Rainfall and river flow ensemble verification: Phase 2. Final report

This document is the Final Report for the “Rainfall and River Flow Ensemble Verification: Phase 2” (EnsVerP2) project forming part of the project “Improving confidence in Flood Guidance through verification of rainfall and river flow ensembles”. Forecasting the weather and floods is a challenging task and inherently uncertain. Acknowledging and accounting for the uncertainty in precipitation and flood forecasts has become increasingly important. This has partly been driven by the move of warning and guidance services to risk-based approaches that combine the likelihood of flooding with its potential impact on society and the environment. In the UK, such risk-based approaches underpin the National Severe Weather Warning Service delivered by the Met Office, and the Flood Guidance Statements produced by the Flood Forecasting Centre (FFC) and Scottish Flood Forecasting Service (SFFS). A standard approach to accounting for forecast uncertainty is to use ensemble methods. For a number of years, FFC and SFFS have used precipitation ensembles coupled with the national Grid-to-Grid (G2G) model of river flow to underpin the Flood Guidance Statement. However, the performance of the overall end-to-end ensemble precipitation and river flow forecasting system is currently not verified routinely. This ensemble verification information and evidence is essential: its absence can limit end-user confidence and inhibit full exploitation for flood-risk guidance. In addition, the local flood forecasting systems - used by the Environment Agency (EA), Scottish Environment Protection Agency (SEPA) and Natural Resources Wales (NRW) - are planned to transition to ensemble forecasting and will have similar requirements for verification information. A first step in addressing this operational gap has been to bring together existing expertise in meteorological and hydrological model performance assessment to design and develop a new, holistic Ensemble Verification Framework. Then to consider how this Framework could be used to develop an operational end-end interactive Ensemble Forecast Visualisation and Verification System. The Framework has been designed so that the operational system developed from it would help forecasters answer the following two key questions. • How well has the ensemble precipitation and flood forecasting system performed in the (recent) past? Particularly for flood events of interest. • What does this mean for interpreting today’s forecast? Forecasters could then make more informed decisions and increase their confidence in the use of ensembles for forecasting the severity and likelihood of precipitation and flooding. To develop and test the potential verification approaches and operational displays, 16-months of precipitation and river flow ensemble forecasts have been processed and verified. Specific case-studies, identified with the help of stakeholders, have been used to prototype, demonstrate, assess and refine the verification tools. The Best Medium Range (BMR) precipitation ensemble is used as input to the national-scale G2G model of river flow across Great Britain and to a small selection of catchment-scale PDM local models of river flow. This approach has allowed rigorous scientific exploration of how to provide robust verification statistics of the ensemble precipitation inputs to the river flow modelling and of its ensemble river flow outputs. The scientific analysis allowed identification of several points relevant to the underpinning verification methodology part of the Framework. • Three different precipitation accumulation time-intervals were evaluated: 15 min (the temporal resolution of the river flow model and its precipitation inputs), hourly and daily. Daily precipitation accumulations appear to provide the best guidance in terms of rain volume for hydrological impacts. One reason for this may well be because it removes the impact of timing errors at the sub-daily scale. Sub-daily precipitation can be more closely related to river flow on an ensemble member-by-member basis. • The source of observed precipitation (raingauge, radar or merged raingauge-radar) has an impact on the verification analyses and G2G river flow performance. • The change in precipitation-intensity characteristics with lead-time between the STEPS, MOGREPS-UK and MOGREPS-G components of the BMR precipitation ensemble, are evident in both rainfall and river flow analysis. • The length of period used for ensemble verification is an important factor: generally longer than two years is recommended if possible. The 16-month test period was sufficient for generating enough precipitation threshold-exceedances for the 95th percentile thresholds: but insufficient for higher thresholds and for considering river flow thresholds above one half the median annual maximum flood at sub-regional scales. • New methods of presenting the precipitation forecast probabilities have been developed for precipitation thresholds that are hydrologically relevant. The verification of these Time-Window Probabilities (TWPs) has shown that the probabilities are larger, and also more reliable: so users can have greater confidence in using them. For new real-time displays to be of value in operational settings, it is important that users (e.g. FFC hydrometeorologists or flood forecasting officers) find the displays understandable and easy to deploy in support of flood guidance and warning. Operational users have been engaged in co-design of the real-time forecast displays through the Project Board and a Workshop. These interactions have identified that the real-time displays need to be flexible and informative, with varying layers of detail. Viewing the precipitation and river flow together, however, is the most important ingredient along with using common methods for conveying information on both. Prototype joint rainfall and river flow displays have been created. Further co-design of interactive displays is recommended during future implementation and interactions should include operational users, researchers and system developers. Case-studies have been used to highlight the potential benefits of these new real-time displays. They have demonstrated how the ensemble verification information can help users make more informed decisions when ensemble verification information is included. For example, knowing whether a forecast is over- or under-confident for different lead-times and severity-thresholds can be very helpful, particularly in marginal cases. That is if a forecast has a tendency to predict too high or low a probability of precipitation, or of river flow, exceeding a given level of severity. Summary and key recommendation: Realising the benefit and value of probabilistic flood-risk information for decision-making was a key motivator for the “Rainfall and River Flow Ensemble Verification: Phase 2” project. The project succeeded in bringing together the meteorology and hydrology to define, test and demonstrate a joint Ensemble Verification Framework for ensemble precipitation and river flow forecasts. The outcomes of the project demonstrate how the subsequent verification information can be used to enhance the user’s perception and ability to deploy ensemble forecasts and derived probabilities in day-to-day flood risk decision-making. Overall, the key finding is that joint precipitation and river flow ensemble verification is possible and useful. The primary recommendation is that an end-to-end interactive Ensemble Forecast Visualisation and Verification System for FFC (and SFFS) be implemented as soon as is practicable. The Ensemble Verification Framework provides the blueprint for the system and the Joint Coding Framework developed and applied here provides the basis for the algorithm and code. A detailed set of recommendations have been provided, including what is required for operational implementation. This also includes a priority list of recommendations for developing a minimum system. The proposed system would address the current urgent operational gap in ensemble forecast verification capability for FFC and SFFS. It would mark a significant addition to the forecasters’ toolkit by providing real-time displays that incorporate ensemble verification information for the first time, and in a usable form. In turn, this will facilitate enhanced and more informed decision-making at times of potential flood-risk. Local model systems have ensemble and probabilistic flood forecasting as an aspiration in their future plans. These systems would eventually benefit from the operationally urgent developments recommended here for the national-scale G2G model used by FFC and SFFS. Local model users could play an early and active part in system co-design as part of a staged implementation process for local model systems

Longitudinal exchange: an alternative strategy towards quantification of dynamics parameters in ZZ exchange spectroscopy

Longitudinal exchange experiments facilitate the quantification of the rates of interconversion between the exchanging species, along with their longitudinal relaxation rates, by analyzing the time-dependence of direct correlation and exchange cross peaks. Here we present a simple and robust alternative to this strategy, which is based on the combination of two complementary experiments, one with and one without resolving exchange cross peaks. We show that by combining the two data sets systematic errors that are caused by differential line-broadening of the exchanging species are avoided and reliable quantification of kinetic and relaxation parameters in the presence of additional conformational exchange on the ms–μs time scale is possible. The strategy is applied to a bistable DNA oligomer that displays different line-broadening in the two exchanging species

Anthropology in conversation with an Islamic tradition : Emmanuel Levinas and the practice of critique

Funded by the Carnegie Trust for the Universities of Scotland This research was funded by the Carnegie Trust for the Universities of Scotland. I would like to thank Arnar Arnason, Alison Brown, Tim Ingold, Jo Vergunst, and the anonymous JRAI readers for their critical feedback, which greatly improved the quality and coherence of this article.Peer reviewedPostprin

Visualizing spatially correlated dynamics that directs RNA conformational transitions

RNAs fold into three- dimensional ( 3D) structures that subsequently undergo large, functionally important, conformational transitions in response to a variety of cellular signals(1-3). RNA structures are believed to encode spatially tuned flexibility that can direct transitions along specific conformational pathways(4,5). However, this hypothesis has proved difficult to examine directly because atomic movements in complex biomolecules cannot be visualized in 3D by using current experimental methods. Here we report the successful implementation of a strategy using NMR that has allowed us to visualize, with complete 3D rotational sensitivity, the dynamics between two RNA helices that are linked by a functionally important trinucleotide bulge over timescales extending up to milliseconds. The key to our approach is to anchor NMR frames of reference onto each helix and thereby directly measure their dynamics, one relative to the other, using 'relativistic' sets of residual dipolar couplings ( RDCs)(6,7). Using this approach, we uncovered super- large amplitude helix motions that trace out a surprisingly structured and spatially correlated 3D dynamic trajectory. The two helices twist around their individual axes by approximately 536 and 1106 in a highly correlated manner ( R = 0.97) while simultaneously ( R = 0.81 - 0.92) bending by about 94 degrees. Remarkably, the 3D dynamic trajectory is dotted at various positions by seven distinct ligand- bound conformations of the RNA. Thus even partly unstructured RNAs can undergo structured dynamics that directs ligand- induced transitions along specific predefined conformational pathways.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62506/1/nature06389.pd

Accessing ns–μs side chain dynamics in ubiquitin with methyl RDCs

This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098–6107, 2001; Lakomek in J Biomol NMR 34:101–115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-τc dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type, distance to backbone and solvent exposure, and that considerable additional dynamics are effective at rates slower than the correlation time τc. In fact, the average amplitude of motion expressed in terms of order parameters S2 associated with the supra-τc window brings evidence to the existence of fluctuations contributing as much additional mobility as those already present in the faster ps-ns time scale measured from relaxation data. Comparison to previous results on ubiquitin demonstrates that the RDC-derived order parameters are dominated both by rotameric interconversions and faster libration-type motions around equilibrium positions. They match best with those derived from a combined J-coupling and residual dipolar coupling approach (Chou in J Am Chem Soc 125:8959–8966, 2003) taking backbone motion into account. In order to appreciate the dynamic scale of side chains over the entire protein, the methyl group order parameters are compared to existing dynamic ensembles of ubiquitin. Of those recently published, the broadest one, namely the EROS ensemble (Lange in Science 320:1471–1475, 2008), fits the collection of methyl group order parameters presented here best. Last, we used the MFA-derived averaged spherical harmonics to perform highly-parameterized rotameric searches of the side chains conformation and find expanded rotamer distributions with excellent fit to our data. These rotamer distributions suggest the presence of concerted motions along the side chains

Mathematical treatment of adiabatic fast passage pulses for the computation of nuclear spin relaxation rates in proteins with conformational exchange

Although originally designed for broadband inversion and decoupling in NMR spectroscopy, recent methodological developments have introduced adiabatic fast passage (AFP) pulses into the field of protein dynamics. AFP pulses employ a frequency sweep, and have not only superior inversion properties with respect to offset effects, but they are also easily implemented into a pulse sequence. As magnetization is dragged from the +z to the −z direction, Larmor precession is impeded since magnetization becomes spin-locked, which is a potentially useful feature for the investigation of microsecond to millisecond dynamics. A major drawback of these pulses as theoretical prediction is concerned, however, results from their time-dependent offset: simulations of spin density matrices under the influence of a time-dependent Hamiltonian with non-commuting elements are costly in terms of computational time, rendering data analysis impracticable. In this paper we suggest several ways to reduce the computational time without compromising accuracy with respect to effects such as cross-correlated relaxation and modulation of the chemical shift

Probing Microsecond Time Scale Dynamics in Proteins by Methyl 1H Carr−Purcell−Meiboom−Gill Relaxation Dispersion NMR Measurements. Application to Activation of the Signaling Protein NtrCr

To study microsecond processes by relaxation dispersion NMR spectroscopy, low power deposition and short pulses are crucial and encourage the development of experiments that employ H-1 Carr-Purcell-Meiboom-Gill (CPMG) pulse trains. Herein, a method is described for the comprehensive study of microsecond to millisecond time scale dynamics of methyl groups in proteins, exploiting their high abundance and favorable relaxation properties. In our approach, protein samples are produced using [H-1, C-13]-D-glucose in similar to 100% D2O, which yields CHD2 methyl groups for alanine, valine, threonine, isoleucine, leucine, and methionine residues with high abundance, in an otherwise largely deuterated background. Methyl groups in such samples can be sequence-specifically assigned to near completion, using C-13 TOCSY NMR spectroscopy, as was recently demonstrated (Often, R.; et al. J. Am. Chem. Soc. 2010, 132, 2952-2960). In this Article, NMR pulse schemes are presented to measure H-1 CPMG relaxation dispersion profiles for CHD2 methyl groups, in a vein similar to that of backbone relaxation experiments. Because of the high deuteration level of methyl-bearing side chains, artifacts arising from proton scalar coupling during the CPMG pulse train are negligible, with the exception of Ile-delta 1 and Thr-gamma 2 methyl groups, and a pulse scheme is described to remove the artifacts for those residues. Strong C-13 scalar coupling effects, observed for several leucine residues, are removed by alternative biochemical and NMR approaches. The methodology is applied to the transcriptional activator NtrC(r), for which an inactive/active state transition was previously measured and the motions in the microsecond time range were estimated through a combination of backbone N-15 CPMG dispersion NMR spectroscopy and a collection of experiments to determine the exchange-free component to the transverse relaxation rate. Exchange contributions to the H-1 line width were detected for 21 methyl groups, and these probes were found to collectively report on a local structural rearrangement around the phosphorylation site, with a rate constant of (15.5 +/- 0.5) x 10(3) per second (i.e., tau(ex) = 64.7 +/- 1.9 mu s). The affected methyl groups indicate that, already before phosphorylation, a substantial, transient rearrangement takes place between helices 3 and 4 and strands 4 and 5. This conformational equilibrium allows the protein to gain access to the active, signaling state in the absence of covalent modification through a shift in a pre-existing dynamic equilibrium. Moreover, the conformational switching maps exactly to the regions that differ between the solution NMR structures of the fully inactive and active states. These results demonstrate that a cost-effective and quantitative study of protein methyl group dynamics by H-1 CPMG relaxation dispersion NMR spectroscopy is possible and can be applied to study functional motions on the microsecond time scale that cannot be accessed by backbone N-15 relaxation dispersion NMR. The use of methyl groups as dynamics probes extends such applications also to larger proteins

Determination of Conformational Equilibria in Proteins Using Residual Dipolar Couplings

In order to carry out their functions, proteins often undergo significant conformational fluctuations that enable them to interact with their partners. The accurate characterization of these motions is key in order to understand the mechanisms by which macromolecular recognition events take place. Nuclear magnetic resonance spectroscopy offers a variety of powerful methods to achieve this result. We discuss a method of using residual dipolar couplings as replica-averaged restraints in molecular dynamics simulations to determine large amplitude motions of proteins, including those involved in the conformational equilibria that are established through interconversions between different states. By applying this method to ribonuclease A, we show that it enables one to characterize the ample fluctuations in interdomain orientations expected to play an important functional role

Manipulating Protein Conformations By Single-molecule Afm-fret Nanoscopy

Combining atomic force microscopy and fluorescence resonance energy transfer spectroscopy (AFM-FRET), we have developed a single-molecule AFM-FRET nanoscopy approach capable of effectively pinpointing and mechanically manipulating a targeted dye-labeled single protein in a large sampling area and simultaneously monitoring the conformational changes of the targeted protein by recording single-molecule FRET time trajectories. We have further demonstrated an application of using this nanoscopy on manipulation of single-molecule protein conformation and simultaneous single-molecule FRET measurement of a Cy3-Cy5-labeled kinase enzyme, HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase). By analyzing time-resolved FRET trajectories and correlated AFM force pulling curves of the targeted single-molecule enzyme, we are able to observe the protein conformational changes of a specific coordination by AFM mechanic force pulling