The interplay between facilitation and habitat type drives spatial vegetation patterns in global drylands

The spatial configuration of vascular vegetation has been linked to variations in land degradation and ecosystem functioning in drylands. However, most studies on spatial patterns conducted to date have focused on a single or a few study sites within a particular region, specific vegetation types, or in landscapes characterized by a certain type of spatial patterns. Therefore, little is known on the general typology and distribution of plant spatial patterns in drylands worldwide, and on the relative importance of biotic and abiotic factors as predictors of their variations across geographical regions and habitat types. We analyzed 115 dryland plant communities from all continents except Antarctica to: 1) investigate the general typology of spatial patterns, and 2) assess the relative importance of biotic (plant cover, frequency of facilitation, soil amelioration, height of the dominant species) and abiotic (aridity, rainfall seasonality and sand content) factors as predictors of spatial patterns (median patch size, shape of patch‐size distribution and regularity) across contrasting habitat types (shrublands and grasslands). Precipitation during the warmest period and sand content were particularly strong predictors of plant spatial patterns in grasslands and shrublands, respectively. Facilitation associated with power‐law like and irregular spatial patterns in both shrublands and grasslands, although it was mediated by different mechanisms (respectively soil ammelioration and percentage of facilitated species). The importance of biotic attributes as predictors of the shape of patch‐size distributions declined with aridity in both habitats, leading to the emergence of more regular patterns under the most arid conditions. Our results expand our knowledge about patch formation in drylands and the habitat‐dependency of their drivers. They also highlight different ways in which facilitation affects ecosystem structure through the formation of plant spatial patterns.     

Algae sediment dynamics are mediated by herbivorous fishes on a nearshore coral reef

Coral Reefs - Epilithic algae are a ubiquitous component of coral reefs. Components of the epilithic algal matrix (EAM) can have a significant influence on coral settlement and benthic feeding by...     

Dynamics of Fusarium solani cutinase investigated through structural comparison among different crystal forms of its variants

In characterizing mutants and covalently inhibited complexes of Fusarium solani cutinase, which is a 197-residue lipolytic enzyme, 34 variant structures, crystallizing in 8 different crystal forms, have been determined, mostly at high resolution. Taking advantage of this considerable body of information, a structural comparative analysis was carried out to investigate the dynamics of cutinase. Surface loops were identified as the major flexible protein regions, particularly those forming the active-site groove, whereas the elements constituting the protein scaffold were found to retain the same conformation in all the cutinase variants studied. Flexibility turned out to be correlated with thermal motion. With a given crystal packing environment, a high flexibility turned out to be correlated with a low involvement in crystal packing contacts. The high degree of crystal polymorphism, which allowed different conformations with similar energy to be detected, made it possible to identify motions which would have remained unidentified if only a single crystal form had been available. Fairly good agreement was found to exist between the data obtained from the structural comparison and those from a molecular dynamics (MD) simulation carried out on the native enzyme. The crystallographic approach used in this study turned out to be a suitable tool for investigating cutinase dynamics. Because of the availability of a set of closely related proteins in different crystal environments, the intrinsic drawback of a crystallographic approach was bypassed. By combining several static pictures, the dynamics of the protein could be monitored much more realistically than what can be achieved on the basis of static pictures alone. Proteins 26:442–458 © 1996 Wiley-Liss, Inc.     

Mast cells in the developing avian eye

Mast cells are present in the eye of Gallus domesticus, appearing in the anterior uvea in embryos at stage 39 HH (13th day). In hatching and adult birds, they are present in the sclera, uvea, pectinate ligament, and conjunctiva. Mast cells are absent in the cornea, retina, and pecten oculi. Maturing mast cells in the anterior eye segment appear as round cells having eccentric nuclei and a few cytoplasmic metachromatic granules, whose fluorescence increases during development. Mature cells are more numerous in late development, and their cytoplasm is rich in metachromatic and intensely fluorescent granules. Ultrastructurally, maturing mast cells display progranules and a few electron dense and homogeneous granules on one side of the cell. Mast cells of adult birds possess homogeneous cytoplasmic granules, some of which display protuberances that penetrate hollows of adjoining granules. Heterogeneous granules exhibiting latticed and mottled patterns are also present. The existence of mast cells in the anterior eye segment indicates that these cells might perform a physiological role during development and in aqueous humor outflow. They might modulate exchanges between blood and aqueous humor through chemical mediators present in their granules. © 1996 Wiley-Liss, Inc.     

In vivo observations of timecourse and distribution of morphological dynamics in Xenopus retinotectal axon arbors

Changes in neuronal structure can contribute to the plasticity of neuronal connections in the developing and mature nervous system. However, the expectation that they would occur slowly precluded many from considering structural changes as a mechanism underlying synaptic plasticity that occurs over a period of minutes to hours. We took time-lapse confocal images of retinotectal axon arbors to determine the timecourse, magnitude, and distribution of changes in axon arbor structure within living Xenopus tadpoles. Images of axons were collected at intervals of 3 min, 30 min, and 2 h over total observation periods up to 8 h. Branch additions and retractions in arbors imaged at 3- or 30-min intervals were confined to shorter branches. Sites of additions and retractions were distributed throughout the arbor. The average lifetime of branches was about 10 min. Branches of up to 10 μm could be added to the arbor within a single 3-min observation interval. Observations of arbors at 3-min intervals showed rapid changes in the structure of branchtips, including transitions from lamellar growth cones to more streamlined tips, growth cone collapse, and re-extension. Simple branchtips were motile and appeared capable of exploratory behavior when viewed in time-lapse movies. In arbors imaged at 2-h intervals over a total of 8 h, morphological changes included longer branches, tens of microns in length. An average of 50% of the total branch length in the arbor was remodeled within 8 h. The data indicate that the elaboration of the arbor occurs by the random addition of branches throughout the arbor, followed by the selective stabilization of a small fraction of the new branches and the retraction of the majority of branches. Stabilized branches can then elongate and support the addition of more branches. These data show that structural changes in presynaptic axons can occur very rapidly even in complex arbors and can therefore play a role in forms of neuronal plasticity that operate on a timescale of minutes. © 1996 John Wiley & Sons, Inc.     

Predicting the subcellular localization of human proteins using machine learning and exploratory data analysis

Identifying the subcellular localization of proteins is particularly helpful in the functional annotation of gene products. In this study, we use Machine Learning and Exploratory Data Analysis （EDA） techniques to examine and characterize amino acid sequences of human proteins localized in nine cellular compartments. A dataset of 3,749 protein sequences representing human proteins was extracted from the SWISS-PROT database. Feature vectors were created to capture specific amino acid sequence characteristics. Relative to a Support Vector Machine, a Multi-layer Perceptron, and a Naive Bayes classifier, the C4.5 Decision Tree algorithm was the most consistent performer across all nine compartments in reliably predicting the subcellular localization of proteins based on their amino acid sequences （average Precision=0.88; average Sensitivity=0.86）. Furthermore, EDA graphics characterized essential features of proteins in each compartment. As examples, proteins localized to the plasma membrane had higher proportions of hydrophobic amino acids; cytoplasmic proteins had higher proportions of neutral amino acids; and mitochondrial proteins had higher proportions of neutral amino acids and lower proportions of polar amino acids. These data showed that the C4.5 classifier and EDA tools can be effective for characterizing and predicting the subcellular localization of human proteins based on their amino acid sequences.     

FtsZ filament structures in different nucleotide states reveal the mechanism of assembly dynamics

Treadmilling protein filaments perform essential cellular functions by growing from one end while shrinking from the other, driven by nucleotide hydrolysis. Bacterial cell division relies on the primitive tubulin homolog FtsZ, a target for antibiotic discovery that assembles into single treadmilling filaments that hydrolyse GTP at an active site formed upon subunit association. We determined high-resolution filament structures of FtsZ from the pathogen Staphylococcus aureus in complex with different nucleotide analogs and cations, including mimetics of the ground and transition states of catalysis. Together with mutational and biochemical analyses, our structures reveal interactions made by the GTP γ-phosphate and Mg²⁺ at the subunit interface, a K⁺ ion stabilizing loop T7 for co-catalysis, new roles of key residues at the active site and a nearby crosstalk area, and rearrangements of a dynamic water shell bridging adjacent subunits upon GTP hydrolysis. We propose a mechanistic model that integrates nucleotide hydrolysis signaling with assembly-associated conformational changes and filament treadmilling. Equivalent assembly mechanisms may apply to more complex tubulin and actin cytomotive filaments that share analogous features with FtsZ.

Bacterial cell division critically relies on the tubulin homolog FtsZ, which assembles into filaments that treadmill, fuelled by GTP hydrolysis. This structural and biochemical study of FtsZ from Staphylocuccus aureus reveals the mechanism of GTP hydrolysis and its connection with filament dynamics.