Environmental Research Institute

We provide here a list of 481 P450 genes and 22 pseudogenes, plus all accession numbers that have been reported as of October 18, 1995. These genes have been described in 85 eukaryote (including vertebrates, invertebrates, fungi, and plants) and 20 prokaryote species. Of 74 gene families so far described, 14 families exist in all mammals examined to date. These 14 families comprise 26 mammalian subfamilies, of which 20 and 15 have been mapped in the human genome and the mouse genome, respectively. Each subfamily usually represents a cluster of tightly linked genes widely scattered throughout the genome, but there are exceptions. Interestingly, the CYP51 family has been found in mammals, filamentous fungi and yeast, and plants-attesting to the fact that this P450 gene family is very ancient. One functional CYP51 gene and two processed pseudogenes, which are the first examples of intronless pseudogenes within the P450 superfamily, have been mapped to three different human chromosomes. This revision supersedes the four previous updates in which a nomenclature system, based on divergent evolution of the superfamily, has been described. For the gene, we recommend that the italicized root symbol "CYP' for human ("Cyp' for mouse and Drosophila), representing "cytochrome P450', be followed by an Arabic number denoting the family, a letter designating the subfamily (when two or more exist), and an Arabic numeral representing the individual gene within the subfamily. A hyphen is no longer recommended in mouse gene nomenclature. "P' ("ps' in mouse and Drosophila) after the gene number denotes a pseudogene; "X' after the gene number means its use has been discontinued. If a gene is the sole member of a family, the subfamily letter and gene number would be helpful but need not be included. The human nomenclature system should be used for all species other than mouse and Drosophila. The cDNAs, mRNAs and enzymes in all species (including mouse) should include all capital letters, and without italics or hyphens. This nomenclature system is similar to that proposed in our previous updates.

Driven by the high demand for sensitive and specific tools for optical sensing and imaging, bioprobes with various working mechanisms and advanced functionalities are flourishing at an incredible speed. Conventional fluorescent probes suffer from the notorious effect of aggregation-caused quenching that imposes limitation on their labelling efficiency or concentration to achieve desired sensitivity. The recently emerged fluorogens with an aggregation-induced emission (AIE) feature offer a timely remedy to tackle the challenge. Utilizing the unique properties of AIE fluorogens (AIEgens), specific light-up probes have been constructed through functionalization with recognition elements, showing advantages such as low background interference, a high signal to noise ratio and superior photostability with activatable therapeutic effects. In this tutorial review, we summarize the recent progress in the development of specific AIEgen-based light-up bioprobes. Through illustration of their operation mechanisms and application examples, we hope to provide guidelines for the design of more advanced AIE sensing and imaging platforms with high selectivity, great sensitivity and wide adaptability to a broad range of biomedical applications.

Abstract Drought events are increasing globally, and reports of consequent forest mortality are widespread. However, due to a lack of a quantitative global synthesis, it is still not clear whether drought‐induced mortality rates differ among global biomes and whether functional traits influence the risk of drought‐induced mortality. To address these uncertainties, we performed a global meta‐analysis of 58 studies of drought‐induced forest mortality. Mortality rates were modelled as a function of drought, temperature, biomes, phylogenetic and functional groups and functional traits. We identified a consistent global‐scale response, where mortality increased with drought severity [log mortality (trees trees −1 year −1 ) increased 0.46 (95% CI = 0.2–0.7) with one SPEI unit drought intensity]. We found no significant differences in the magnitude of the response depending on forest biomes or between angiosperms and gymnosperms or evergreen and deciduous tree species. Functional traits explained some of the variation in drought responses between species (i.e. increased from 30 to 37% when wood density and specific leaf area were included). Tree species with denser wood and lower specific leaf area showed lower mortality responses. Our results illustrate the value of functional traits for understanding patterns of drought‐induced tree mortality and suggest that mortality could become increasingly widespread in the future.

Standardised recommendations for a physiologically relevant, semi-dynamic <italic>in vitro</italic> simulation of upper GI tract digestion.

Abstract The ocean is a sink for ~25% of the atmospheric CO 2 emitted by human activities, an amount in excess of 2 petagrams of carbon per year (PgC yr −1 ). Time-resolved estimates of global ocean-atmosphere CO 2 flux provide an important constraint on the global carbon budget. However, previous estimates of this flux, derived from surface ocean CO 2 concentrations, have not corrected the data for temperature gradients between the surface and sampling at a few meters depth, or for the effect of the cool ocean surface skin. Here we calculate a time history of ocean-atmosphere CO 2 fluxes from 1992 to 2018, corrected for these effects. These increase the calculated net flux into the oceans by 0.8–0.9 PgC yr −1 , at times doubling uncorrected values. We estimate uncertainties using multiple interpolation methods, finding convergent results for fluxes globally after 2000, or over the Northern Hemisphere throughout the period. Our corrections reconcile surface uptake with independent estimates of the increase in ocean CO 2 inventory, and suggest most ocean models underestimate uptake.

Factors controlling the anaerobic oxidation of ammonium with nitrate and nitrite were explored in a marine sediment from the Skagerrak in the Baltic-North Sea transition. In anoxic incubations with the addition of nitrite, approximately 65% of the nitrogen gas formation was due to anaerobic ammonium oxidation with nitrite, with the remainder being produced by denitrification. Anaerobic ammonium oxidation with nitrite exhibited a biological temperature response, with a rate optimum at 15 degrees C and a maximum temperature of 37 degrees C. The biological nature of the process and a 1:1 stoichiometry for the reaction between nitrite and ammonium indicated that the transformations might be attributed to the anammox process. Attempts to find other anaerobic ammonium-oxidizing processes in this sediment failed. The apparent K(m) of nitrite consumption was less than 3 microM, and the relative importance of ammonium oxidation with nitrite and denitrification for the production of nitrogen gas was independent of nitrite concentration. Thus, the quantitative importance of ammonium oxidation with nitrite in the jar incubations at elevated nitrite concentrations probably represents the in situ situation. With the addition of nitrate, the production of nitrite from nitrate was four times faster than its consumption and therefore did not limit the rate of ammonium oxidation. Accordingly, the rate of this process was the same whether nitrate or nitrite was added as electron acceptor. The addition of organic matter did not stimulate denitrification, possibly because it was outcompeted by manganese reduction or because transport limitation was removed due to homogenization of the sediment.

The oxidation of elemental mercury (Hg0) to the divalent gaseous mercury dibromide (HgBr2) has been proposed to account for the removal of Hg0 during depletion events in the springtime Arctic. The mechanism of this process is explored in this paper by theoretical calculations of the relevant rate coefficients. Rice-Ramsberger-Kassel-Marcus (RRKM) theory, together with ab initio quantum calculations where required, are used to estimate the following: recombination rate coefficients of Hg with Br, I, and O; the thermal dissociation rate coefficient of HgBr; and the recombination rate coefficients of HgBr with Br, I, OH, and O2. A mechanism based on the initial recombination of Hg with Br, followed by the addition of a second radical (Br, I, or OH) in competition with thermal dissociation of HgBr, is able to account for the observed rate of Hg0 removal, both in Arctic depletion events and at lower latitudes.

Plastics and other artificial materials pose new risks to the health of the ocean. Anthropogenic debris travels across large distances and is ubiquitous in the water and on shorelines, yet, observations of its sources, composition, pathways, and distributions in the ocean are very sparse and inaccurate. Total amounts of plastics and other man-made debris in the ocean and on the shore, temporal trends in these amounts under exponentially increasing production, as well as degradation processes, vertical fluxes, and time scales are largely unknown. Present ocean circulation models are not able to accurately simulate drift of debris because of its complex hydrodynamics. In this paper we discuss the structure of the future integrated marine debris observing system (IMDOS) that is required to provide long-term monitoring of the state of this anthropogenic pollution and support operational activities to mitigate impacts on the ecosystem and on the safety of maritime activity. The proposed observing system integrates remote sensing and in situ observations. Also, models are used to optimize the design of the system and, in turn, they will be gradually improved using the products of the system. Remote sensing technologies will provide spatially coherent coverage and consistent surveying time series at local to global scale. Optical sensors, including high-resolution imaging, multi-and hyperspectral, fluorescence, and Raman technologies, as well as SAR will be used to measure different types of debris. They will be implemented in a variety of platforms, from hand-held tools to ship-, buoy-, aircraft-, and satellite-based sensors. A network of in situ observations, including reports from volunteers, citizen scientists and ships of opportunity, will be developed to provide data for calibration/validation of remote sensors and to monitor the spread of plastic pollution and other marine debris. IMDOS will interact with other observing systems monitoring physical, chemical, and biological processes in the ocean and on shorelines as well as the state of the ecosystem, maritime activities and safety, drift of sea ice, etc. The synthesized data will support innovative multi-disciplinary research and serve a diverse community of users.

Three endemic vulture species Gyps bengalensis, Gyps indicus and Gyps tenuirostris are critically endangered following dramatic declines in South Asia resulting from exposure to diclofenac, a veterinary drug present in the livestock carcasses that they scavenge. Diclofenac is widely used globally and could present a risk to Gyps species from other regions. In this study, we test the toxicity of diclofenac to a Eurasian (Gyps fulvus) and an African (Gyps africanus) species, neither of which is threatened. A dose of 0.8 mg kg(-1) of diclofenac was highly toxic to both species, indicating that they are at least as sensitive to diclofenac as G. bengalensis, for which we estimate an LD50 of 0.1-0.2 mg kg(-1). We suggest that diclofenac is likely to be toxic to all eight Gyps species, and that G. africanus, which is phylogenetically close to G. bengalensis, would be a suitable surrogate for the safety testing of alternative drugs to diclofenac.

The shallow-water reef coral Goniastrea aspera Verill 1865 has previously been reported to demonstrate differences in within-colony susceptibility to bleaching at elevated sea temperatures; parts of the colony which are exposed to the highest solar radiation are more thermotolerant than areas which are less exposed. In this paper, we show that at elevated experimental sea temperature the 'high light' surfaces lose fewer symbiotic algae, have lower levels of oxidative stress, higher levels of host antioxidant-enzyme copper zinc superoxidase dismutase (CuZnSOD), and host heat-shock proteins 60 and 70, compared to the less exposed surfaces. In addition, 'high light' surfaces show less chronic photoinhibition and greater Photosystem II (PS II) recovery potential when exposed to high irradiance at ambient sea temperature. In contrast, no differences were noted in algal defences (e.g. antioxidant enzymes and stress protein production, and xanthophyll cycling) either at elevated or ambient temperatures. These results are noteworthy because they suggest that corals which acclimatise to high irradiance can, as a result, develop increased thermotolerance which may prevent bleaching at high sea temperatures. Importantly, they also demonstrate the significance of the host tissues in maintaining the intact symbiosis of G. aspera under thermal stress.

Gray, S. A., S. Gray, J. L. De Kok, A. E. R. Helfgott, B. O'Dwyer, R. Jordan, and A. Nyaki. 2015. Using fuzzy cognitive mapping as a participatory approach to analyze change, preferred states, and perceived resilience of social-ecological systems. Ecology and Society 20(2): 11. https://doi.org/10.5751/ES-07396-200211

RATIONALE: Exposure to particulate matter is associated with risk of cardiovascular events, possibly through endothelial dysfunction, and indoor air may be most important. OBJECTIVES: We investigated effects of controlled exposure to indoor air particles on microvascular function (MVF) as the primary endpoint and biomarkers of inflammation and oxidative stress as secondary endpoints in a healthy elderly population. METHODS: A total of 21 nonsmoking couples participated in a randomized, double-blind, crossover study with two consecutive 48-hour exposures to either particle-filtered or nonfiltered air (2,533-4,058 and 7,718-12,988 particles/cm(3), respectively) in their homes. MEASUREMENTS AND MAIN RESULTS: MVF was assessed noninvasively by measuring digital peripheral artery tone after arm ischemia. Secondary endpoints included hemoglobin, red blood cells, platelet count, coagulation factors, P-selectin, plasma amyloid A, C-reactive protein, fibrinogen, IL-6, tumor necrosis factor-alpha, protein oxidation measured as 2-aminoadipic semialdehyde in plasma, urinary 8-iso-prostaglandin F(2alpha), and blood pressure. Indoor air filtration significantly improved MVF by 8.1% (95% confidence interval, 0.4-16.3%), and the particulate matter (diameter < 2.5 mum) mass of the indoor particles was more important than the total number concentration (10-700 nm) for these effects. MVF was significantly associated with personal exposure to iron, potassium, copper, zinc, arsenic, and lead in the fine fraction. After Bonferroni correction, none of the secondary biomarkers changed significantly. CONCLUSIONS: Reduction of particle exposure by filtration of recirculated indoor air for only 48 hours improved MVF in healthy elderly citizens, suggesting that this may be a feasible way of reducing the risk of cardiovascular disease.

OBJECTIVE: This review provides an in-depth overview of diagnostic schema and risk factors influencing recovery during the acute, subacute (operationally defined as up to 3 months postinjury), and chronic injury phases across the full spectrum of individuals (e.g., athletes to neurosurgery patients) with mild traumatic brain injury (mTBI). Particular emphasis is placed on the complex differential diagnoses for patients with prolonged postconcussive symptoms. METHODS: Select literature review and synthesis. RESULTS: In spite of an increase in public awareness surrounding the acute and potential long-term effects of mTBI, the medical field remains fragmented both in terms of the diagnostic (different criteria proffered by multiple medical organizations) and prognostic factors that influence patient care. CONCLUSIONS: Given the lack of objective biomarkers and the spectrum of different disorders that likely encompass mTBI, clinicians are encouraged to adopt a probabilistic, rather than definitive, diagnostic and prognostic framework. The relevance of accurately diagnosing and managing the different manifestations of mTBI becomes clear when one considers the overall incidence of the disorder (42 million people each year worldwide), and the different treatment implications for patients with a true neurodegenerative disorder (e.g., chronic traumatic encephalopathy; rare) vs potentially treatable conditions (e.g., depression or posttraumatic headache; frequent).

Global environmental change has influenced lake surface temperatures, a key driver of ecosystem structure and function. Recent studies have suggested significant warming of water temperatures in individual lakes across many different regions around the world. However, the spatial and temporal coherence associated with the magnitude of these trends remains unclear. Thus, a global data set of water temperature is required to understand and synthesize global, long-term trends in surface water temperatures of inland bodies of water. We assembled a database of summer lake surface temperatures for 291 lakes collected in situ and/or by satellites for the period 1985-2009. In addition, corresponding climatic drivers (air temperatures, solar radiation, and cloud cover) and geomorphometric characteristics (latitude, longitude, elevation, lake surface area, maximum depth, mean depth, and volume) that influence lake surface temperatures were compiled for each lake. This unique dataset offers an invaluable baseline perspective on global-scale lake thermal conditions as environmental change continues.

Knowing how people think about public participation processes and knowing what people want from these processes is essential to crafting a legitimate and effective process and delivering a program that is widely viewed as meaningful and successful. This article reports on research to investigate the nature of diversity among participants' perceptions of what is the most appropriate public participation process for environmental assessment and decision making in 10 different cases. Results show that there are clearly distinct perspectives on what an appropriate public participation process should be. We identified four perspectives: Science‐Centered Stakeholder Consultation, Egalitarian Deliberation, Efficient Cooperation, and Informed Collaboration. The literature on public participation tends to presume that there are clear and universal criteria on how to “do” public participation correctly or that context is the critical factor. This study has revealed that even within a specific assessment or decision‐making effort, there may be different perspectives about what is viewed as appropriate, which poses a challenge for both theorists and practitioners. Among the active participants in these 10 case studies, we found limited agreement and strong differences of opinions for what is a good process. Points of consensus across these cases are that good processes reach out to all stakeholders, share information openly and readily, engage people in meaningful interaction, and attempt to satisfy multiple interest positions. Differences appeared about how strongly to emphasize science and information, how much leadership and direction the process needs, what is the proper behavior of participants, how to tackle issues of power and trust, and what are the outcome‐related goals of the process. These results challenge researchers and practitioners to consider the diversity of participant needs in addition to the broad context when conceptualizing or carrying out participatory processes.

Preface and acknowledgements. Answers to some important questions. Decision-making in ecotoxicology: science and society meet. Measuring ecotoxicological effects on populations, communities and ecosystems. Room for improvement. Integrated ecotoxicolgy: linking fate and effect within a biological hierarchy. Ecotoxicology: past, present and future. References. Tables. List of figure captions. Figures.

Photoacclimation was examined in the marine diatom Skeletonema costatum, which was subjected to reciprocal shifts between irradiances of 50 (low‐light) and 1,200 (high‐light) µmol photons m −2 s −1 . Cell chlorophyll a and fucoxanthin contents were higher but diadinoxanthin and diatoxanthin contents lower in cells grown at 50 µmol photons m −2 s −1 than in cells shifted to 1200 µmol photons m −2 s −1 . Cell carbon contents measured at the start of the light period were similar in both high‐light an low‐light treatments. However, by 6 h into the light period, the carbon contents in the high‐light cells were about twofold higher than in the low‐light cells. Dark respiration rates, dark Chl a synthesis rates, and dark cell‐division rates were greater in the high‐light acclimated cells than in the low‐light cells. Thus, there was a greater uncoupling of carbon assimilation from cell division during the day in the high‐light cells, but pigment synthesis and cell division continued in darkness. Cell‐specific, light saturated photosynthesis rates, and chlorophyll a specific lightlimited photosynthesis rates were constant during reciprocal shifts between growth irradiances of 50 and 1200 µmol photons m −2 s −1 . Thus, differences of photosynthesis versus irradiance curves between cells acclimated to high‐light versus low‐light could be accounted for largely in terms of changes in cell chlorophyll a contents. Although the chlorophyll a‐specific initial slope, α chl , was constant, the chlorophyll a‐specific light absorbtion coeffecient, a chl , increased and the maximum quantum efficiency of photosynthesis (φ m ) declined following the shift to high light. The increase of a chl was most likely due to a decreased package effect. The decline of φ m was most likely due to accumulation of xanthophyll cycle pigments. Carbon‐specific, light‐saturated photosynthesis rates were lower in high‐light than in low‐light cells; this observation may indicate that control of light‐saturated photosynthesis shifts from enzymes of the carbon dioxide reduction cycle (Calvin cycle) in low‐light cells to the photosynthetic electron transfer chain in high‐light cells.

PURPOSE: To continuously measure core temperature (T(c)) and heart rate(HR), and quantify fluid balance during a 21-km mass-participation road racein warm, humid environmental conditions. METHODS: Eighteen heat-acclimatized male soldiers ingested a telemetric Tc sensor on the evening prior to the race and wore an ambulatory T(c) data recorder and HR monitor during the race. Pre- to postrace changes in nude body mass quantified fluid balance. RESULTS: Environmental wet bulb globe temperature averaged 26.5 degrees C. All runners finished the race asymptomatic of heat illness in a mean +/- SD (range) time of 118 +/- 13 (105-146) min, corresponding to an average running speed of 10.8 +/- 1.1 (8.6-12.0) km.h(-1). All runners recorded peak T(c) > 39 degrees C; 56% (N = 10) > 40 degrees C; and 11% (N = 2) > 41 degrees C. Peak T(c) was 40.1 +/- 0.7 (39.3-41.7) degrees C at 86 +/- 36 (13-130) min, with T(c) 39.9 +/- 0.8 (38.3-41.7) degrees C at race finish. The magnitude of T(c) response was unrelated (P > 0.05) to running time or fluid balance (e.g., fluid intake, % dehydration). Cumulative heat strain index was 2790 +/- 1112 (1046-5144) units at race finish. CONCLUSION: Ingestible telemetric temperature sensors demonstrated utility for continuous measurement of T(c) during mass-participation running. Successful application of this technology has highlighted the magnitude and duration of T(c) elevation that runners will voluntarily achieve during mass-participation distance races in heat and high humidity without medical consequence.

Sustained observations are required to determine the marine plastic debris mass balance and to support effective policy for planning remedial action. However, observations currently remain scarce at the global scale. A satellite remote sensing system could make a substantial contribution to tackling this problem. Here, we make initial steps towards the potential design of such a remote sensing system by: (1) identifying the properties of marine plastic debris amenable to remote sensing methods and (2) highlighting the oceanic processes relevant to scientific questions about marine plastic debris. Remote sensing approaches are reviewed and matched to the optical properties of marine plastic debris and the relevant spatio-temporal scales of observation to identify challenges and opportunities in the field. Finally, steps needed to develop marine plastic debris detection by remote sensing platforms are proposed in terms of fundamental science as well as linkages to ongoing planning for satellite systems with similar observation requirements.

We report the design and synthesis of a red fluorescent AIE light-up probe for selective recognition, naked-eye detection, and image-guided photodynamic killing of Gram-positive bacteria, including vancomycin-resistant Enterococcus strains.