Annual Rainfall and Seasonality Predict Pan-tropical Patterns of Liana Density and Basal Area

We test the hypotheses proposed by Gentry and Schnitzer that liana density and basal area in tropical forests vary negatively with mean annual precipitation (MAP) and positively with seasonality. Previous studies correlating liana abundance with these climatic variables have produced conflicting results, warranting a new analysis of drivers of liana abundance based on a different dataset. We compiled a pan-tropical dataset containing 28,953 lianas (≥2.5 cm diam.) from studies conducted at 13 Neotropical and 11 Paleotropical dry to wet lowland tropical forests. The ranges in MAP and dry season length (DSL) (number of months with mean rainfall <100 mm) represented by these datasets were 860–7250 mm/yr and 0–7 mo, respectively. Pan-tropically, liana density and basal area decreased significantly with increasing annual rainfall and increased with increasing DSL, supporting the hypotheses of Gentry and Schnitzer. Our results suggest that much of the variation in liana density and basal area in the tropics can be accounted for by the relatively simple metrics of MAP and DSL.     

Lipoic acid effects on established atherosclerosis

AimsAlpha-lipoic acid (LA) is a commonly used dietary supplement that exerts anti-oxidant and anti-inflammatory effects in vivo and in vitro. We investigated the mechanisms by which LA may confer protection in models of established atherosclerosis.Main methodsWatanabe heritable hyperlipidemic (WHHL) rabbits were fed with high cholesterol chow for 6 weeks and then randomized to receive either high cholesterol diet alone or combined with LA (20 mg/kg/day) for 12 weeks. Vascular function was analyzed by myography. The effects of LA on T cell migration to chemokine gradients was assessed by Boyden chamber. NF-κB activation was determined by measuring translocation and electrophoresis migration shift assay (EMSA).Key findingsLA decreased body weight by 15 ± 5% without alterations in lipid parameters. Magnetic Resonance Imaging (MRI) analysis demonstrated that LA reduced atherosclerotic plaques in the abdominal aorta, with morphological analysis revealing reduced lipid and inflammatory cell content. Consistent with its effect on atherosclerosis, LA improved vascular reactivity (decreased constriction to angiotensin II and increased relaxation to acetylcholine and insulin), inhibited NF-κB activation, and decreased oxidative stress and expression of key adhesion molecules in the vasculature. LA reduced T cell content in atherosclerotic plaque in conjunction with decreasing ICAM and CD62L (l-selectin) expression. These effects were confirmed by demonstration of a direct effect of LA in reducing T cell migration in response to CCL5 and SDF-1 and decreasing T cell adhesion to the endothelium by intra-vital microscopy.SignificanceThe present findings offer a mechanistic insight into the therapeutic effects of LA on atherosclerosis.     

Structures of PHR Domains from Mus musculus Phr1 (Mycbp2) Explain the Loss-of-Function Mutation (Gly1092 → Glu) of the C. elegans Ortholog RPM-1

PHR [PAM (protein associated with Myc)-HIW (Highwire)-RPM-1 (regulator of presynaptic morphology 1)] proteins are conserved, large multi-domain E3 ubiquitin ligases with modular architecture. PHR proteins presynaptically control synaptic growth and axon guidance and postsynaptically regulate endocytosis of glutamate receptors. Dysfunction of neuronal ubiquitin-mediated proteasomal degradation is implicated in various neurodegenerative diseases. PHR proteins are characterized by the presence of two PHR domains near the N-terminus, which are essential for proper localization and function. Structures of both the first and second PHR domains of Mus musculus (mouse) Phr1 (MYC binding protein 2, Mycbp2) have been determined, revealing a novel β sandwich fold composed of 11 antiparallel β-strands. Conserved loops decorate the apical side of the first PHR domain (MmPHR1), yielding a distinct conserved surface feature. The surface of the second PHR domain (MmPHR2), in contrast, lacks significant conservation. Importantly, the structure of MmPHR1 provides insights into a loss-of-function mutation, Gly1092 → Glu, observed in the Caenorhabditis elegans ortholog RPM-1.     

A model-based approach for mining membrane protein crystallization trials

MOTIVATION: Membrane proteins are known to play crucial roles in various cellular functions. Information about their function can be derived from their structure, but knowledge of these proteins is limited, as their structures are difficult to obtain. Crystallization has proved to be an essential step in the determination of macromolecular structure. Unfortunately, the bottleneck is that the crystallization process is quite complex and extremely sensitive to experimental conditions, the selection of which is largely a matter of trial and error. Even under the best conditions, it can take a large amount of time, from weeks to years, to obtain diffraction-quality crystals. Other issues include the time and cost involved in taking multiple trials and the presence of very few positive samples in a wide and largely undetermined parameter space. Therefore, any help in directing scientists' attention to the hot spots in the conceptual crystallization space would lead to increased efficiency in crystallization trials. RESULTS: This work is an application case study on mining membrane protein crystallization trials to predict novel conditions that have a high likelihood of leading to crystallization. We use suitable supervised learning algorithms to model the data-space and predict a novel set of crystallization conditions. Our preliminary wet laboratory results are very encouraging and we believe this work shows great promise. We conclude with a view of the crystallization space that is based on our results, which should prove useful for future studies in this area.     

Tree diversity and distribution in undisturbed and human-impacted sites of tropical wet evergreen forest in southern Western Ghats, India

The composition, abundance, population structure and distribution patterns of all woody species ( 30 cm gbh) were investigated in an undisturbed and two adjacent human-impacted sites of a tropical wet evergreen forest in Kalakad National Park, Western Ghats, south India. Three 1-ha plots were established, one each in (i) an undisturbed site (named site UD), (ii) in a site selectively felled 35 years ago (site SF – small stems felled leaving the large trees (as shade) for developing it into a cardamom estate, on the failure of which the site was abandoned) and (iii) a frequently disturbed site (site FD – round woods logged for use in ovens for curing cardamom). These sites are 1 to 3 km apart in the same wet evergreen forest. In the three study plots a total of 2150 stems (mean density 716 ha^–1) covering 122 species in 89 genera and 41 families were enumerated. Species richness was greatest (85 species ha^–1) in the undisturbed site UD, intermediate (83) in SF and lowest (80) in FD. Tree density was greatest (855 stems ha^–1) in site SF, intermediate (720) in UD and lowest (575) in FD. The forest stand was exceptionally voluminous in site UD (basal area 94.64 m² ha^–1), intermediate (66.9 m²) in SF and least (61.7 m²) in FD, due to tree removal for fuel in the latter sites. Species composition and abundance patterns markedly varied between the three sites. In UD and SF, primary forest species (Cryptocarya bourdillonii , Cullenia exarillata Myristica dactyloides etc.) occurred in greater density. In FD heliophilic secondary forest species (Elaeocarpus venustus, Litsea wightiana, Viburnum punctatum and Vitex altissima) were abundant, while these were absent in UD and SF. The species–area curve did not reach an asymptote in any of the sites on the 1-ha scale. The stand population structure was clearly reverse J shaped in UD and SF, while small stems were 2- to 3-fold fewer in FD. Most trees exhibited clumped distribution of individuals on the 1-ha scale. Variation in the kind and richness of species and their abundance is related to human interference and the need for forest conservation is emphasized.     

Liana diversity and distribution in four tropical dry evergreen forests on the Coromandel coast of south India

Liana diversity was inventoried in four tropical dry evergreen forest sites that are characterized by numerous trees, of short stature and small diameter, and a varying degree of anthropogenic disturbance, on the Coromandel coast of south India. A 1-ha plot was established in each of the four sites and was subdivided into 100 quadrats of 10 m× 10 m. All lianas 1 cm diameter at breast height (dbh) rooted within the plot were enumerated. The species richness and density of lianas, with respect to site disturbance and forest stature, varied across the sites. Liana density totaled 3307 individuals (range 497–1163 individuals ha^–1) and species richness totaled 39 species (range 24–29 species ha^–1) representing 34 genera and 24 families. Combretaceae, Asclepiadaceae, Capparaceae and Vitaceae were the well-represented families. The top five species Strychnos minor, Combretum albidum, Derris ovalifolia, Jasminum angustifolium and Reissantia indica contributed 55% of total density. The slopes of the species–area curves were different for each of the four sites and the curve stabilized in only one site. Of the four climbing modes recognized among the total 39 species, 18 were twiners (56% of the total density). Eight species (24% of density) were tendril climbers and 12 species (16% of density) were scramblers. Hugonia mystax was the only hook climber. All the 39 species and 88% of liana density were encountered within a category of 6 cm dbh or less, and a similar pattern prevailed in the individual sites. Of the three diaspore dispersal modes found among the 39 liana species, animal (64%) and wind (23%) dispersal were predominant over the autochorous mode (13%). Liana diversity and distribution in dry forest communities appear to be influenced by forest stature and site disturbance levels. In the light of the extent of liana diversity and sacred grove status of the study sites, the need for forest conservation, involving local people, is emphasized.     

Structure of Plasmodium falciparum triose-phosphate isomerase-2-phosphoglycerate complex at 1.1-A resolution

Triose-phosphate isomerase, a key enzyme of the glycolytic pathway, catalyzes the isomerization of dihydroxy acetone phosphate and glyceraldehyde 3-phosphate. In this communication we report the crystal structure of Plasmodium falciparum triose-phosphate isomerase complexed to the inhibitor 2-phosphoglycerate at 1.1-A resolution. The crystallographic asymmetric unit contains a dimeric molecule. The inhibitor bound to one of the subunits in which the flexible catalytic loop 6 is in the open conformation has been cleaved into two fragments presumably due to radiation damage. The cleavage products have been tentatively identified as 2-oxoglycerate and meta-phosphate. The intact 2-phosphoglycerate bound to the active site of the other subunit has been observed in two different orientations. The active site loop in this subunit is in both open and "closed" conformations, although the open form is predominant. Concomitant with the loop closure, Phe-96, Leu-167, and residues 208-211 (YGGS) are also observed in dual conformations in the B-subunit. Detailed comparison of the active-site geometry in the present case to the Saccharomyces cerevisiae triose-phosphate isomerase-dihydroxy acetone phosphate and Leishmania mexicana triose-phosphate isomerase-phosphoglycolate complexes, which have also been determined at atomic resolution, shows that certain interactions are common to the three structures, although 2-phosphoglycerate is neither a substrate nor a transition state analogue.