenobiotic detoxification, sarcomere structure, and energy transfer. TCDD-modulation of selected genes was verified by RT-PCR. Induction of mitochondrial electron transfer genes was variable and modest; such induction provides a possible pathway to reactive oxygen generation and cardiac pathology. Sarcomere genes were generally robustly induced, but RT-PCR indicated suppression of cardiac troponin T2. The current data suggest that TCDD causes cardiomyopathy in zebrafish embryos. Investigation of a TCDD-induced EST cluster led to the discovery of a novel retroelement, EZR1. EZR1 elements lack genes necessary for autonomous retrotransposition, but are highly expressed in normal and TCDD-exposed cardiac tissue. Putative regulatory elements in LTR sequences may account for observed expression patterns. The function, if any, of EZR1 remains open to speculation.This research was supported in part by the WHOI Academic Programs Office, an NSF Coastal Research Traineeship, NIH Superfund Basic Research Program grant 5-P42-ES07381, EPA grant R827102-01-0, and WHOI Ocean Life Institute and Coastal Ocean Institute grant 39591300

Geochemical and Sr-Nd-Hf-O isotopic constraints on volcanic petrogenesis at the Sunda arc, Indonesia

The Sunda island arc of Indonesia formed as a result of the northward subduction of the Indo- Australian Plate beneath the Eurasian Plate. Along-arc variations in the composition and thickness of the overriding Eurasian plate and variation in the type and amount of sediment deposited on the subducting plate create differential effects on Sunda arc lava geochemistry. Detailed study of volcanic rocks from Salak, Gede Volcanic Complex (GVC) in West Java and Ijen Volcanic Complex (IVC) in East Java was carried out in order to establish the relative importance and contributions of various potential source components and composition-modifying processes at individual volcanic centres, prior to investigating petrogenetic variation along the arc. Differentiation processes play a major role in modifying the geochemical composition of Sunda arc magmas. However, the relative importance and traceable impact of the different processes varies at each volcanic centre. Fractional crystallisation of a typical Javan island arc mineral assemblage exerts the largest control on major and trace element composition of the volcanic rocks. Distinct intra-volcanic complex differentiation trends at rvc and Salak are spatially controlled and are explained by independent conduits and multiple magma reservoirs at different depths in the crust - linked to sub-volcanic structure. Shallow level contamination by typical upper-crustal continental material is insignificant during magmatic differentiation at Salak, GVC and IVC. However, at Salak there is some evidence for assimilation of material similar in composition to the volcanic rocks. Deep fractionation of a phase in which HFSE and HREE are compatible (e.g. amphibole) is inferred in the evolution of most Javan magmas. Magmatism at Salak, GVC and IVC is the product of shallow, relatively homogeneous, fertile, Indian Ocean MORB-like mantle that has been enriched by slab- derived component(s) sourced from the altered oceanic crust and subducted sediment. Hf and Nd isotope ratios of Javan lavas show that the subducted sedimentary source component is heterogeneous and reflects spatial variations in sediment compositions on the down-going plate along the Java Trench. A progressive eastward increase in Sr isotope ratio of volcanic rocks across West and Central Java broadly correlates with inferred lithospheric thickness. A significant change in crustal architecture (i.e. thickness) occurs between Central and East Java. This transition may represent the south-eastern boundary of Sundaland (pre-Tertiary arc basement)

Cardiovascular gene expression profiles of dioxin exposure in zebrafish embryos

Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of Society of Toxicology for personal use, not for redistribution. The definitive version was published in Toxicological Sciences 85 (2005): 683-693, doi:10.1093/toxsci/kfi116.2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a widespread environmental contaminant that causes altered heart morphology, circulatory impairment, edema, hemorrhage, and early life stage mortality in fish. TCDD toxicity is largely dependent upon the aryl hydrocarbon receptor, but understanding of the molecular mechanism of cardiovascular embryotoxicity remains incomplete. In order to identify genes potentially involved in cardiovascular impacts, we constructed custom cDNA microarrays consisting of 4,896 zebrafish adult heart cDNA clones and over 200 genes with known developmental, toxicological, and housekeeping roles. Gene expression profiles were obtained for 3-day old zebrafish following early embryonic exposure to either 0.5 or 5.0 nM TCDD. 516 clones were significantly differentially expressed (p-value < 0.005) under at least one treatment condition; 123 high-priority clones were selected for further investigation. CYP1A, CYP1B1, and other members of the AHR gene battery, were strongly and dose-dependently induced by TCDD. Importantly, altered expression of cardiac sarcomere components, including cardiac troponin T2 and multiple myosin isoforms, was consistent with the hypothesis that TCDD causes dilated cardiomyopathy. Observed increases in expression levels of mitochondrial energy transfer genes also may be related to cardiomyopathy. Other TCDD-responsive genes included fatty acid and steroid metabolism enzymes, ribosomal and signal transduction proteins, and 18 ESTs with no known protein homologs. As the first broadscale study of TCDD-modulated gene expression in a non-mammalian system, this work provides an important perspective on mechanisms of TCDD toxicity.This work was supported by funding from the National Institutes of Health

Considerations for U-series dating of sediments: insights from the Flinders Ranges, South Australia

Uranium isotope ratios have been determined for the fine-grained detrital fraction of Pleistocene Wilkawillina valley-fill sediments, four local Proterozoic bedrock samples and fine-grained aeolian material from a sand dune deposit of the Flinders Ranges, South Australia. The aim was to quantify the comminution age, i.e. the time elapsed since physical weathering of the bedrock, and residence time of the valley-fill sediments and to place tighter constraints on input parameters for the comminution age calculation. Despite using two independent approaches for determination of the recoil lost fraction of 234U from the sediment (weighted geometric and surface area estimates), samples fail to produce realistic comminution ages and hence, residence times. The issues involved in the ability to determine sediment comminution ages are discussed. The (234U/238U) activity ratio of the local bedrock is not in secular equilibrium, despite the bedrock being much older than 1Ma, i.e. the timeframe for 234U and 238U to reach secular equilibrium in a closed system. Using the average Flinders Ranges bedrock (234U/238U) ratio instead of an assumed (234U/238U) activity ratio of unity for the source would significantly reduce calculated residence times. This result warrants concern for future studies using the comminution approach for which a secular equilibrium source (234U/238U) activity ratio is assumed. Significant input of aeolian material may modify the measured (234U/238U) activity ratios. Such input may be more tightly constrained in future studies using rare earth element and radiogenic isotopic data. Future comminution studies would benefit from further consideration of the importance of 1) leaching lost 234U from source rock and bulk sediment samples, 2) wind deposition of fine-grained material and 3) the appropriateness and robustness of sample pre-treatment procedures

Living in uncertain times: trajectories to death in residential care homes.

BACKGROUND: Older people living in care homes often have limited life expectancy. Practitioners and policymakers are increasingly questioning the appropriateness of many acute hospital admissions and the quality of end-of-life care provided in care homes. AIM: To describe care home residents' trajectories to death and care provision in their final weeks of life. DESIGN AND SETTING: Prospective study of residents in six residential care homes in three sociodemographically varied English localities: Hertfordshire, Essex, and Cambridgeshire. METHOD: Case note reviews and interviews with residents, care home staff, and healthcare professionals. RESULTS: Twenty-three out of 121 recruited residents died during the study period. Four trajectories to death were identified: 'anticipated dying' with an identifiable end-of-life care period and death in the care home (n = 9); 'unexpected dying' with death in the care home that was not anticipated and often sudden (n = 3); 'uncertain dying' with a period of diagnostic uncertainty or difficult symptom management leading to hospital admission and inpatient death (n = 7); and 'unpredictable dying' with an unexpected event leading to hospital admission and inpatient death (n = 4). End-of-life care tools were rarely used. Most residents who had had one or more acute hospital admission were still alive at the end of the study. CONCLUSION: For some care home residents there was an identifiable period when they were approaching the end-of-life and planned care was put in place. For others, death came unexpectedly or during a period of considerable uncertainty, with care largely unplanned and reactive to events

Dynamics and timescales of mafic–silicic magma interactions at Soufrière Hills Volcano, Montserrat

Mafic magma intrusions into silica-rich magmatic reservoirs are commonly proposed to drive the eruptions of andesitic hybrid magmas that characterise many arc volcanoes. However, interactions between contrasting magmas involve large gradients of physical and chemical properties that change over time, and the details of such processes have proven difficult to constrain. In this paper we investigate the dynamics of magma mingling and mixing using chemical and textural zoning patterns recorded in plagioclase crystals from the February 2010 eruption at Soufrière Hills Volcano, Montserrat. This eruption is considered a classic example of interactions between the andesite magma that constitutes the bulk of the erupted volume and the basaltic andesite that occurs as enclaves. We find that plagioclase crystals are characterised by two well-defined zones that record mafic–silicic magma interaction: a crystal interior, often identified by a patchy, dusty and oscillatory zoning, and an overgrowth zone (rim) of a different composition. We use the anorthite and Mg contents to track the thermal and compositional changes experienced by the crystals over time. Our results reveal that the crystal rims formed a few hours to days prior to eruption, during co-eruptive magmatic interactions. The interaction between the two magmas with contrasting rheology is likely increased by a narrowing conduit geometry towards the surface, which facilitates convection and additional interface contact of the two magmas. Our findings shed new light on the nature and timing of magmatic interactions driving the final eruptive phase at Soufrière Hills Volcano and help to propose an interpretative framework of the monitoring signals

Valuing the urban trees in Bridgend county borough

Urban forests provide a range of services, often termed ecosystem services, that help alleviate problems associated with urbanisation. Trees improve local air quality, capture carbon, reduce flooding and cool urban environments. They provide habitat for animals,and can improve social cohesion in communities. Ecosystem service provision is directly influenced by management actions that affect the overall structure of an urban forest.The first step to improve the management of an urban forest is to better understand its current structure, composition and distribution in order to obtain a baseline from which to set goals and to monitor progress. By measuring the structure of the urban forest (the tree species present, their size and condition), the benefits of the urban forest can be determined and the value of these benefits calculated and expressed in monetary terms.Valuing services provided by the urban trees in Bridgend County Borough (Bridgend CB) could allow Bridgend County Borough Council (Bridgend CBC) and Natural Resources Wales (NRW) to increase the profile of the urban forest thereby helping to ensure its value is maintained and improved upon. The Bridgend CB, as described in this study, is spread across 5 separate urban districts with a total area of 4,400 ha. In order to gain a better understanding of the urban trees in Bridgend CB and to value the services they provide, an i-Tree Eco survey was undertaken in the summer of 2014. i-Tree Eco is a model developed by the US Forest Service to measure a range of ecosystem services provided by urban trees. This study was funded by NRW and Bridgend CBC and the survey was carried out by Barton Trees. This report presents a baseline quantitative assessment of the air pollution removal, carbon storage and sequestration, rainfall interception and visual amenity of the urban forest of Bridgend CB, and is accompanied with detailed information on the forest’s structure and composition. Residents in Bridgend CB benefit significantly from the urban trees present, including the provision of ecosystem services worth £950,000 per year. This value, however, excludes many of the ecosystem services of trees that are mnot currently assessed by i-Tree Eco, including cooling local air temperatures and reducing noise pollution. Therefore, this value is a conservative estimate of the ecosystem services provided. This study captures a snapshot-in-time ‘picture’ of the urban forest. It does not consider how the urban forest has changed over time or the reasons for this. Decisions on how the structure and composition of Bridgend CB’s urban forest should change in the future or how to ensure that it is resilient to the effects of a changing climate are beyond the scope of this report, though this study goes a long way to providing the necessary baseline data required to inform such decision making

The Impact of a Six‐Year Climate Anomaly on the “Spanish Flu” Pandemic and WWI

The H1N1 “Spanish influenza” pandemic of 1918–1919 caused the highest known number of deaths recorded for a single pandemic in human history. Several theories have been offered to explain the virulence and spread of the disease, but the environmental context remains underexamined. In this study, we present a new environmental record from a European, Alpine ice core, showing a significant climate anomaly that affected the continent from 1914 to 1919. Incessant torrential rain and declining temperatures increased casualties in the battlefields of World War I (WWI), setting the stage for the spread of the pandemic at the end of the conflict. Multiple independent records of temperature, precipitation, and mortality corroborate these findings

A case study using 2019 pre-monsoon snow and stream chemistry in the Khumbu region, Nepal

This case study provides a framework for future monitoring and evidence for human source pollution in the Khumbu region, Nepal. We analyzed the chemical composition (major ions, major/trace elements, black carbon, and stable water isotopes) of pre-monsoon stream water (4300–5250 m) and snow (5200–6665 m) samples collected from Mt. Everest, Mt. Lobuche, and the Imja Valley during the 2019 pre-monsoon season, in addition to a shallow ice core recovered from the Khumbu Glacier (5300 m). In agreement with previous work, pre-monsoon aerosol deposition is dominated by dust originating from western sources and less frequently by transport from southerly air mass sources as demonstrated by evidence of one of the strongest recorded pre-monsoon events emanating from the Bay of Bengal, Cyclone Fani. Elevated concentrations of human-sourced metals (e.g., Pb, Bi, As) are found in surface snow and stream chemistry collected in the Khumbu region. As the most comprehensive case study of environmental chemistry in the Khumbu region, this research offers sufficient evidence for increased monitoring in this watershed and surrounding areas