A morphometric analysis of vegetation patterns in dryland ecosystems

Vegetation in dryland ecosystems often forms remarkable spatial patterns. These range from regular bands of vegetation alternating with bare ground, to vegetated spots and labyrinths, to regular gaps of bare ground within an otherwise continuous expanse of vegetation. It has been suggested that spotted vegetation patterns could indicate that collapse into a bare ground state is imminent, and the morphology of spatial vegetation patterns, therefore, represents a potentially valuable source of information on the proximity of regime shifts in dryland ecosystems. In this paper, we have developed quantitative methods to characterize the morphology of spatial patterns in dryland vegetation. Our approach is based on algorithmic techniques that have been used to classify pollen grains on the basis of textural patterning, and involves constructing feature vectors to quantify the shapes formed by vegetation patterns. We have analysed images of patterned vegetation produced by a computational model and a small set of satellite images from South Kordofan (South Sudan), which illustrates that our methods are applicable to both simulated and real-world data. Our approach provides a means of quantifying patterns that are frequently described using qualitative terminology, and could be used to classify vegetation patterns in large-scale satellite surveys of dryland ecosystems

In vivo reprogramming of pancreatic acinar cells to three islet endocrine subtypes

Direct lineage conversion of adult cells is a promising approach for regenerative medicine. A major challenge of lineage conversion is to generate specific cell subtypes. The pancreatic islets contain three major hormone-secreting endocrine subtypes: insulin+ β-cells, glucagon+ α-cells, and somatostatin+ δ-cells. We previously reported that a combination of three transcription factors, Ngn3, Mafa, and Pdx1, directly reprograms pancreatic acinar cells to β-cells. We now show that acinar cells can be converted to δ-like and α-like cells by Ngn3 and Ngn3+Mafa respectively. Thus, three major islet endocrine subtypes can be derived by acinar reprogramming. Ngn3 promotes establishment of a generic endocrine state in acinar cells, and also promotes δ-specification in the absence of other factors. δ-specification is in turn suppressed by Mafa and Pdx1 during α- and β-cell induction. These studies identify a set of defined factors whose combinatorial actions reprogram acinar cells to distinct islet endocrine subtypes in vivo. DOI: http://dx.doi.org/10.7554/eLife.01846.00

Global well-posedness for Schr\"odinger equation with derivative in H1/2(R)H^{{1/2}}(\R)

In this paper, we consider the Cauchy problem of the cubic nonlinear Schr\"{o}dinger equation with derivative in $H^s(\R)$. This equation was known to be the local well-posedness for $s\geq \frac12$ (Takaoka,1999), ill-posedness for $s<\frac12$ (Biagioni and Linares, 2001, etc.) and global well-posedness for $s>\frac12$ (I-team, 2002). In this paper, we show that it is global well-posedness in H^{1/2(\R). The main approach is the third generation I-method combined with some additional resonant decomposition technique. The resonant decomposition is applied to control the singularity coming from the resonant interaction.Comment: 31pages; In this version, we change some expressions in Englis

Interpreting the functional role of a novel interaction motif in prokaryotic sodium channels

Voltage-gated sodium channels enable the translocation of sodium ions across cell membranes and play crucial roles in electrical signaling by initiating the action potential. In humans, mutations in sodium channels give rise to several neurological and cardiovascular diseases, and hence they are targets for pharmaceutical drug developments. Prokaryotic sodium channel crystal structures have provided detailed views of sodium channels, which by homology have suggested potentially important functionally related structural features in human sodium channels. A new crystal structure of a full-length prokaryotic channel, NavMs, in a conformation we proposed to represent the open, activated state, has revealed a novel interaction motif associated with channel opening. This motif is associated with disease when mutated in human sodium channels and plays an important and dynamic role in our new model for channel activation

Alignment of transmembrane regions in the cystic fibrosis transmembrane conductance regulator chloride channel pore

Different transmembrane (TM) α helices are known to line the pore of the cystic fibrosis TM conductance regulator (CFTR) Cl− channel. However, the relative alignment of these TMs in the three-dimensional structure of the pore is not known. We have used patch-clamp recording to investigate the accessibility of cytoplasmically applied cysteine-reactive reagents to cysteines introduced along the length of the pore-lining first TM (TM1) of a cysteine-less variant of CFTR. We find that methanethiosulfonate (MTS) reagents irreversibly modify cysteines substituted for TM1 residues K95, Q98, P99, and L102 when applied to the cytoplasmic side of open channels. Residues closer to the intracellular end of TM1 (Y84–T94) were not apparently modified by MTS reagents, suggesting that this part of TM1 does not line the pore. None of the internal MTS reagent-reactive cysteines was modified by extracellular [2-(trimethylammonium)ethyl] MTS. Only K95C, closest to the putative intracellular end of TM1, was apparently modified by intracellular [2-sulfonatoethyl] MTS before channel activation. Comparison of these results with recent work on CFTR-TM6 suggests a relative alignment of these two important TMs along the axis of the pore. This alignment was tested experimentally by formation of disulfide bridges between pairs of cysteines introduced into these two TMs. Currents carried by the double mutants K95C/I344C and Q98C/I344C, but not by the corresponding single-site mutants, were inhibited by the oxidizing agent copper(II)-o-phenanthroline. This inhibition was irreversible on washing but could be reversed by the reducing agent dithiothreitol, suggesting disulfide bond formation between the introduced cysteine side chains. These results allow us to develop a model of the relative positions, functional contributions, and alignment of two important TMs lining the CFTR pore. Such functional information is necessary to understand and interpret the three-dimensional structure of the pore

Rhodium nanoflowers stabilized by a nitrogen-rich PEG-tagged substrate as recyclable catalyst for the stereoselective hydrosilylation of internal alkynes

Morphology and size controllable rhodium nanoparticles stabilized by a nitrogen-rich polyoxyethylenated derivative have been prepared by reduction of RhCl3 with NaBH4 in water at room temperature and fully characterized. The flower-like Rh NPs are effective and recyclable catalysts for the stereoselective hydrosilylation of challenging internal alkynes and diynes, affording the (E)-vinylsilanes in quantitative yields for a wide range of substrates. The insolubility of the nanocatalyst in diethyl ether allows its easy separation and recycling

Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences

The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics

The Role of Alveolar Epithelial Cells in Initiating and Shaping Pulmonary Immune Responses: Communication between Innate and Adaptive Immune Systems

Macrophages and dendritic cells have been recognized as key players in the defense against mycobacterial infection. However, more recently, other cells in the lungs such as alveolar epithelial cells (AEC) have been found to play important roles in the defense and pathogenesis of infection. In the present study we first compared AEC with pulmonary macrophages (PuM) isolated from mice in their ability to internalize and control Bacillus Calmette-Guérin (BCG) growth and their capacity as APCs. AEC were able to internalize and control bacterial growth as well as present antigen to primed T cells. Secondly, we compared both cell types in their capacity to secrete cytokines and chemokines upon stimulation with various molecules including mycobacterial products. Activated PuM and AEC displayed different patterns of secretion. Finally, we analyzed the profile of response of AEC to diverse stimuli. AEC responded to both microbial and internal stimuli exemplified by TLR ligands and IFNs, respectively. The response included synthesis by AEC of several factors, known to have various effects in other cells. Interestingly, TNF could stimulate the production of CCL2/MCP-1. Since MCP-1 plays a role in the recruitment of monocytes and macrophages to sites of infection and macrophages are the main producers of TNF, we speculate that both cell types can stimulate each other. Also, another cell-cell interaction was suggested when IFNs (produced mainly by lymphocytes) were able to induce expression of chemokines (IP-10 and RANTES) by AEC involved in the recruitment of circulating lymphocytes to areas of injury, inflammation, or viral infection. In the current paper we confirm previous data on the capacity of AEC regarding internalization of mycobacteria and their role as APC, and extend the knowledge of AEC as a multifunctional cell type by assessing the secretion of a broad array of factors in response to several different types of stimuli