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| | 1. |
2012 Jul |
Effect of Biodiversity Changes in Disease Risk: Exploring Disease Emergence in a Plant-Virus System
Pagán, González-Jara, Moreno-Letelier, Rodelo-Urrego, Fraile, Piñero, García-Arenal
PLoS Pathog 2012 Jul;8(7).
Abstract
The effect of biodiversity on the ability of parasites to infect their host and cause disease (i.e. disease risk) is a major question in pathology, which is central to understand the emergence of infectious diseases, and to develop strategies for their management. Two hypotheses, which can be considered as extremes of a continuum, relate biodiversity to disease risk: One states that biodiversity is positively correlated with disease risk (Amplification Effect), and the second predicts a negative correlation between biodiversity and disease risk (Dilution Effect). Which of them applies better to different host-parasite systems is still a source of debate, due to limited experimental or empirical data. This is especially the case for viral diseases of plants. To address this subject, we have monitored for three years the prevalence of several viruses, and virus-associated symptoms, in populations of wild pepper (chiltepin) under different levels of human management. For each population, we also measured the habitat species diversity, host plant genetic diversity and host plant density. Results indicate that disease and infection risk increased with the level of human management, which was associated with decreased species diversity and host genetic diversity, and with increased host plant density. Importantly, species diversity of the habitat was the primary predictor of disease risk for wild chiltepin populations. This changed in managed populations where host genetic diversity was the primary predictor. Host density was generally a poorer predictor of disease and infection risk. These results support the dilution effect hypothesis, and underline the relevance of different ecological factors in determining disease/infection risk in host plant populations under different levels of anthropic influence. These results are relevant for managing plant diseases and for establishing conservation policies for endangered plant species.
[Pubmed: 22792068]
| | 2. |
2012 Jul 13 |
Molecular Detection of Eukaryotes in a Single Human Stool Sample from Senegal
Hamad, Sokhna, Raoult, Bittar
PLoS One 2012 Jul 13;7(7). published online before print
Abstract
Microbial eukaryotes represent an important component of the human gut microbiome, with different beneficial or harmful roles; some species are commensal or mutualistic, whereas others are opportunistic or parasitic. The diversity of eukaryotes inhabiting humans remains relatively unexplored because of either the low abundance of these organisms in human gut or because they have received limited attention from a whole-community perspective.
[Pubmed: 22808282]
| | 3. |
2012 Jul |
Update on sumoylation: defining core components of the plant SUMO conjugation system by phylogenetic comparison.
Novatchkova M, Tomanov K, Hofmann K, Stuible HP, Bachmair A
New Phytol. 2012 Jul;195(1):23-31.
Abstract
The conjugation of the small ubiquitin-related modifier, SUMO, to substrate proteins is a reversible and dynamic process, and an important response of plants to environmental challenges. Nevertheless, reliable data have so far been restricted largely to the model plant Arabidopsis thaliana. The increasing availability of genome information for other plant species offers the possibility to identify a core set of indispensable components, and to discover species-specific features of the sumoylation pathway. We analyzed the enzymes responsible for the conjugation of SUMO to substrates for their conservation between dicots and monocots. We thus assembled gene sets that relate the Arabidopsis SUMO conjugation system to that of the dicot species tomato, grapevine and poplar, and to four plant species from the monocot class: rice, Brachypodium distachyon, Sorghum bicolor and maize. We found that a core set of genes with clear assignment in Arabidopsis had highly conserved homologs in all tested plants. However, we also observed a variation in the copy number of homologous genes, and sequence variations that suggested monocot-specific variants. Generally, SUMO ligases and proteases showed the most pronounced differences. Finally, we identified potential SUMO chain-binding ubiquitin ligases, pointing to an in vivo function of SUMO chains as degradation signals in plants.
[Pubmed: 22799003]
| | 4. |
2012 Jul 16 |
“Scanning mutagenesis” of the amino acid sequences flanking phosphorylation site 1 of the mitochondrial pyruvate dehydrogenase complex
Ahsan, Swatek, Zhang, Miernyk, Xu, Thelen
Front Plant Sci 2012 Jul 16;3. published online before print
Abstract
The mitochondrial pyruvate dehydrogenase complex (mtPDC) is regulated by reversible seryl-phosphorylation of the E1α subunit by a dedicated, intrinsic kinase. The phospho-complex is reactivated when dephosphorylated by an intrinsic PP2C-type protein phosphatase. Both the position of the phosphorylated Ser-residue and the sequences of the flanking amino acids are highly conserved. We have used the synthetic peptide-based kinase client (KiC) assay plus recombinant pyruvate dehydrogenase E1α and E1α-kinase to perform “scanning mutagenesis” of the residues flanking the site of phosphorylation. Consistent with the results from “phylogenetic analysis” of the flanking sequences, the direct peptide-based kinase assays tolerated very few changes. Even conservative changes such as Leu, Ile, or Val for Met, or Glu for Asp, gave very marked reductions in phosphorylation. Overall the results indicate that regulation of the mtPDC by reversible phosphorylation is an extreme example of multiple, interdependent instances of co-evolution.
[Pubmed: 22811682]
| | 5. |
2012 Jul 10 |
Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato
Sim, Durstewitz, Plieske, Wieseke, Ganal, Van Deynze, Hamilton, Buell, Causse, Wijeratne, Francis
PLoS One 2012 Jul 10;7(7). published online before print
Abstract
The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F2 populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.
[Pubmed: 22802968]
| | 6. |
2012 Jul 13 |
Modeling the Hydrodynamics of Phloem Sieve Plates
Jensen, Mullendore, Holbrook, Bohr, Knoblauch, Bruus
Front Plant Sci 2012 Jul 13;3. published online before print
Abstract
Sieve plates have an enormous impact on the efficiency of the phloem vascular system of plants, responsible for the distribution of photosynthetic products. These thin plates, which separate neighboring phloem cells, are perforated by a large number of tiny sieve pores and are believed to play a crucial role in protecting the phloem sap from intruding animals by blocking flow when the phloem cell is damaged. The resistance to the flow of viscous sap in the phloem vascular system is strongly affected by the presence of the sieve plates, but the hydrodynamics of the flow through them remains poorly understood. We propose a theoretical model for quantifying the effect of sieve plates on the phloem in the plant, thus unifying and improving previous work in the field. Numerical simulations of the flow in real and idealized phloem channels verify our model, and anatomical data from 19 plant species are investigated. We find that the sieve plate resistance is correlated to the cell lumen resistance, and that the sieve plate and the lumen contribute almost equally to the total hydraulic resistance of the phloem translocation pathway.
[Pubmed: 22811681]
| | 7. |
2012 Jul 17 |
Two Unique Ligand-Binding Clamps of Rhizopus oryzae Starch Binding Domain for Helical Structure Disruption of Amylose
Jiang, Ci, Chou, Lee, Sun, Chou, Li, Chang
PLoS One 2012 Jul 17;7(7). published online before print
Abstract
The N-terminal starch binding domain of Rhizopus oryzae glucoamylase (RoSBD) has a high binding affinity for raw starch. RoSBD has two ligand-binding sites, each containing a ligand-binding clamp: a polyN clamp residing near binding site I is unique in that it is expressed in only three members of carbohydrate binding module family 21 (CBM21) members, and a Y32/F58 clamp located at binding site II is conserved in several CBMs. Here we characterized different roles of these sites in the binding of insoluble and soluble starches using an amylose-iodine complex assay, atomic force microscopy, isothermal titration calorimetry, site-directed mutagenesis, and structural bioinformatics. RoSBD induced the release of iodine from the amylose helical cavity and disrupted the helical structure of amylose type III, thereby significantly diminishing the thickness and length of the amylose type III fibrils. A point mutation in the critical ligand-binding residues of sites I and II, however, reduced both the binding affinity and amylose helix disruption. This is the first molecular model for structure disruption of the amylose helix by a non-hydrolytic CBM21 member. RoSBD apparently twists the helical amylose strands apart to expose more ligand surface for further SBD binding. Repeating the process triggers the relaxation and unwinding of amylose helices to generate thinner and shorter amylose fibrils, which are more susceptible to hydrolysis by glucoamylase. This model aids in understanding the natural roles of CBMs in protein-glycan interactions and contributes to potential molecular engineering of CBMs.
[Pubmed: 22815939]
| | 8. |
2012 Jul 17 |
Complexity and Variability of Gut Commensal Microbiota in Polyphagous Lepidopteran Larvae
Tang, Freitak, Vogel, Ping, Shao, Cordero, Andersen, Westermann, Heckel, Boland
PLoS One 2012 Jul 17;7(7). published online before print
Abstract
The gut of most insects harbours nonpathogenic microorganisms. Recent work suggests that gut microbiota not only provide nutrients, but also involve in the development and maintenance of the host immune system. However, the complexity, dynamics and types of interactions between the insect hosts and their gut microbiota are far from being well understood.
[Pubmed: 22815679]
| | 9. |
2012 Jul 11 |
An Automated Flow for Directed Evolution Based on Detection of Promiscuous Scaffolds Using Spatial and Electrostatic Properties of Catalytic Residues
Chakraborty
PLoS One 2012 Jul 11;7(7). published online before print
Abstract
The aspiration to mimic and accelerate natural evolution has fueled interest in directed evolution experiments, which endow or enhance functionality in enzymes. Barring a few de novo approaches, most methods take a template protein having the desired activity, known active site residues and structure, and proceed to select a target protein which has a pre-existing scaffold congruent to the template motif. Previously, we have established a computational method (CLASP) based on spatial and electrostatic properties to detect active sites, and a method to quantify promiscuity in proteins. We exploit the prospect of promiscuous active sites to serve as the starting point for directed evolution and present a method to select a target protein which possesses a significant partial match with the template scaffold (DECAAF). A library of partial motifs, constructed from the active site residues of the template protein, is used to rank a set of target proteins based on maximal significant matches with the partial motifs, and cull out the best candidate from the reduced set as the target protein. Considering the scenario where this ‘incubator’ protein lacks activity, we identify mutations in the target protein that will mirror the template motif by superimposing the target and template protein based on the partial match. Using this superimposition technique, we analyzed the less than expected gain of activity achieved by an attempt to induce β-lactamase activity in a penicillin binding protein (PBP) (PBP-A from T. elongatus), and attributed this to steric hindrance from neighboring residues. We also propose mutations in PBP-5 from E. coli, which does not have similar steric constraints. The flow details have been worked out in an example which aims to select a substitute protein for human neutrophil elastase, preferably related to grapevines, in a chimeric anti-microbial enzyme which bolsters the innate immune defense system of grapevines.
[Pubmed: 22811760]
| | 10. |
2012 Jul 17 |
Shifting Preference between Oviposition vs. Host-Feeding under Changing Host Densities in Two Aphelinid Parasitoids
Yang, Ji, Lövei, Wan
PLoS One 2012 Jul 17;7(7). published online before print
Abstract
Destructive host-feeding is common in hymenopteran parasitoids. Such feeding may be restricted to host stages not preferred for oviposition. However, whether this is a fixed strategy or can vary according to resource levels or parasitoid needs is less clear. We tested the trade-off between host feeding and oviposition on two whitefly parasitoids under varying host densities. Females of two aphelinid parasitoids, Eretmocerus hayati and Encarsia sophia were exposed to nine different densities of their whitefly host, Bemisia tabaci, in single-instar tests to identify their functional response. Mixed-instar host choice tests were also conducted by exposing whiteflies at four densities to the parasitoids. We hypothesized that the parasitoid females can detect different host densities, and decide on oviposition vs. host-feeding accordingly. The results showed that both Er. hayati and En. sophia females tended to increase both oviposition and host-feeding with increased host density within a certain range. Oviposition reached a plateau at lower host density than host-feeding in Er. hayati, while En. sophia reached its oviposition plateau at higher densities. At low densities, Er. hayati parasitized most on first and second (the optimal ones), and fed most on third nymphal instars (the suboptimal one) of the whitefly host as theory predicts, while at high densities, both parasitism and host-feeding occurred on first and second instars which are preferred for oviposition. En. sophia parasitized most on third and fourth (the optimal ones), while fed on first instars (the suboptimal one) at low densities, and utilized third and fourth instars for both at high densities. In conclusion, oviposition vs. host-feeding strategy of parasitoid females was found to vary at different host densities. The balance between reserving optimal hosts for oviposition or using them for host-feeding depended on parasitoid life history and the availability of host resources.
[Pubmed: 22815964]
| | 11. |
2012 Jul 06 |
Cell wall evolution and diversity
Fangel, Ulvskov, Knox, Mikkelsen, Harholt, Popper, Willats
Front Plant Sci 2012 Jul 06;3. published online before print
Abstract
Plant cell walls display a considerable degree of diversity in their compositions and molecular architectures. In some cases the functional significance of a particular cell wall type appears to be easy to discern: secondary cells walls are often reinforced with lignin that provides durability; the thin cell walls of pollen tubes have particular compositions that enable their tip growth; lupin seed cell walls are characteristically thickened with galactan used as a storage polysaccharide. However, more frequently the evolutionary mechanisms and selection pressures that underpin cell wall diversity and evolution are unclear. For diverse green plants (chlorophytes and streptophytes) the rapidly increasing availability of transcriptome and genome data sets, the development of methods for cell wall analyses which require less material for analysis, and expansion of molecular probe sets, are providing new insights into the diversity and occurrence of cell wall polysaccharides and associated biosynthetic genes. Such research is important for refining our understanding of some of the fundamental processes that enabled plants to colonize land and to subsequently radiate so comprehensively. The study of cell wall structural diversity is also an important aspect of the industrial utilization of global polysaccharide bio-resources.
[Pubmed: 22783271]
| | 12. |
2012 Jul 27 |
Potential Distribution of the Australian Native Chloris truncata Based on Modelling Both the Successful and Failed Global Introductions
Michael, Yeoh, Scott
PLoS One 2012 Jul 27;7(7). published online before print
Abstract
Our aim was to model the current and future potential global distribution of Chloris truncata (windmill grass) based on the plant's biology, soil requirements and colonisation success. The growth response of C. truncata to constant temperatures and soil moisture levels were measured and estimated respectively, to develop parameters for a CLIMEX bioclimatic model of potential distribution. The native distribution in eastern Australia and naturalised distribution in Western Australia was also used to inform the model. Associations with soil types were assessed within the suitable bioclimatic region in Australia. The global projection of the model was tested against the distribution of soil types and the known successful and failed global introductions. The verified model was then projected to future conditions due to climate change. Optimal temperature for plant development was 28°C and the plant required 970 degree-days above a threshold of 10°C. Early collection records indicate that the species is native to Queensland, New South Wales and Victoria. The plant has been introduced elsewhere in Australia and throughout the world as a wool contaminant and as a potential pasture species, but some of the recorded establishments have failed to persist. The CLIMEX model projected to the world reflected effectively both the successful and failed distributions. The inclusion of soil associations improved the explanation of the observed distribution in Australia, but did not improve the ability to determine the potential distribution elsewhere, due to lack of similarity of soil types between continents. The addition of a climate change projection showed decreased suitability for this species in Australia, but increased suitability for other parts of the world, including regions where the plant previously failed to establish.
[Pubmed: 22848733]
| | 13. |
2012 Jul 27 |
Diversity and Relationships of Eggplants from Three Geographically Distant Secondary Centers of Diversity
Hurtado, Vilanova, Plazas, Gramazio, Fonseka, Fonseka, Prohens
PLoS One 2012 Jul 27;7(7). published online before print
Abstract
Eggplant (Solanum melongena L.) was domesticated in the Indo-Birmanian region, which is also the primary center of diversity for this crop. From there eggplant spread to other regions, and diversity accumulated in several secondary centers of diversity. We have assessed the diversity and relationships of 52 accessions of eggplant from three geographically distant secondary centers of diversity (China, Spain, and Sri Lanka) using 28 morphological descriptors and 12 highly polymorphic genomic SSRs. A wide variation was found for most morphological traits, and significant differences among the three centers of diversity were detected for 22 of these traits. The PCA analysis showed that eggplants from the three origins were morphologically differentiated, and accessions from each of the three secondary centers of diversity presented a typical combination of morphological characteristics. In this respect, discriminant analysis showed that accessions could be correctly classified to their origin using only six traits. The SSR characterization identified 110 alleles and allowed obtaining a unique genetic fingerprint for each accession. Many alleles were found to be private to each origin, but no universal alleles were found for any of the origins. The PCA analysis showed that the genetic differentiation among origins was less clear than for morphological traits, although the analysis of the population structure shows that accessions mostly group according to the origin, but also provides evidence of migration among the three secondary centers of diversity. The genetic diversity (HT) within each origin was high, ranging between HT = 0.5400 (Sri Lanka) and HT = 0.4943 (China), while the standardized genetic differentiation (G’ST) among origins was moderate (G’ST = 0.2657). The correlation between morphological and SSR distances was non-significant (r = 0.044), indicating that both data are complementary for the conservation of germplasm and breeding of eggplant. These results are relevant for the management of genetic resources, breeding programmes, and evolutionary studies of eggplant.
[Pubmed: 22848589]
| | 14. |
2012 Jul 18 |
Evolution of the Land Plant Exocyst Complexes
Cvrčková, Grunt, Bezvoda, Hála, Kulich, Rawat, Žárský
Front Plant Sci 2012 Jul 18;3. published online before print
Abstract
Exocyst is an evolutionarily conserved vesicle tethering complex functioning especially in the last stage of exocytosis. Homologs of its eight canonical subunits – Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70, and Exo84 – were found also in higher plants and confirmed to form complexes in vivo, and to participate in cell growth including polarized expansion of pollen tubes and root hairs. Here we present results of a phylogenetic study of land plant exocyst subunits encoded by a selection of completely sequenced genomes representing a variety of plant, mostly angiosperm, lineages. According to their evolution histories, plant exocyst subunits can be divided into several groups. The core subunits Sec6, Sec8, and Sec10, together with Sec3 and Sec5, underwent few, if any fixed duplications in the tracheophytes (though they did amplify in the moss Physcomitrella patens), while others form larger families, with the number of paralogs ranging typically from two to eight per genome (Sec15, Exo84) to several dozens per genome (Exo70). Most of the diversity, which can be in some cases traced down to the origins of land plants, can be attributed to the peripheral subunits Exo84 and, in particular, Exo70. As predicted previously, early land plants (including possibly also the Rhyniophytes) encoded three ancestral Exo70 paralogs which further diversified in the course of land plant evolution. Our results imply that plants do not have a single “Exocyst complex” – instead, they appear to possess a diversity of exocyst variants unparalleled among other organisms studied so far. This feature might perhaps be directly related to the demands of building and maintenance of the complicated and spatially diverse structures of the endomembranes and cell surfaces in multicellular land plants.
[Pubmed: 22826714]
| | 15. |
2012 Jul 25 |
ATP Hydrolyzing Salivary Enzymes of Caterpillars Suppress Plant Defenses
Wu, Peiffer, Luthe, Felton
PLoS One 2012 Jul 25;7(7). published online before print
Abstract
The oral secretions of herbivores are important recognition cues that can be used by plants to mediate induced defenses. In this study, a degradation of adenosine-5′-triphosphate (ATP) in tomato leaves was detected after treatment with Helicoverpa zea saliva. Correspondingly, a high level of ATPase activity in saliva was detected and three ATP hydrolyzing enzymes: apyrase, ATP synthase and ATPase 13A1 were identified in salivary glands. To determine the functions of these proteins in mediating defenses, they were cloned from H. zea and expressed in Escherichia coli. By applying the purified expressed apyrase, ATP synthase or ATPase 13A1 to wounded tomato leaves, it was determined that these ATP hydrolyzing enzymes suppressed the defensive genes regulated by the jasmonic acid and ethylene pathways in tomato plant. Suppression of glandular trichome production was also observed after treatment. Blood-feeding arthropods employ 5′-nucleotidase family of apyrases to circumvent host responses and the H. zea apyrase, is also a member of this family. The comparatively high degree of sequence similarity of the H. zea salivary apyrase with mosquito apyrases suggests a broader evolutionary role for salivary apyrases than previously envisioned.
[Pubmed: 22848670]
| | 16. |
2012 Jul 31 |
Modification of Seed Oil Composition in Arabidopsis by Artificial microRNA-Mediated Gene Silencing
Belide, Petrie, Shrestha, Singh
Front Plant Sci 2012 Jul 31;3. published online before print
Abstract
Various post transcriptional gene silencing strategies have been developed and exploited to study gene function or engineer disease resistance. The recently developed artificial microRNA strategy is an alternative method of effectively silencing target genes. The Δ12-desaturase (FAD2), Fatty acid elongase (FAE1), and Fatty acyl-ACP thioesterase B (FATB) were targeted with amiR159b-based constructs in Arabidopsis
thaliana to evaluate changes in oil composition when expressed with the seed-specific Brassica napus truncated napin (FP1) promoter. Fatty acid profiles from transgenic homozygous seeds reveal that the targeted genes were silenced. The down-regulation of the AtFAD-2 gene substantially increased oleic acid from the normal levels of ∼15% to as high as 63.3 and reduced total PUFA content (18:2Δ9,12 + 18:3Δ9,12,15 + 20:2Δ11,14 + 20:3Δ11,14,17) from 46.8 to 4.8%. Δ12-desaturase activity was reduced to levels as low as those in the null fad-2-1 and fad-2-2 mutants. Silencing of the FAE1 gene resulted in the reduction of eicosenoic acid (20:1Δ11) to 1.9 from 15.4% and silencing of FATB resulted in the reduction of palmitic acid (16:0) to 4.4% from 8.0%. Reduction in FATB activity is comparable with a FATB knock-out mutant. These results demonstrate for the first time amiR159b constructs targeted against three endogenous seed-expressed genes are clearly able to down-regulate and generate genotypic changes that are inherited stably over three generations.
[Pubmed: 22866055]
| | 17. |
2012 Jul 30 |
Proteome Analysis of the Wild and YX-1 Male Sterile Mutant Anthers of Wolfberry (Lycium barbarum L.)
Zheng, Sijun Yue, Xu, Liu, Xu, Wang, Han, Yu
PLoS One 2012 Jul 30;7(7). published online before print
Abstract
Pollen development is disturbed in the early tetrad stage of the YX-1 male sterile mutant of wolfberry (Lycium barbarum L.). The present study aimed to identify differentially expressed anther proteins and to reveal their possible roles in pollen development and male sterility. To address this question, the proteomes of the wild-type (WT) and YX-1 mutant were compared. Approximately 1760 protein spots on two-dimensional differential gel electrophoresis (2D-DIGE) gels were detected. A number of proteins whose accumulation levels were altered in YX-1 compared with WT were identified by mass spectrometry and the NCBInr and Viridiplantae EST databases. Proteins down-regulated in YX-1 anthers include ascorbate peroxidase (APX), putative glutamine synthetase (GS), ATP synthase subunits, chalcone synthase (CHS), CHS-like, putative callose synthase catalytic subunit, cysteine protease, 5B protein, enoyl-ACP reductase, 14-3-3 protein and basic transcription factor 3 (BTF3). Meanwhile, activities of APX and GS, RNA expression levels of apx and atp synthase beta subunit were low in YX-1 anthers which correlated with the expression of male sterility. In addition, several carbohydrate metabolism-related and photosynthesis-related enzymes were also present at lower levels in the mutant anthers. In contrast, 26S proteasome regulatory subunits, cysteine protease inhibitor, putative S-phase Kinase association Protein 1(SKP1), and aspartic protease, were expressed at higher levels in YX-1 anthers relative to WT anthers. Regulation of wolfberry pollen development involves a complex network of differentially expressed genes. The present study lays the foundation for future investigations of gene function linked with wolfberry pollen development and male sterility.
[Pubmed: 22860020]
| | 18. |
2012 Jul 18 |
Sexual Compatibility among Different Host-Originated Isolates of Aphelenchoides besseyi and the Inheritance of the Parasitism
Hsieh, Lin, Chen
PLoS One 2012 Jul 18;7(7). published online before print
Abstract
Nine isolates of Aphelenchoides besseyi from two different hosts were studied. The isolates were identified at the species level according to morphometrics and fine structures observed under a scanning electron microscope. Two fern-originated isolates, Fu, and Fm, one rice-originated isolate, Rl, were not able to reproduce from a single juvenile, based on at least 50 replicates. The other six isolates were able to develop into a small population when inoculated with a single juvenile, demonstrating parthenogenesis. Crosses between isolates were conducted. In a compatibility cross experiment, three fern-originated isolates were selfed and crossed reciprocally, and all nine crossings had viable offspring. When fern isolates were used as paternal lines, the only two successful crosses were with the Rd line, and as maternal lines, only the Ff x Re and Fu x Rn crosses had viable offspring. Rl was used as the maternal line and Fm as the paternal line to study the inheritance of the bird’s-nest fern parasitism. Twenty of the 80 attempted crosses resulted in viable offspring and among these; six lines had the ability to parasitize on the bird’s-nest fern. When the F1 lines were back-crossed to the Rl maternal line, 20 viable offspring lines were obtained and among them 4 were able to parasitize bird’s-nest fern. These results indicate that bird’s-nest fern parasitism can be transferred to new generations by cross fertilization.
[Pubmed: 22815854]
| | 19. |
2012 Jun |
Antisense Inhibition of the 2-Oxoglutarate Dehydrogenase Complex in Tomato Demonstrates Its Importance for Plant Respiration and during Leaf Senescence and Fruit Maturation[W][OA]
Araújo, Tohge, Osorio, Lohse, Balbo, Krahnert, Sienkiewicz-Porzucek, Usadel, Nunes-Nesi, Fernie
Plant Cell 2012 Jun;24(6):2328-2351.
Abstract
Here, antisense inhibition of the E1 subunit of the 2-oxoglutarate dehydrogenase complex in tomato was associated with generally accelerated development. This report reveals the importance of this mitochondrial enzyme in both photosynthetic and respiratory metabolism, highlighting its significance in programs of plant development connected to carbon–nitrogen interactions.
[Pubmed: 22751214]
| | 20. |
2012 Jul |
An aerobiological perspective in allergy and asthma
Singh, Mathur
Asia Pac Allergy 2012 Jul;2(3):210-222.
Abstract
Allergic diseases are amongst the most common chronic disorders worldwide. Today, more than 300 million of the population is known to suffer from one or other allergic ailments affecting the socio-economic quality of life. Major causative agents implicated are pollen grains, fungal spores, dust mites, insect debris, animal epithelia, etc. Several aerobiological studies have been conducted in different parts of the world to ascertain aerial concentration and seasonality of pollen grains and fungi. Especially from clinical point of view, it is important to know the details about the pollen season and pollen load in the atmosphere. The flowering time of higher plants are events that come periodically in each season, but the time of blooming may differ from year to year, in different geographic locations. Based on differences recorded in several years of observations in airborne pollen, pollen calendars are drawn as an aid to allergy diagnosis and management. This review article emphasises on various aerobiological parameters of environmental pollen from different parts of the world with special emphasis from India. The role of aerobiology in the diagnosis and management of allergic diseases is reviewed briefly in this article.
[Pubmed: 22872824]
| | 21. |
2012 Aug 3 |
Sight or Scent: Lemur Sensory Reliance in Detecting Food Quality Varies with Feeding Ecology
Rushmore, Leonhardt, Drea
PLoS One 2012 Aug 3;7(8). published online before print
Abstract
Visual and olfactory cues provide important information to foragers, yet we know little about species differences in sensory reliance during food selection. In a series of experimental foraging studies, we examined the relative reliance on vision versus olfaction in three diurnal, primate species with diverse feeding ecologies, including folivorous Coquerel's sifakas (Propithecus coquereli), frugivorous ruffed lemurs (Varecia variegata spp), and generalist ring-tailed lemurs (Lemur catta). We used animals with known color-vision status and foods for which different maturation stages (and hence quality) produce distinct visual and olfactory cues (the latter determined chemically). We first showed that lemurs preferentially selected high-quality foods over low-quality foods when visual and olfactory cues were simultaneously available for both food types. Next, using a novel apparatus in a series of discrimination trials, we either manipulated food quality (while holding sensory cues constant) or manipulated sensory cues (while holding food quality constant). Among our study subjects that showed relatively strong preferences for high-quality foods, folivores required both sensory cues combined to reliably identify their preferred foods, whereas generalists could identify their preferred foods using either cue alone, and frugivores could identify their preferred foods using olfactory, but not visual, cues alone. Moreover, when only high-quality foods were available, folivores and generalists used visual rather than olfactory cues to select food, whereas frugivores used both cue types equally. Lastly, individuals in all three of the study species predominantly relied on sight when choosing between low-quality foods, but species differed in the strength of their sensory biases. Our results generally emphasize visual over olfactory reliance in foraging lemurs, but we suggest that the relative sensory reliance of animals may vary with their feeding ecology.
[Pubmed: 22870229]
| | 22. |
2012 Aug 1 |
Transgenic Resistance Confers Effective Field Level Control of Bacterial Spot Disease in Tomato
Horvath, Stall, Jones, Pauly, Vallad, Dahlbeck, Staskawicz, Scott
PLoS One 2012 Aug 1;7(8). published online before print
Abstract
We investigated whether lines of transgenic tomato (Solanum lycopersicum) expressing the Bs2 resistance gene from pepper, a close relative of tomato, demonstrate improved resistance to bacterial spot disease caused by Xanthomonas species in replicated multi-year field trials under commercial type growing conditions. We report that the presence of the Bs2 gene in the highly susceptible VF 36 background reduced disease to extremely low levels, and VF 36-Bs2 plants displayed the lowest disease severity amongst all tomato varieties tested, including commercial and breeding lines with host resistance. Yields of marketable fruit from transgenic lines were typically 2.5 times that of the non-transformed parent line, but varied between 1.5 and 11.5 fold depending on weather conditions and disease pressure. Trials were conducted without application of any copper-based bactericides, presently in wide use despite negative impacts on the environment. This is the first demonstration of effective field resistance in a transgenic genotype based on a plant R gene and provides an opportunity for control of a devastating pathogen while eliminating ineffective copper pesticides.
[Pubmed: 22870280]
| | 23. |
2012 Jul 23 |
Development and Characterization of a New TILLING Population of Common Bread Wheat (Triticum aestivum L.)
Chen, Huang, Min, Phillips, Wang, Madgwick, Parry, Hu
PLoS One 2012 Jul 23;7(7). published online before print
Abstract
Mutagenesis is an important tool in crop improvement. However, the hexaploid genome of wheat (Triticum aestivum L.) presents problems in identifying desirable genetic changes based on phenotypic screening due to gene redundancy. TILLING (Targeting Induced Local Lesions IN Genomes), a powerful reverse genetic strategy that allows the detection of induced point mutations in individuals of the mutagenized populations, can address the major challenge of linking sequence information to the biological function of genes and can also identify novel variation for crop breeding. Wheat is especially well-suited for TILLING due to the high mutation densities tolerated by polyploids. However, only a few wheat TILLING populations are currently available in the world, which is far from satisfying the requirement of researchers and breeders in different growing environments. In addition, current TILLING screening protocols require costly fluorescence detection systems, limiting their use, especially in developing countries. We developed a new TILLING resource comprising 2610 M2 mutants in a common wheat cultivar ‘Jinmai 47’. Numerous phenotypes with altered morphological and agronomic traits were observed from the M2 and M3 lines in the field. To simplify the procedure and decrease costs, we use unlabeled primers and either non-denaturing polyacrylamide gels or agarose gels for mutation detection. The value of this new resource was tested using PCR with RAPD and Intron-spliced junction (ISJ) primers, and also TILLING in three selected candidate genes, in 300 and 512 mutant lines, revealing high mutation densities of 1/34 kb by RAPD/ISJ analysis and 1/47 kb by TILLING. In total, 31 novel alleles were identified in the 3 targeted genes and confirmed by sequencing. The results indicate that this mutant population represents a useful resource for the wheat research community. We hope that the use of this reverse genetics resource will provide novel allelic diversity for wheat improvement and functional genomics.
[Pubmed: 22844501]
| | 24. |
2012 Jul |
Balancing Selection at the Tomato RCR3 Guardee Gene Family Maintains Variation in Strength of Pathogen Defense
Hörger, Ilyas, Stephan, Tellier, van der Hoorn, Rose
PLoS Genet 2012 Jul;8(7).
Abstract
Coevolution between hosts and pathogens is thought to occur between interacting molecules of both species. This results in the maintenance of genetic diversity at pathogen antigens (or so-called effectors) and host resistance genes such as the major histocompatibility complex (MHC) in mammals or resistance (R) genes in plants. In plant–pathogen interactions, the current paradigm posits that a specific defense response is activated upon recognition of pathogen effectors via interaction with their corresponding R proteins. According to the “Guard-Hypothesis,” R proteins (the “guards”) can sense modification of target molecules in the host (the “guardees”) by pathogen effectors and subsequently trigger the defense response. Multiple studies have reported high genetic diversity at R genes maintained by balancing selection. In contrast, little is known about the evolutionary mechanisms shaping the guardee, which may be subject to contrasting evolutionary forces. Here we show that the evolution of the guardee RCR3 is characterized by gene duplication, frequent gene conversion, and balancing selection in the wild tomato species Solanum peruvianum. Investigating the functional characteristics of 54 natural variants through in vitro and in planta assays, we detected differences in recognition of the pathogen effector through interaction with the guardee, as well as substantial variation in the strength of the defense response. This variation is maintained by balancing selection at each copy of the RCR3 gene. Our analyses pinpoint three amino acid polymorphisms with key functional consequences for the coevolution between the guardee (RCR3) and its guard (Cf-2). We conclude that, in addition to coevolution at the “guardee-effector” interface for pathogen recognition, natural selection acts on the “guard-guardee” interface. Guardee evolution may be governed by a counterbalance between improved activation in the presence and prevention of auto-immune responses in the absence of the corresponding pathogen.
[Pubmed: 22829777]
| | 25. |
2012 Jul 17 |
The In Planta Transcriptome of Ralstonia solanacearum: Conserved Physiological and Virulence Strategies during Bacterial Wilt of Tomato
Jacobs, Babujee, Meng, Milling, Allen
mBio 2012 Jul 17;3(4). published online before print
Abstract
Plant xylem fluid is considered a nutrient-poor environment, but the bacterial wilt pathogen Ralstonia solanacearum is well adapted to it, growing to 108 to 109 CFU/g tomato stem. To better understand how R. solanacearum succeeds in this habitat, we analyzed the transcriptomes of two phylogenetically distinct R. solanacearum strains that both wilt tomato, strains UW551 (phylotype II) and GMI1000 (phylotype I). We profiled bacterial gene expression at ~6 × 108 CFU/ml in culture or in plant xylem during early tomato bacterial wilt pathogenesis. Despite phylogenetic differences, these two strains expressed their 3,477 common orthologous genes in generally similar patterns, with about 12% of their transcriptomes significantly altered in planta versus in rich medium. Several primary metabolic pathways were highly expressed during pathogenesis. These pathways included sucrose uptake and catabolism, and components of these pathways were encoded by genes in the scrABY cluster. A UW551 scrA mutant was significantly reduced in virulence on resistant and susceptible tomato as well as on potato and the epidemiologically important weed host Solanum dulcamara. Functional scrA contributed to pathogen competitive fitness during colonization of tomato xylem, which contained ~300 µM sucrose. scrA expression was induced by sucrose, but to a much greater degree by growth in planta. Unexpectedly, 45% of the genes directly regulated by HrpB, the transcriptional activator of the type 3 secretion system (T3SS), were upregulated in planta at high cell densities. This result modifies a regulatory model based on bacterial behavior in culture, where this key virulence factor is repressed at high cell densities. The active transcription of these genes in wilting plants suggests that T3SS has a biological role throughout the disease cycle.
[Pubmed: 22807564]
| | 26. |
2012 Jul 16 |
Effector-triggered post-translational modifications and their role in suppression of plant immunity
Howden, Huitema
Front Plant Sci 2012 Jul 16;3. published online before print
Abstract
Plant–pathogen interactions feature complex signaling exchanges between host and microbes that ultimately determine association outcomes. Plants deploy pattern recognition receptors to perceive pathogen-associated molecular patterns, mount pattern-triggered immunity (PTI), and fend off potential pathogens. In recent years an increasing number of defense-signaling components have been identified along with a mechanistic understanding of their regulation during immune responses. Post-translational modifications (PTMs) are now thought to play a crucial role in regulating defense signaling. In a bid to suppress PTI and infect their host, pathogens have evolved large repertoires of effectors that trigger susceptibility and allow colonization of host tissues. While great progress has been made in elucidating defense-signaling networks in plants and the activities of effectors in immune suppression, a critical gap exists in our understanding of effector mechanism-of-action. Given the importance of PTMs in the regulation of defense signaling, we will explore the question: how do effectors modify the post-translational status of host proteins and thus interfere with host processes required for immunity? We will consider how emerging proteomics-based experimental strategies may help us answer this important question and ultimately open the pathogens’ effector black box.
[Pubmed: 22811685]
| | 27. |
2012 Jul 04 |
Analytical technologies for identification and characterization of the plant N-glycoproteome
Ruiz-May, Thannhauser, Zhang, Rose
Front Plant Sci 2012 Jul 04;3. published online before print
Abstract
N-glycosylation is one of the most common and complex post-translational modifications of eukaryotic proteins and one that has numerous roles, such as modulating protein stability, sorting, folding, enzyme activity, and ligand interactions. In plants, the functional significance of N-glycosylation is typically obscure, although it is a feature of most secreted proteins and so is potentially of considerable interest to plant cell wall biologists. While analytical pipelines have been established to characterize yeast, mammalian, and bacterial N-glycoproteomes, such large-scale approaches for the study of plant glycoproteins have yet to be reported. Indeed, the N-glycans that decorate plant and mammalian or yeast proteins are structurally distinct and so modification of existing analytical approaches are needed to tackle plant N-glycoproteomes. In this review, we summarize a range of existing technologies for large-scale N-glycoprotein analysis and highlight promising future approaches that may provide a better understanding of the plant N-glycoproteome, and therefore the cell wall proteome and other proteins associated with the secretory pathway.
[Pubmed: 22783270]
| | 28. |
2012 Jul 1 |
A Sequence-Anchored Linkage Map of the Plant–Parasitic Nematode Meloidogyne hapla Reveals Exceptionally High Genome-Wide Recombination
Thomas, Fudali, Schaff, Liu, Scholl, Opperman, Bird, Williamson
G3 (Bethesda) 2012 Jul 1;2(7):815-824. published online before print
Abstract
Root-knot nematodes (Meloidogyne spp.) cause major yield losses to many of the world’s crops, but efforts to understand how these pests recognize and interact with their hosts have been hampered by a lack of genetic resources. Starting with progeny of a cross between inbred strains (VW8 and VW9) of Meloidogyne hapla that differed in host range and behavioral traits, we exploited the novel, facultative meiotic parthenogenic reproductive mode of this species to produce a genetic linkage map. Molecular markers were derived from SNPs identified between the sequenced and annotated VW9 genome and de novo sequence of VW8. Genotypes were assessed in 183 F2 lines. The colinearity of the genetic and physical maps supported the veracity of both. Analysis of local crossover intervals revealed that the average recombination rate is exceptionally high compared with that in other metazoans. In addition, F2 lines are largely homozygous for markers flanking crossover points, and thus resemble recombinant inbred lines. We suggest that the unusually high recombination rate may be an adaptation to generate within-population genetic diversity in this organism. This work presents the most comprehensive linkage map of a parasitic nematode to date and, together with genomic and transcript sequence resources, empowers M. hapla as a tractable model. Alongside the molecular map, these progeny lines can be used for analyses of genome organization and the inheritance of phenotypic traits that have key functions in modulating parasitism, behavior, and survival and for the eventual identification of the responsible genes.
[Pubmed: 22870404]
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