Proteomic method for the quantification of methionine sulfoxide

Glycoxidation and lipoxidation reactions contribute to the chemical modification of proteins during the Maillard reaction. Reactive oxygen species, produced during the oxidation of sugars and lipids in these processes, irreversibly oxidize proteins. Methionine is particularly susceptible to oxidation, yielding the oxidation product methionine sulfoxide (MetSO). Here we describe a method for the analysis of MetSO using proteomic techniques. Using these techniques, we measured MetSO formation on the model protein RNase during aerobic incubations with glucose and arachidonate. We also evaluated the susceptibility of MetSO to reduction by NaBH4, a commonly used reductant in the analysis of Maillard reaction products.

Agonist-dependent internalization of D2 receptors: Imaging quantification by confocal microscopy

In positron emission tomography and single photon emission computed tomography studies using D2 dopamine (DA) receptor radiotracers, a decrease in radiotracer binding potential (BP) is usually interpreted in terms of increased competition with synaptic DA. However, some data suggest that this signal may also reflect agonist (DA)-induced increases in D2 receptor (D2R) internalization, a process which would presumably also decrease the population of receptors available for binding to hydrophilic radioligands. To advance interpretation of alterations in D2 radiotracer BP, direct methods of assessment of D2R internalization are required. Here, we describe a confocal microscopy-based approach for the quantification of agonist-dependent receptor internalization. The method relies upon double-labeling of the receptors with antibodies directed against intracellular as well as extracellular epitopes. Following agonist stimulation, DA D2R internalization was quantified by differentiating, in optical cell sections, the signal due to the staining of the extracellular from intracellular epitopes of D2Rs. Receptor internalization was increased in the presence of the D2 agonists DA and bromocriptine, but not the D1 agonist SKF38393. Pretreatment with either the D2 antagonist sulpiride, or inhibitors of internalization (phenylarsine oxide and high molarity sucrose), blocked D2-agonist induced receptor internalization, thus validating this method in vitro. This approach therefore provides a direct and streamlined methodology for investigating the pharmacological and mechanistic aspects of D2R internalization, and should inform the interpretation of results from in vivo receptor imaging studies.

Quantification of boundary definition using pulsed terahertz radiation for wedged geometries

The interaction of a terahertz beam with a sample containing a material boundary across the profile of the terahertz beam produces characteristic spectroscopic detail. A full vectorial model is presented to quantify boundary definition for a series of wedged geometries. As a result of this work, using simple geometric forms, we wish to be able to extend these ideas to characterize boundaries in more irregular samples, impacting most application areas of pulsed terahertz radiation.

Quantification of mitochondrial DNA mutation load

Mitochondrial DNA (mtDNA) mutations are an important cause of genetic disease and have been proposed to play a role in the ageing process. Quantification of total mtDNA mutation load in ageing tissues is difficult as mutational events are rare in a background of wild-type molecules, and detection of individual mutated molecules is beyond the sensitivity of most sequencing based techniques. The methods currently most commonly used to document the incidence of mtDNA point mutations in ageing include post-PCR cloning, single-molecule PCR and the random mutation capture assay. The mtDNA mutation load obtained by these different techniques varies by orders of magnitude, but direct comparison of the three techniques on the same ageing human tissue has not been performed. We assess the procedures and practicalities involved in each of these three assays and discuss the results obtained by investigation of mutation loads in colonic mucosal biopsies from ten human subjects.

Transport impacts on atmosphere and climate: metrics

The transport sector emits a wide variety of gases and aerosols, with distinctly different characteristics which influence climate directly and indirectly via chemical and physical processes. Tools that allow these emissions to be placed on some kind of common scale in terms of their impact on climate have a number of possible uses such as: in agreements and emission trading schemes; when considering potential trade-offs between changes in emissions resulting from technological or operational developments; and/or for comparing the impact of different environmental impacts of transport activities. Many of the non-CO2 emissions from the transport sector are short-lived substances, not currently covered by the Kyoto Protocol. There are formidable difficulties in developing metrics and these are particularly acute for such short-lived species. One difficulty concerns the choice of an appropriate structure for the metric (which may depend on, for example, the design of any climate policy it is intended to serve) and the associated value judgements on the appropriate time periods to consider; these choices affect the perception of the relative importance of short- and long-lived species. A second difficulty is the quantification of input parameters (due to underlying uncertainty in atmospheric processes). In addition, for some transport-related emissions, the values of metrics (unlike the gases included in the Kyoto Protocol) depend on where and when the emissions are introduced into the atmosphere – both the regional distribution and, for aircraft, the distribution as a function of altitude, are important. In this assessment of such metrics, we present Global Warming Potentials (GWPs) as these have traditionally been used in the implementation of climate policy. We also present Global Temperature Change Potentials (GTPs) as an alternative metric, as this, or a similar metric may be more appropriate for use in some circumstances. We use radiative forcings and lifetimes from the literature to derive GWPs and GTPs for the main transport-related emissions, and discuss the uncertainties in these estimates. We find large variations in metric (GWP and GTP) values for NOx, mainly due to the dependence on location of emissions but also because of inter-model differences and differences in experimental design. For aerosols we give only global-mean values due to an inconsistent picture amongst available studies regarding regional dependence. The uncertainty in the presented metric values reflects the current state of understanding; the ranking of the various components with respect to our confidence in the given metric values is also given. While the focus is mostly on metrics for comparing the climate impact of emissions, many of the issues are equally relevant for stratospheric ozone depletion metrics, which are also discussed.

A simple, coherent framework for partitioning uncertainty in climate predictions

A simple and coherent framework for partitioning uncertainty in multi-model climate ensembles is presented. The analysis of variance (ANOVA) is used to decompose a measure of total variation additively into scenario uncertainty, model uncertainty and internal variability. This approach requires fewer assumptions than existing methods and can be easily used to quantify uncertainty related to model-scenario interaction - the contribution to model uncertainty arising from the variation across scenarios of model deviations from the ensemble mean. Uncertainty in global mean surface air temperature is quantified as a function of lead time for a subset of the Coupled Model Intercomparison Project phase 3 ensemble and results largely agree with those published by other authors: scenario uncertainty dominates beyond 2050 and internal variability remains approximately constant over the 21st century. Both elements of model uncertainty, due to scenario-independent and scenario-dependent deviations from the ensemble mean, are found to increase with time. Estimates of model deviations that arise as by-products of the framework reveal significant differences between models that could lead to a deeper understanding of the sources of uncertainty in multi-model ensembles. For example, three models are shown diverging pattern over the 21st century, while another model exhibits an unusually large variation among its scenario-dependent deviations.

Uncertainty in the relationship between climate forcing and hydrological response in UK catchments

This paper assesses the relationship between amount of climate forcing – as indexed by global mean temperature change – and hydrological response in a sample of UK catchments. It constructs climate scenarios representing different changes in global mean temperature from an ensemble of 21 climate models assessed in the IPCC AR4. The results show a considerable range in impact between the 21 climate models, with – for example - change in summer runoff at a 2oC increase in global mean temperature varying between -40% and +20%. There is evidence of clustering in the results, particularly in projected changes in summer runoff and indicators of low flows, implying that the ensemble mean is not an appropriate generalised indicator of impact, and that the standard deviation of responses does not adequately characterise uncertainty. The uncertainty in hydrological impact is therefore best characterised by considering the shape of the distribution of responses across multiple climate scenarios. For some climate model patterns, and some catchments, there is also evidence that linear climate change forcings produce non-linear hydrological impacts. For most variables and catchments, the effects of climate change are apparent above the effects of natural multi-decadal variability with an increase in global mean temperature above 1oC, but there are differences between catchments. Based on the scenarios represented in the ensemble, the effect of climate change in northern upland catchments will be seen soonest in indicators of high flows, but in southern catchments effects will be apparent soonest in measures of summer and low flows. The uncertainty in response between different climate model patterns is considerably greater than the range due to uncertainty in hydrological model parameterisation.

Uncertainty in climate change impacts on basin-scale freshwater resources – preface to the special issue: the QUEST-GSI methodology and synthesis of results

This paper presents a preface to this Special Issue on the results of the QUEST-GSI (Global Scale Impacts) project on climate change impacts on catchment-scale water resources. A detailed description of the unified methodology, subsequently used in all studies in this issue, is provided. The project method involved running simulations of catchment-scale hydrology using a unified set of past and future climate scenarios, to enable a consistent analysis of the climate impacts around the globe. These scenarios include "policy-relevant" prescribed warming scenarios. This is followed by a synthesis of the key findings. Overall, the studies indicate that in most basins the models project substantial changes to river flow, beyond that observed in the historical record, but that in many cases there is considerable uncertainty in the magnitude and sign of the projected changes. The implications of this for adaptation activities are discussed.