TY - JOUR AB - Plants maintain capacity to form new organs such as leaves, flowers, lateral shoots and roots throughout their postembryonic lifetime. Lateral roots (LRs) originate from a few pericycle cells that acquire attributes of founder cells (FCs), undergo series of anticlinal divisions, and give rise to a few short initial cells. After initiation, coordinated cell division and differentiation occur, giving rise to lateral root primordia (LRP). Primordia continue to grow, emerge through the cortex and epidermal layers of the primary root, and finally a new apical meristem is established taking over the responsibility for growth of mature lateral roots [for detailed description of the individual stages of lateral root organogenesis see Malamy and Benfey (1997)]. To examine this highly dynamic developmental process and to investigate a role of various hormonal, genetic and environmental factors in the regulation of lateral root organogenesis, the real time imaging based analyses represent extremely powerful tools (Laskowski et al., 2008; De Smet et al., 2012; Marhavy et al., 2013 and 2014). Herein, we describe a protocol for real time lateral root primordia (LRP) analysis, which enables the monitoring of an onset of the specific gene expression and subcellular protein localization during primordia organogenesis, as well as the evaluation of the impact of genetic and environmental perturbations on LRP organogenesis. AU - Peter Marhavy AU - Eva Benková ID - 832 IS - 8 JF - Bio-protocol TI - Real time analysis of lateral root organogenesis in arabidopsis VL - 5 ER - TY - JOUR AB - The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking’ motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments. AU - Ma, Peixiang AU - Xue, Yi AU - Coquelle, Nicolas AU - Haller, Jens D. AU - Yuwen, Tairan AU - Ayala, Isabel AU - Mikhailovskii, Oleg AU - Willbold, Dieter AU - Colletier, Jacques-Philippe AU - Skrynnikov, Nikolai R. AU - Schanda, Paul ID - 8456 JF - Nature Communications KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Physics and Astronomy KW - General Chemistry SN - 2041-1723 TI - Observing the overall rocking motion of a protein in a crystal VL - 6 ER - TY - JOUR AB - We review recent advances in methodologies to study microseconds‐to‐milliseconds exchange processes in biological molecules using magic‐angle spinning solid‐state nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS ssNMR, as compared to solution‐state NMR, are elucidated using numerical simulations and experimental data. These simulations reveal the potential of MAS NMR to provide detailed insight into short‐lived conformations of biological molecules. Recent studies of conformational exchange dynamics in microcrystalline ubiquitin are discussed. AU - Ma, Peixiang AU - Schanda, Paul ID - 8457 IS - 3 JF - eMagRes SN - 9780470034590 TI - Conformational exchange processes in biological systems: Detection by solid-state NMR VL - 4 ER - TY - JOUR AB - The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution. AU - Usmanova, Dinara AU - Ferretti, Luca AU - Povolotskaya, Inna AU - Vlasov, Peter AU - Kondrashov, Fyodor ID - 848 IS - 2 JF - Molecular Biology and Evolution TI - A model of substitution trajectories in sequence space and long-term protein evolution VL - 32 ER - TY - JOUR AB - In the present note we announce a proof of a strong form of Arnold diffusion for smooth convex Hamiltonian systems. Let ${\mathbb T}^2$ be a 2-dimensional torus and B2 be the unit ball around the origin in ${\mathbb R}^2$ . Fix ρ > 0. Our main result says that for a 'generic' time-periodic perturbation of an integrable system of two degrees of freedom $H_0(p)+\varepsilon H_1(\theta,p,t),\quad \ \theta\in {\mathbb T}^2,\ p\in B^2,\ t\in {\mathbb T}={\mathbb R}/{\mathbb Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in ${\mathbb T}^2 \times B^2 \times {\mathbb T}$ , namely, a ρ-neighborhood of the orbit contains ${\mathbb T}^2 \times B^2 \times {\mathbb T}$ . Our proof is a combination of geometric and variational methods. The fundamental elements of the construction are the usage of crumpled normally hyperbolic invariant cylinders from [9], flower and simple normally hyperbolic invariant manifolds from [36] as well as their kissing property at a strong double resonance. This allows us to build a 'connected' net of three-dimensional normally hyperbolic invariant manifolds. To construct diffusing orbits along this net we employ a version of the Mather variational method [41] equipped with weak KAM theory [28], proposed by Bernard in [7]. AU - Kaloshin, Vadim AU - Zhang, K ID - 8498 IS - 8 JF - Nonlinearity KW - Mathematical Physics KW - General Physics and Astronomy KW - Applied Mathematics KW - Statistical and Nonlinear Physics SN - 0951-7715 TI - Arnold diffusion for smooth convex systems of two and a half degrees of freedom VL - 28 ER - TY - JOUR AB - We consider the cubic defocusing nonlinear Schrödinger equation in the two dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka proved the existence of solutions with s-Sobolev norm growing in time. We establish the existence of solutions with polynomial time estimates. More exactly, there is c>0 such that for any K≫1 we find a solution u and a time T such that ∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0−1. However, there are major spatial differences both between glaciers and within any single glacier, exhibiting a very distinct nonlinear mass-balance profile with elevation. Through analysis of surface velocities derived from Landsat ETM+ imagery, we show that thinning occurs in areas of low velocity and low slope. These areas are prone to a general, dynamic decay of surface features and to the development of supraglacial lakes and ice cliffs, which may be responsible for a considerable increase in overall glacier ablation. AU - Pellicciotti, Francesca AU - Stephan, Christa AU - Miles, Evan AU - Herreid, Sam AU - Immerzeel, Walter W. AU - Bolch, Tobias ID - 12628 IS - 226 JF - Journal of Glaciology KW - Earth-Surface Processes SN - 0022-1430 TI - Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999 VL - 61 ER - TY - JOUR AB - Air temperature is one of the most relevant input variables for snow and ice melt calculations. However, local meteorological conditions, complex topography, and logistical concerns in glacierized regions make the measuring and modeling of air temperature a difficult task. In this study, we investigate the spatial distribution of 2 m air temperature over mountain glaciers and propose a modification to an existing model to improve its representation. Spatially distributed meteorological data from Haut Glacier d'Arolla (Switzerland), Place (Canada), and Juncal Norte (Chile) Glaciers are used to examine approximate flow line temperatures during their respective ablation seasons. During warm conditions (off-glacier temperatures well above 0°C), observed air temperatures in the upper reaches of Place Glacier and Haut Glacier d'Arolla decrease down glacier along the approximate flow line. At Juncal Norte and Haut Glacier d'Arolla, an increase in air temperature is observed over the glacier tongue. While the temperature behavior over the upper part can be explained by the cooling effect of the glacier surface, the temperature increase over the glacier tongue may be caused by several processes induced by the surrounding warm atmosphere. In order to capture the latter effect, we add an additional term to the Greuell and Böhm (GB) thermodynamic glacier wind model. For high off-glacier temperatures, the modified GB model reduces root-mean-square error up to 32% and provides a new approach for distributing air temperature over mountain glaciers as a function of off-glacier temperatures and approximate glacier flow lines. AU - Ayala, A. AU - Pellicciotti, Francesca AU - Shea, J. M. ID - 12631 IS - 8 JF - Journal of Geophysical Research: Atmospheres KW - Space and Planetary Science KW - Earth and Planetary Sciences (miscellaneous) KW - Atmospheric Science KW - Geophysics SN - 2169-897X TI - Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming VL - 120 ER - TY - JOUR AB - Meteorological studies in high-mountain environments form the basis of our understanding of catchment hydrology and glacier accumulation and melt processes, yet high-altitude (>4000 m above sea level, asl) observatories are rare. This research presents meteorological data recorded between December 2012 and November 2013 at seven stations in Nepal, ranging in elevation from 3860 to 5360 m asl. Seasonal and diurnal cycles in air temperature, vapour pressure, incoming short-wave and long-wave radiation, atmospheric transmissivity, wind speed, and precipitation are compared between sites. Solar radiation strongly affects diurnal temperature and vapour pressure cycles, but local topography and valley-scale circulations alter wind speed and precipitation cycles. The observed diurnal variability in vertical temperature gradients in all seasons highlights the importance of in situ measurements for melt modelling. The monsoon signal (progressive onset and sharp end) is visible in all data-sets, and the passage of the remnants of Typhoon Phailin in mid-October 2013 provides an interesting case study on the possible effects of such storms on glaciers in the region. AU - Shea, J.M. AU - Wagnon, P. AU - Immerzeel, W.W. AU - Biron, R. AU - Brun, F. AU - Pellicciotti, Francesca ID - 12629 IS - 2 JF - International Journal of Water Resources Development KW - Water Science and Technology KW - Development SN - 0790-0627 TI - A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya VL - 31 ER - TY - JOUR AB - Ice cliffs have been identified as a reason for higher ablation rates on debris-covered glaciers than are implied by the insulation effects of the debris. This study aims to improve our understanding of cliff backwasting, and the role of radiative fluxes in particular. An energy-balance model is forced with new data gathered in May and October 2013 on Lirung Glacier, Nepalese Himalaya. Observations show substantial variability in melt between cliffs, between locations on any cliff and between seasons. Using a high-resolution digital elevation model we calculate longwave fluxes incident to the cliff from surrounding terrain and include the effect of local shading on shortwave radiation. This is an advance over previous studies, that made simplified assumptions on cliff geometry and radiative fluxes. Measured melt rates varied between 3.25 and 8.6 cm d−1 in May and 0.18 and 1.34 cm d−1 in October. Model results reproduce the strong variability in space and time, suggesting considerable differences in radiative fluxes over one cliff. In October the model fails to reproduce stake readings, probably due to the lack of a refreezing component. Disregarding local topography can lead to overestimation of melt at the point scale by up to ∼9%. AU - Steiner, Jakob F. AU - Pellicciotti, Francesca AU - Buri, Pascal AU - Miles, Evan S. AU - Immerzeel, Walter W. AU - Reid, Tim D. ID - 12626 IS - 229 JF - Journal of Glaciology SN - 0022-1430 TI - Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya VL - 61 ER - TY - JOUR AB - Spatial evolution of supraglacial debris cover on mountain glaciers is a largely unmonitored and poorly understood phenomenon that directly affects glacier melt. Supraglacial debris cover for 93 glaciers in the Karakoram, northern Pakistan, was mapped from Landsat imagery acquired in 1977, 1998, 2009 and 2014. Surge-type glaciers occupy 41% of the study area and were considered separately. The time series of debris-covered surface area change shows a mean value of zero or near-zero change for both surging and non-surging glaciers. An increase in debris-covered area is often associated with negative regional mass balances. We extend this logic to suggest that the stable regional mass balances in the Karakoram explain the zero or near-zero change in debris-covered area. This coupling of trends combined with our 37 year time series of data suggests the Karakoram anomaly extends further back in time than previously known. AU - Herreid, Sam AU - Pellicciotti, Francesca AU - Ayala, Alvaro AU - Chesnokova, Anna AU - Kienholz, Christian AU - Shea, Joseph AU - Shrestha, Arun ID - 12627 IS - 227 JF - Journal of Glaciology SN - 0022-1430 TI - Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014 VL - 61 ER - TY - JOUR AB - CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed. AU - Veldkamp, Christopher AU - Kiermaier, Eva AU - Gabel Eissens, Skylar AU - Gillitzer, Miranda AU - Lippner, David AU - Disilvio, Frank AU - Mueller, Casey AU - Wantuch, Paeton AU - Chaffee, Gary AU - Famiglietti, Michael AU - Zgoba, Danielle AU - Bailey, Asha AU - Bah, Yaya AU - Engebretson, Samantha AU - Graupner, David AU - Lackner, Emily AU - Larosa, Vincent AU - Medeiros, Tysha AU - Olson, Michael AU - Phillips, Andrew AU - Pyles, Harley AU - Richard, Amanda AU - Schoeller, Scott AU - Touzeau, Boris AU - Williams, Larry AU - Sixt, Michael K AU - Peterson, Francis ID - 1618 IS - 27 JF - Biochemistry TI - Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites VL - 54 ER -