@article{12633, abstract = {We use two hydrological models of varying complexity to study the Juncal River Basin in the Central Andes of Chile with the aim to understand the degree of conceptualization and the spatial structure that are needed to model present and future streamflows. We use a conceptual semi-distributed model based on elevation bands [Water Evaluation and Planning (WEAP)], frequently used for water management, and a physically oriented, fully distributed model [Topographic Kinematic Wave Approximation and Integration ETH Zurich (TOPKAPI-ETH)] developed for research purposes mainly. We evaluate the ability of the two models to reproduce the key hydrological processes in the basin with emphasis on snow accumulation and melt, streamflow and the relationships between internal processes. Both models are capable of reproducing observed runoff and the evolution of Moderate-resolution Imaging Spectroradiometer snow cover adequately. In spite of WEAP's simple and conceptual approach for modelling snowmelt and its lack of glacier representation and snow gravitational redistribution as well as a proper routing algorithm, this model can reproduce historical data with a similar goodness of fit as the more complex TOPKAPI-ETH. We show that the performance of both models can be improved by using measured precipitation gradients of higher temporal resolution. In contrast to the good performance of the conceptual model for the present climate, however, we demonstrate that the simplifications in WEAP lead to error compensation, which results in different predictions in simulated melt and runoff for a potentially warmer future climate. TOPKAPI-ETH, using a more physical representation of processes, depends less on calibration and thus is less subject to a compensation of errors through different model components. Our results show that data obtained locally in ad hoc short-term field campaigns are needed to complement data extrapolated from long-term records for simulating changes in the water cycle of high-elevation catchments but that these data can only be efficiently used by a model applying a spatially distributed physical representation of hydrological processes.}, author = {Ragettli, S. and Cortés, G. and McPhee, J. and Pellicciotti, Francesca}, issn = {0885-6087}, journal = {Hydrological Processes}, keywords = {Water Science and Technology}, number = {23}, pages = {5674--5695}, publisher = {Wiley}, title = {{An evaluation of approaches for modelling hydrological processes in high-elevation, glacierized Andean watersheds}}, doi = {10.1002/hyp.10055}, volume = {28}, year = {2013}, } @article{12638, abstract = {Central Asian water resources largely depend on melt water generated in the Pamir and Tien Shan mountain ranges. To estimate future water availability in this region, it is necessary to use climate projections to estimate the future glacier extent and volume. In this study, we evaluate the impact of uncertainty in climate change projections on the future glacier extent in the Amu and Syr Darya river basins. To this end we use the latest climate change projections generated for the upcoming IPCC report (CMIP5) and, for comparison, projections used in the fourth IPCC assessment (CMIP3). With these projections we force a regionalized glacier mass balance model, and estimate changes in the basins' glacier extent as a function of the glacier size distribution in the basins and projected temperature and precipitation. This glacier mass balance model is specifically developed for implementation in large scale hydrological models, where the spatial resolution does not allow for simulating individual glaciers and data scarcity is an issue. Although the CMIP5 ensemble results in greater regional warming than the CMIP3 ensemble and the range in projections for temperature as well as precipitation is wider for the CMIP5 than for the CMIP3, the spread in projections of future glacier extent in Central Asia is similar for both ensembles. This is because differences in temperature rise are small during periods of maximum melt (July–September) while differences in precipitation change are small during the period of maximum accumulation (October–February). However, the model uncertainty due to parameter uncertainty is high, and has roughly the same importance as uncertainty in the climate projections. Uncertainty about the size of the decline in glacier extent remains large, making estimates of future Central Asian glacier evolution and downstream water availability uncertain.}, author = {Lutz, A. F. and Immerzeel, W. W. and Gobiet, A. and Pellicciotti, Francesca and Bierkens, M. F. P.}, issn = {1607-7938}, journal = {Hydrology and Earth System Sciences}, keywords = {General Earth and Planetary Sciences, General Engineering, General Environmental Science}, number = {9}, pages = {3661--3677}, publisher = {Copernicus GmbH}, title = {{Comparison of climate change signals in CMIP3 and CMIP5 multi-model ensembles and implications for Central Asian glaciers}}, doi = {10.5194/hess-17-3661-2013}, volume = {17}, year = {2013}, } @article{12639, abstract = {In the headwater catchments of the main Asian rivers, glaciohydrological models are a useful tool to anticipate impacts of climatic changes. However, the reliability of their projections strongly depends on the quality and quantity of data that are available for parameter estimation, model calibration and validation, as well as on the accuracy of climate change projections. In this study the physically oriented, glaciohydrological model TOPKAPI-ETH is used to simulate future changes in snow, glacier, and runoff from the Hunza River Basin in northern Pakistan. Three key sources of model uncertainty in future runoff projections are compared: model parameters, climate projections, and natural climate variability. A novel approach, applicable also to ungauged catchments, is used to determine which model parameters and model components significantly affect the overall model uncertainty. We show that the model is capable of reproducing streamflow and glacier mass balances, but that all analyzed sources of uncertainty significantly affect the reliability of future projections, and that their effect is variable in time and in space. The effect of parametric uncertainty often exceeds the impact of climate uncertainty and natural climate variability, especially in heavily glacierized subcatchments. The results of the uncertainty analysis allow detailed recommendations on network design and the timing and location of field measurements, which could efficiently help to reduce model uncertainty in the future.}, author = {Ragettli, S. and Pellicciotti, Francesca and Bordoy, R. and Immerzeel, W. W.}, issn = {0043-1397}, journal = {Water Resources Research}, keywords = {Water Science and Technology}, number = {9}, pages = {6048--6066}, publisher = {American Geophysical Union}, title = {{Sources of uncertainty in modeling the glaciohydrological response of a Karakoram watershed to climate change}}, doi = {10.1002/wrcr.20450}, volume = {49}, year = {2013}, } @article{12640, abstract = {Greater Himalayan glaciers are retreating and losing mass at rates comparable to glaciers in other regions of the world1,2,3,4,5. Assessments of future changes and their associated hydrological impacts are scarce, oversimplify glacier dynamics or include a limited number of climate models6,7,8,9. Here, we use results from the latest ensemble of climate models in combination with a high-resolution glacio-hydrological model to assess the hydrological impact of climate change on two climatically contrasting watersheds in the Greater Himalaya, the Baltoro and Langtang watersheds that drain into the Indus and Ganges rivers, respectively. We show that the largest uncertainty in future runoff is a result of variations in projected precipitation between climate models. In both watersheds, strong, but highly variable, increases in future runoff are projected and, despite the different characteristics of the watersheds, their responses are surprisingly similar. In both cases, glaciers will recede but net glacier melt runoff is on a rising limb at least until 2050. In combination with a positive change in precipitation, water availability during this century is not likely to decline. We conclude that river basins that depend on monsoon rains and glacier melt will continue to sustain the increasing water demands expected in these areas10.}, author = {Immerzeel, W. W. and Pellicciotti, Francesca and Bierkens, M. F. P.}, issn = {1752-0908}, journal = {Nature Geoscience}, keywords = {General Earth and Planetary Sciences}, number = {9}, pages = {742--745}, publisher = {Springer Nature}, title = {{Rising river flows throughout the twenty-first century in two Himalayan glacierized watersheds}}, doi = {10.1038/ngeo1896}, volume = {6}, year = {2013}, } @article{12641, abstract = {We investigate the sensitivity of a distributed enhanced temperature-index (ETI) melt model, in order to understand which parameters have the largest influence on model outputs and thus need to be accurately known. We use melt and meteorological data from two Alpine glaciers and one glacier in the Andes of Chile. Sensitivity analysis is conducted in a systematic way in terms of parameters and the different conditions (day, night, clear-sky, overcast), melt seasons and glaciers examined. The sensitivity of total melt to changes in individual parameters is calculated using a local method around the optimal value of the parameters. We verify that the parameters are optimal at the distributed scale and assess the model uncertainty induced by uncertainty in the parameters using a Monte Carlo technique. Model sensitivity to parameters is consistent across melt seasons, glaciers, different conditions and the daily statistics examined. The parameters to which the model is most sensitive are the shortwave-radiation factor, the temperature lapse rate for extrapolation of air temperature, the albedo parameters, the temperature threshold and the cloud transmittance factor parameters. A parameter uncertainty of 5% results in a model uncertainty of 5.6% of mean melt on Haut Glacier d’Arolla, Switzerland.}, author = {Heynen, Martin and Pellicciotti, Francesca and Carenzo, Marco}, issn = {1727-5644}, journal = {Annals of Glaciology}, number = {63}, pages = {311--321}, publisher = {International Glaciological Society}, title = {{Parameter sensitivity of a distributed enhanced temperature-index melt model}}, doi = {10.3189/2013aog63a537}, volume = {54}, year = {2013}, } @article{12642, abstract = {Near-surface air temperature, typically measured at a height of 2 m, is the most important control on the energy exchange and the melt rate at a snow or ice surface. It is distributed in a simplistic manner in most glacier melt models by using constant linear lapse rates, which poorly represent the actual spatial and temporal variability of air temperature. In this paper, we test a simple thermodynamic model proposed by Greuell and Böhm in 1998 as an alternative, using a new dataset of air temperature measurements from along the flowline of Haut Glacier d’Arolla, Switzerland. The unmodified model performs little better than assuming a constant linear lapse rate. When modified to allow the ratio of the boundary layer height to the bulk heat transfer coefficient to vary along the flowline, the model matches measured air temperatures better, and a further reduction of the root-mean-square error is obtained, although there is still considerable scope for improvement. The modified model is shown to perform best under conditions favourable to the development of katabatic winds – few clouds, positive ambient air temperature, limited influence of synoptic or valley winds and a long fetch – but its performance is poor under cloudy conditions.}, author = {Petersen, Lene and Pellicciotti, Francesca and Juszak, Inge and Carenzo, Marco and Brock, Ben}, issn = {1727-5644}, journal = {Annals of Glaciology}, keywords = {Earth-Surface Processes}, number = {63}, pages = {120--130}, publisher = {International Glaciological Society}, title = {{Suitability of a constant air temperature lapse rate over an Alpine glacier: Testing the Greuell and Böhm model as an alternative}}, doi = {10.3189/2013aog63a477}, volume = {54}, year = {2013}, } @article{12643, abstract = {Parameterizations of incoming longwave radiation are increasingly receiving attention for both low and high elevation glacierized sites. In this paper, we test 13 clear-sky parameterizations combined with seven cloud corrections for all-sky atmospheric emissivity at one location on Haut Glacier d'Arolla. We also analyze the four seasons separately and conduct a cross-validation to test the parameters’ robustness. The best parameterization is the one by Dilley and O'Brien, B for clear-sky conditions combined with Unsworth and Monteith cloud correction. This model is also the most robust when tested in cross-validation. When validated at different sites in the southern Alps of Switzerland and north-western Italian Alps, all parameterizations show a substantial decrease in performance, except for one site, thus suggesting that it is important to recalibrate parameterizations of incoming longwave radiation for different locations. We argue that this is due to differences in the structure of the atmosphere at the sites. We also quantify the effect that the incoming longwave radiation parameterizations have on energy-balance melt modeling, and show that recalibration of model parameters is needed. Using parameters from other sites leads to a significant underestimation of melt and to an error that is larger than that associated with using different parameterizations. Once recalibrated, however, the parameters of most models seem to be stable over seasons and years at the location on Haut Glacier d'Arolla.}, author = {Juszak, I. and Pellicciotti, Francesca}, issn = {2169-897X}, journal = {Journal of Geophysical Research: Atmospheres}, keywords = {Space and Planetary Science, Earth and Planetary Sciences (miscellaneous), Atmospheric Science, Geophysics}, number = {8}, pages = {3066--3084}, publisher = {American Geophysical Union}, title = {{A comparison of parameterizations of incoming longwave radiation over melting glaciers: Model robustness and seasonal variability}}, doi = {10.1002/jgrd.50277}, volume = {118}, year = {2013}, } @article{1304, abstract = {When confronted with a large-field stimulus rotating around the vertical body axis, flies display a following behavior called "optomotor response." As neural control elements, the large tangential horizontal system (HS) cells of the lobula plate have been prime candidates for long. Here, we applied optogenetic stimulation of HS cells to evaluate their behavioral role in Drosophila. To minimize interference of the optical activation of channelrhodopsin-2 with the visual perception of the flies, we used a bistable variant called ChR2-C128S. By applying pulses of blue and yellow light, we first demonstrate electrophysiologically that lobula plate tangential cells can be activated and deactivated repeatedly with no evident change in depolarization strength over trials. We next show that selective optogenetic activation of HS cells elicits robust yaw head movements and yaw turning responses in fixed and tethered flying flies, respectively.}, author = {Haikala, Väinö and Maximilian Jösch and Borst, Alexander and Mauss, Alex S}, journal = {Journal of Neuroscience}, number = {34}, pages = {13927 -- 13934}, publisher = {Society for Neuroscience}, title = {{Optogenetic control of fly optomotor responses}}, doi = {10.1523/JNEUROSCI.0340-13.2013}, volume = {33}, year = {2013}, } @article{1305, abstract = {In the fly Drosophila melanogaster, photoreceptor input to motion vision is split into two parallel pathways as represented by first-order interneurons L1 and L2 (Rister et al., 2007; Joesch et al., 2010). However, how these pathways are functionally specialized remains controversial. One study (Eichner et al., 2011) proposed that the L1-pathway evaluates only sequences of brightness increments (ON-ON), while the L2-pathway processes exclusively brightness decrements (OFF-OFF). Another study (Clark et al., 2011) proposed that each of the two pathways evaluates both ON-ON and OFF-OFF sequences. To decide between these alternatives, we recorded from motionsensitive neurons in flies in which the output from either L1 or L2 was genetically blocked. We found that blocking L1 abolishes ON-ON responses but leaves OFF-OFF responses intact. The opposite was true, when the output from L2 was blocked. We conclude that the L1 and L2 pathways are functionally specialized to detect ON-ON and OFF-OFF sequences, respectively.}, author = {Maximilian Jösch and Weber, Franz and Eichner, Hubert and Borst, Alexander}, journal = {Journal of Neuroscience}, number = {3}, pages = {902 -- 905}, publisher = {Society for Neuroscience}, title = {{Functional specialization of parallel motion detection circuits in the fly}}, doi = {10.1523/JNEUROSCI.3374-12.2013}, volume = {33}, year = {2013}, } @article{1307, abstract = {We prove uniqueness of solutions of the DLSS equation in a class of sufficiently regular functions. The global weak solutions of the DLSS equation constructed by Jüngel and Matthes belong to this class of uniqueness. We also show uniqueness of solutions for the quantum drift-diffusion equation, which contains additional drift and second-order diffusion terms. The results hold in case of periodic or Dirichlet-Neumann boundary conditions. Our proof is based on a monotonicity property of the DLSS operator and sophisticated approximation arguments; we derive a PDE satisfied by the pointwise square root of the solution, which enables us to exploit the monotonicity property of the operator.}, author = {Julian Fischer}, journal = {Communications in Partial Differential Equations}, number = {11}, pages = {2004 -- 2047}, publisher = {Taylor & Francis}, title = {{Uniqueness of solutions of the Derrida-Lebowitz-Speer-Spohn equation and quantum drift diffusion models}}, doi = {10.1080/03605302.2013.823548}, volume = {38}, year = {2013}, } @article{1308, abstract = {We derive sufficient conditions for advection-driven backward motion of the free boundary in a chemotaxis model with degenerate mobility. In this model, a porous-medium-type diffusive term and an advection term are in competition. The former induces forward motion, the latter may induce backward motion of the free boundary depending on the direction of advection. We deduce conditions on the growth of the initial data at the free boundary which ensure that at least initially the advection term is dominant. This implies local backward motion of the free boundary provided the advection is (locally) directed appropriately. Our result is based on a new class of moving test functions and Stampacchia's lemma. As a by-product of our estimates, we obtain quantitative bounds on the spreading of the support of solutions for the chemotaxis model and provide a proof for the finite speed of the support propagation property of solutions.}, author = {Julian Fischer}, journal = {SIAM Journal on Mathematical Analysis}, number = {3}, pages = {1585 -- 1615}, publisher = {Society for Industrial and Applied Mathematics }, title = {{Advection-driven support shrinking in a chemotaxis model with degenerate mobility}}, doi = {10.1137/120874291}, volume = {45}, year = {2013}, } @article{1310, abstract = {We derive lower bounds on asymptotic support propagation rates for strong solutions of the Cauchy problem for the thin-film equation. The bounds coincide up to a constant factor with the previously known upper bounds and thus are sharp. Our results hold in case of at most three spatial dimensions and n∈. (1, 2.92). The result is established using weighted backward entropy inequalities with singular weight functions to yield a differential inequality; combined with some entropy production estimates, the optimal rate of propagation is obtained. To the best of our knowledge, these are the first lower bounds on asymptotic support propagation rates for higher-order nonnegativity-preserving parabolic equations.}, author = {Julian Fischer}, journal = {Journal of Differential Equations}, number = {10}, pages = {3127 -- 3149}, publisher = {Academic Press}, title = {{Optimal lower bounds on asymptotic support propagation rates for the thin-film equation}}, doi = {10.1016/j.jde.2013.07.028}, volume = {255}, year = {2013}, } @article{8245, abstract = {Background: Monoclonal antibodies (mAb), such as trastuzumab are a valuable addition to breast cancer therapy. Data obtained from neoadjuvant settings revealed that antibody-dependent cell-mediated cytotoxicity (ADCC) is a major mechanism of action for the mAb trastuzumab. Conflicting results still call into question whether disease progression, prolonged treatment or concomitant chemotherapy influences ADCC and related immunological phenomena. Methods: We analyzed the activity of ADCC and antibody-dependent cell-mediated phagocytosis (ADCP) of peripheral blood mononuclear cells (PBMCs) from human epidermal growth factor receptor 2 (HER2/neu) positive breast cancer patients receiving trastuzumab therapy either in an adjuvant (n = 13) or metastatic (n = 15) setting as well as from trastuzumab treatment-naive (t-naive) HER2/neu negative patients (n = 15). PBMCs from healthy volunteers (n = 24) were used as controls. ADCC and ADCP activity was correlated with the expression of antibody binding Fc-gamma receptor (FcγR)I (CD64), FcγRII (CD32) and FcγRIII (CD16) on CD14+ (monocytes) and CD56+ (NK) cells, as well as the expression of CD107a+ (LAMP-1) on CD56+ cells and the total amount of CD4+CD25+FOXP3+ (Treg) cells. In metastatic patients, markers were correlated with progression-free survival (PFS). Results: ADCC activity was significantly down regulated in metastatic, adjuvant and t-naive patient cohorts as compared to healthy controls. Reduced ADCC activity was inversely correlated with the expression of CD107a on CD56+ cells in adjuvant patients. ADCC and ADCP activity of the patient cohorts were similar, regardless of treatment duration or additional chemotherapy. PFS in metastatic patients inversely correlated with the number of peripheral Treg cells. Conclusion: The reduction of ADCC in patients as compared to healthy controls calls for adjuvant strategies, such as immune-enhancing agents, to improve the activity of trastuzumab. However, efficacy of trastuzumab-specific ADCC and ADCP appears not to be affected by treatment duration, disease progression or concomitant chemotherapy. This finding supports the application of trastuzumab at any stage of the disease.}, author = {Petricevic, Branka and Laengle, Johannes and Singer, Josef and Sachet, Monika and Fazekas, Judit and Steger, Guenther and Bartsch, Rupert and Jensen-Jarolim, Erika and Bergmann, Michael}, issn = {1479-5876}, journal = {Journal of Translational Medicine}, publisher = {Springer Nature}, title = {{Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients}}, doi = {10.1186/1479-5876-11-307}, volume = {11}, year = {2013}, } @article{827, abstract = {As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed.}, author = {O'Brien, José and Benková, Eva}, journal = {Frontiers in Plant Science}, publisher = {Frontiers Research Foundation}, title = {{Cytokinin cross talking during biotic and abiotic stress responses}}, doi = {10.3389/fpls.2013.00451}, volume = {4}, year = {2013}, } @article{828, abstract = {The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed.}, author = {Cuesta, Candela and Wabnik, Krzysztof T and Benková, Eva}, journal = {Frontiers in Plant Science}, publisher = {Frontiers Research Foundation}, title = {{Systems approaches to study root architecture dynamics}}, doi = {10.3389/fpls.2013.00537}, volume = {4}, year = {2013}, } @article{830, abstract = {Upon hormonal signaling, ovules develop as lateral organs from the placenta. Ovule numbers ultimately determine the number of seeds that develop, and thereby contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule primordia formation. We show that expression of the CUC1 and CUC2 genes is required to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required for ovule primordia formation. Furthermore, our results suggest that the auxin response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and promote their transcription. Based on our findings, we propose an integrative model to describe the molecular mechanisms of the early stages of ovule development.}, author = {Galbiati, Francesca and Sinha Roy, Dola and Simonini, Sara and Cucinotta, Mara and Ceccato, Luca and Cuesta, Candela and Šimášková, Mária and Benková, Eva and Kamiuchi, Yuri and Aida, Mitsuhiro and Weijers, Dolf and Simon, Rüdiger and Masiero, Simona and Colombo, Lucia}, journal = {The Plant journal for cell and molecular biology}, number = {3}, pages = {446 -- 455}, publisher = {Wiley-Blackwell}, title = {{An integrative model of the control of ovule primordia formation}}, doi = {10.1111/tpj.12309}, volume = {76}, year = {2013}, } @article{831, abstract = {In Arabidopsis, lateral roots originate from pericycle cells deep within the primary root. New lateral root primordia (LRP) have to emerge through several overlaying tissues. Here, we report that auxin produced in new LRP is transported towards the outer tissues where it triggers cell separation by inducing both the auxin influx carrier LAX3 and cell-wall enzymes. LAX3 is expressed in just two cell files overlaying new LRP. To understand how this striking pattern of LAX3 expression is regulated, we developed a mathematical model that captures the network regulating its expression and auxin transport within realistic three-dimensional cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression to be robust to natural variations in root tissue geometry, an efflux carrier is required--later identified to be PIN3. To prevent LAX3 from being transiently expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively, which we later demonstrated to be the case. Our study exemplifies how mathematical models can be used to direct experiments to elucidate complex developmental processes.}, author = {Péret, Benjamin and Middleton, Alistair M and French, Andrew P and Larrieu, Antoine and Bishopp, Anthony and Njo, Maria and Wells, Darren M and Porco, Silvana and Mellor, Nathan and Band, Leah R and Casimiro, Ilda and Kleine-Vehn, Jürgen and Vanneste, Steffen and Sairanen, Ilkka and Mallet, Romain and Sandberg, Göran and Ljung, Karin and Beeckman, Tom and Eva Benková and Jirí Friml and Kramer, Eric and King, John R and De Smet, Ive and Pridmore, Tony and Owen, Markus and Bennett, Malcolm J}, journal = {Molecular Systems Biology}, publisher = {Nature Publishing Group}, title = {{Sequential induction of auxin efflux and influx carriers regulates lateral root emergence}}, doi = {10.1038/msb.2013.43}, volume = {9}, year = {2013}, } @article{8461, abstract = {Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps–μs motions in proteins by solid-state NMR.}, author = {Haller, Jens D. and Schanda, Paul}, issn = {0925-2738}, journal = {Journal of Biomolecular NMR}, keywords = {Spectroscopy, Biochemistry}, number = {3}, pages = {263--280}, publisher = {Springer Nature}, title = {{Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin}}, doi = {10.1007/s10858-013-9787-x}, volume = {57}, year = {2013}, } @article{8462, abstract = {The transition of proteins from their soluble functional state to amyloid fibrils and aggregates is associated with the onset of several human diseases. Protein aggregation often requires some structural reshaping and the subsequent formation of intermolecular contacts. Therefore, the study of the conformation of excited protein states and their ability to form oligomers is of primary importance for understanding the molecular basis of amyloid fibril formation. Here, we investigated the oligomerization processes that occur along the folding of the amyloidogenic human protein β2-microglobulin. The combination of real-time two-dimensional NMR data with real-time small-angle X-ray scattering measurements allowed us to derive thermodynamic and kinetic information on protein oligomerization of different conformational states populated along the folding pathways. In particular, we could demonstrate that a long-lived folding intermediate (I-state) has a higher propensity to oligomerize compared to the native state. Our data agree well with a simple five-state kinetic model that involves only monomeric and dimeric species. The dimers have an elongated shape with the dimerization interface located at the apical side of β2-microglobulin close to Pro32, the residue that has a trans conformation in the I-state and a cis conformation in the native (N) state. Our experimental data suggest that partial unfolding in the apical half of the protein close to Pro32 leads to an excited state conformation with enhanced propensity for oligomerization. This excited state becomes more populated in the transient I-state due to the destabilization of the native conformation by the trans-Pro32 configuration.}, author = {Rennella, E. and Cutuil, T. and Schanda, Paul and Ayala, I. and Gabel, F. and Forge, V. and Corazza, A. and Esposito, G. and Brutscher, B.}, issn = {0022-2836}, journal = {Journal of Molecular Biology}, keywords = {Molecular Biology}, number = {15}, pages = {2722--2736}, publisher = {Elsevier}, title = {{Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure}}, doi = {10.1016/j.jmb.2013.04.028}, volume = {425}, year = {2013}, } @article{894, abstract = {Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons. Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene. Conclusions: Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.}, author = {Derelle, Romain and Kondrashov, Fyodor and Arkhipov, Vladimir and Corbel, Hélène and Frantz, Adrien and Gasparini, Julien and Jacquin, Lisa and Jacob, Gwenaël and Thibault, Sophie and Baudry, Emmanuelle}, journal = {BMC Research Notes}, number = {1}, publisher = {BioMed Central}, title = {{Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R}}, doi = {10.1186/1756-0500-6-310}, volume = {6}, year = {2013}, }