Gap colonization in the Patagonian semidesert: seed bank and diaspore morphology

We report work on a cold, windy South American steppe dominated by tussock grasses and shrubs of small stature that, together, cover only half of the soil surface. Our objective was to find out why seedlings and juveniles of these dominant species are generally absent from the bare or poorly-populated spots (gaps) that exist between established individuals. We hypothesized that matrix-forming species fail to colonize gaps because of a lack of properly-placed seeds, contained in diaspores which because of their morphology are blown away from gaps that otherwise would constitute safe sites for recruitment. We evaluated diaspore size and wing loading (weight:area ratio) for all common species in the community, collected seed-bank samples in different occasions and microsites, and performed detailed field observations for one gap-dwelling species during several years. We found that: 1) Seeds of the dominant, matrix-forming species are uncommon in the soil bank of the center of the gaps between established vegetation. 2) Seeds of the dominant species are more abundant towards the edges of the gaps than at their center. 3) Diaspores of those species present in the seed bank of the gaps are smaller than diaspores of absent species; contrary to expectations, not all gap-dwelling species had larger diaspore wing loading than non-gap species. 4) Seeds and adult densities of the most common gap species (the annual Camissonia dentata ), were correlated between them and across subsequent years. We conclude that it is not an overall shortage of seeds that precludes the dominant species from becoming established in the gaps, but rather the seeds' uneven spatial distribution. We further argue that gaps would be suitable sites for recruitment, but large diaspore size makes seeds of the dominant species to be blown away by the strong westerly winds.     

Efficiency of genome-wide association studies in random cross populations

Genome-wide association studies (GWAS) with plant species have employed inbred lines panels. We evaluated the efficiency of GWAS in non-inbred and inbred populations and assessed factors affecting GWAS. Fifty samples of 800 individuals from populations with linkage disequilibrium were simulated. Individuals were genotyped for 10,000 single nucleotide polymorphisms (SNPs) and phenotyped for traits controlled by ten quantitative trait loci (QTLs) and 90 minor genes, assuming different degrees of dominance and broad sense heritabilities of 40 and 80%. The average SNP density was 0.1 centiMorgan (cM) and the QTL heritabilities ranged from 3.2 to 11.8%. The results for random cross populations evidenced that to increase the QTL detection power, the additive-dominance model must be fitted for traits controlled by dominance effects but must not be fitted for traits showing no dominance. The power of detection was maximized by increasing the sample size to 400 and the false discovery rate (FDR) to 5%. The average power of detection for the low, intermediate, and high heritability QTLs achieved 52.4, 87.0, and 100.0%, respectively. Assuming sample sizes of 400 and 800, the observed FDR was equal to or lower than the specified level of significance. The association mapping was highly precise, since at least 97% of the declared QTLs were detected by the SNP inside it (average bias of 0.4 cM). Besides controlling the FDR, relatedness (and identity by state) efficiently controls the number of significant associations outside the QTL interval (not all false positive associations). The analysis of the inbred random cross population provided essentially the same results as the non-inbred populations.     

Dissecting the multifunctional role of the N‐terminal domain of the Melon necrotic spot virus coat protein in RNA packaging,viral movement and interference with antiviral plant defence

The coat protein (CP) of Melon necrotic spot virus (MNSV) is structurally composed of three major domains. The middle S‐domain builds a robust protein shell around the viral genome, whereas the C‐terminal protruding domain, or P‐domain, is involved in the attachment of virions to the transmission vector. Here, we have shown that the N‐terminal domain, or R‐domain, and the arm region, which connects the R‐domain and S‐domain, are involved in different key steps of the viral cycle, such as cell‐to‐cell movement and the suppression of RNA silencing and pathogenesis through their RNA‐binding capabilities. Deletion mutants revealed that the CP RNA‐binding ability was abolished only after complete, but not partial, deletion of the R‐domain and the arm region. However, a comparison of the apparent dissociation constants for the CP RNA‐binding reaction of several partial deletion mutants showed that the arm region played a more relevant role than the R‐domain in in vitro RNA binding. Similar results were obtained in in vivo assays, although, in this case, full‐length CPs were required to encapsidate full‐length genomes. We also found that the R‐domain carboxyl portion and the arm region were essential for efficient cell‐to‐cell movement, for enhancement of Potato virus X pathogenicity, for suppression of systemic RNA silencing and for binding of small RNAs. Therefore, unlike other carmovirus CPs, the R‐domain and the arm region of MNSV CP have acquired, in addition to other essential functions such as genome binding and encapsidation functions, the ability to suppress RNA silencing by preventing systemic small RNA transport.     

Corneal endothelial cell density decreases with age in emmetropic eyes

PURPOSE: To analyze the corneal endothelial cell density in healthy adult emmetropic subjects. METHODS: We analyzed the corneal endothelial cell density of a group made up of 225 emmetropic subjects (n=225). As age-matched control groups we analyzed two other groups, one made up of myopic subjects (n=209) and the other made up of hyperopic subjects (n=203). We recorded the mean of three consecutive measurements of the corneal endothelial cell density using the Topcon SP-2000P non-contact specular microscope (Topcon Corp., Tokyo, Japan). RESULTS: The mean age was 38.6+/-11.8 years, 40.7+/-12.2 years, and 39.2+/-10.5 years for emmetropic, myopic and hyperopic subjects respectively (p=0.994). No significant differences (p=0.920) in endothelial cell density values were found between emmetropic (2985+/-245 cells/mm2), myopic (2936+/-258 cells/mm2) and hyperopic eyes (2946+/-253 cells/mm2). Lower corneal endothelial cell density values were found in older emmetropic (p<0.001), myopic (p<0.001), and hyperopic subjects (p<0.001). A significant correlation between endothelial cell density and age was found in emmetropic (r=-0.958; p<0.001), myopic (r= -0.954; p<0.001) and hyperopic subjects (r= -0.948; p<0.001). CONCLUSIONS: In healthy emmetropic subjects there is a reduction in corneal endothelial cell density with age although there are no differences in corneal endothelial cell density values between emmetropic, myopic and hyperopic subjects.     

Pectinolytic Systems of Two Aerobic Sporogenous Bacterial Strains with High Activity on Pectin

Strains Paenibacillus sp. BP-23 and Bacillus sp. BP-7, previously isolated from soil from a rice field, secreted high levels of pectinase activity in media supplemented with pectin. Production of pectinases in strain Paenibacillus sp. BP-23 showed catabolite repression, while in Bacillus sp. BP-7 production of pectin degrading enzymes was not negatively affected by glucose. The two strains showed lyase activities as the predominant pectinases, while hydrolase activity was very low. Analysis of Paenibacillus sp. BP-23 in SDS–polyacrylamide gels and zymograms showed five pectinase activity bands. The strict requirement of Ca²⁺ for lyase activity of the strain indicates that correspond to pectate lyases. For Bacillus sp. BP-7, zymograms showed four bands of different size. The strain showed a Ca²⁺ requirement for lyase activity on pectate but not on pectin, indicating that the pectinolytic system of Bacillus sp. BP-7 is comprised of pectate lyases and pectin lyases. The results show differences in pectin degrading systems between the two aerobic sporogenous bacterial strains studied.     

The v-SNARE Vti1a regulates insulin-stimulated glucose transport and Acrp30 secretion in 3T3-L1 adipocytes

Regulated exocytosis in adipocytes mediates key functions, exemplified by insulin-stimulated secretion of peptides such as adiponectin and recycling of intracellular membranes containing GLUT4 glucose transporters to the cell surface. Using a proteomics approach, the v-SNARE Vti1a (vps10p tail interacting 1a) was identified by mass spectrometry in purified GLUT4-containing membranes. Insulin treatment of 3T3-L1 adipocytes decreased the amounts of both Vti1a and GLUT4 in these membranes, confirming that Vti1a is a component of insulin-sensitive GLUT4-containing vesicles. In the basal state, endogenous Vti1a colocalizes exclusively with perinuclear GLUT4. Although Vti1a has previously been reported to be a v-SNARE localized in the trans-Golgi network, treatment with brefeldin A failed to significantly modify Vti1a or GLUT4 localization while completely dispersing Golgi and trans-Golgi network marker proteins. Furthermore, depletion of Vti1a protein in cultured adipocytes through small interfering RNA-based gene silencing significantly inhibited both adiponectin secretion and insulin-stimulated deoxyglucose uptake. Taken together, these results suggest that the v-SNARE Vti1a may regulate a step common to both GLUT4 and Acrp30 trafficking in 3T3-L1 adipocytes.     

Mitofusin-2 determines mitochondrial network architecture and mitochondrial metabolism. A novel regulatory mechanism altered in obesity

In many cells and specially in muscle, mitochondria form elongated filaments or a branched reticulum. We show that Mfn2 (mitofusin 2), a mitochondrial membrane protein that participates in mitochondrial fusion in mammalian cells, is induced during myogenesis and contributes to the maintenance and operation of the mitochondrial network. Repression of Mfn2 caused morphological and functional fragmentation of the mitochondrial network into independent clusters. Concomitantly, repression of Mfn2 reduced glucose oxidation, mitochondrial membrane potential, cell respiration, and mitochondrial proton leak. We also show that the Mfn2-dependent mechanism of mitochondrial control is disturbed in obesity by reduced Mfn2 expression. In all, our data indicate that Mfn2 expression is crucial in mitochondrial metabolism through the maintenance of the mitochondrial network architecture, and reduced Mfn2 expression may explain some of the metabolic alterations associated with obesity.     

Structure of the Clade 1 catalase,CatF of Pseudomonas syringae,at 1.8 A resolution

Catalase CatF of Pseudomonas syringae has been identified phylogenetically as a clade 1 catalase, closely related to plant catalases, a group from which no structure has been determined. The structure of CatF has been refined at 1.8 A resolution by using X-ray synchrotron data collected from a crystal flash-cooled with liquid nitrogen. The crystallographic agreement factors R and R(free) are, respectively, 18.3% and 24.0%. The asymmetric unit of the crystal contains a whole molecule that shows accurate 222-point group symmetry. The crystallized enzyme is a homotetramer of subunits with 484 residues, some 26 residues shorter than predicted from the DNA sequence. Mass spectrometry analysis confirmed the absence of 26 N-terminal residues, possibly removed by a periplasmic transport system. The core structure of the CatF subunit was closely related to seven other catalases with root-mean-square deviations (RMSDs) of 368 core Calpha atoms of 0.99-1.30 A. The heme component of CatF is heme b in the same orientation that is found in Escherichia coli hydroperoxidase II, an orientation that is flipped 180 degrees with respect the orientation of the heme in bovine liver catalase. NADPH is not found in the structure of CatF because key residues required for nucleotide binding are missing; 2129 water molecules were refined into the model. Water occupancy in the main or perpendicular channel of CatF varied among the four subunits from two to five in the region between the heme and the conserved Asp150. A comparison of the water occupancy in this region with the same region in other catalases reveals significant differences among the catalases.     

EHD2 and the novel EH domain binding protein EHBP1 couple endocytosis to the actin cytoskeleton

Here we identified two novel proteins denoted EH domain protein 2 (EHD2) and EHD2-binding protein 1 (EHBP1) that link clathrin-mediated endocytosis to the actin cytoskeleton. EHD2 contains an N-terminal P-loop and a C-terminal EH domain that interacts with NPF repeats in EHBP1. Disruption of EHD2 or EHBP1 function by small interfering RNA-mediated gene silencing inhibits endocytosis of transferrin into EEA1-positive endosomes as well as GLUT4 endocytosis into cultured adipocytes. EHD2 localizes with cortical actin filaments, whereas EHBP1 contains a putative actin-binding calponin homology domain. High expression of EHD2 or EHBP1 in intact cells mediates extensive actin reorganization. Thus EHD2 appears to connect endocytosis to the actin cytoskeleton through interactions of its N-terminal domain with membranes and its C-terminal EH domain with the novel EHBP1 protein.