Nucleotide Diversity and Molecular Evolution of the <Emphasis Type="Italic">ALK</Emphasis> Gene in Cultivated Rice and its Wild Relatives

Gelatinization temperature (GT), an important parameter for rice cooking quality, is mainly regulated by the ALK gene encoding starch synthase IIa. Here, we reported the nucleotide diversity of the ALK gene in 122 cultivated accessions and 199 wild rice accessions that were collected around the Pearl River Basin in China. A total of 93 single nucleotide ploymorphisms (SNPs) were identified, with an average of one SNP per 40 bp. Tajima D statistics revealed that the DNA sequences covering the last exon have probably evolved under balancing selection. Based on two functional SNPs (an A to G substitution at 4198 bp and a GC to TT dinucleotide substitution at 4330/4331 bp), three haplotypes, G/GC, G/TT, and A/GC, were identified in both wild and cultivated accessions, with the G/GC haplotype being predominant. Interestingly, the A/GC haplotype was exclusively found in the wild accessions from Guangdong province, while the G/TT haplotype was only present in the wild accessions from Jiangxi province and Hainan Island. This suggests that the G/TT and A/GC variants may have arisen independently and undergone balancing selection on separate haplotypes in multiple populations. Our result supports earlier hypothesis that cultivated rice was independently domesticated from multiple domestication events in China. Our study aids in the understanding of the domestication process that led to the improvement of rice grain quality.     

Designing patterns for profile HMM search

MOTIVATION: Profile HMMs are a powerful tool for modeling conserved motifs in proteins. These models are widely used by search tools to classify new protein sequences into families based on domain architecture. However, the proliferation of known motifs and new proteomic sequence data poses a computational challenge for search, requiring days of CPU time to annotate an organism's proteome. RESULTS: We use PROSITE-like patterns as a filter to speed up the comparison between protein sequence and profile HMM. A set of patterns is designed starting from the HMM, and only sequences matching one of these patterns are compared to the HMM by full dynamic programming. We give an algorithm to design patterns with maximal sensitivity subject to a bound on the false positive rate. Experiments show that our patterns typically retain at least 90% of the sensitivity of the source HMM while accelerating search by an order of magnitude. AVAILABILITY: Contact the first author at the address below.     

Ca2+ entry via TRPC channels is necessary for thrombin-induced NF-kappaB activation in endothelial cells through AMP-activated protein kinase and protein kinase Cdelta

The transient receptor potential canonical (TRPC) family channels are proposed to be essential for store-operated Ca2+ entry in endothelial cells. Ca2+ signaling is involved in NF-kappaB activation, but the role of store-operated Ca2+ entry is unclear. Here we show that thrombin-induced Ca2+ entry and the resultant AMP-activated protein kinase (AMPK) activation targets the Ca2+-independent protein kinase Cdelta (PKCdelta) to mediate NF-kappaB activation in endothelial cells. We observed that thrombin-induced p65/RelA, AMPK, and PKCdelta activation were markedly reduced by knockdown of the TRPC isoform TRPC1 expressed in human endothelial cells and in endothelial cells obtained from Trpc4 knock-out mice. Inhibition of Ca2+/calmodulin-dependent protein kinase kinase beta downstream of the Ca2+ influx or knockdown of the downstream Ca2+/calmodulin-dependent protein kinase kinase beta target kinase, AMPK, also prevented NF-kappaB activation. Further, we observed that AMPK interacted with PKCdelta and phosphorylated Thr505 in the activation loop of PKCdelta in thrombin-stimulated endothelial cells. Expression of a PKCdelta-T505A mutant suppressed the thrombin-induced but not the TNF-alpha-induced NF-kappaB activation. These findings demonstrate a novel mechanism for TRPC channels to mediate NF-kappaB activation in endothelial cells that involves the convergence of the TRPC-regulated signaling at AMPK and PKCdelta and that may be a target of interference of the inappropriate activation of NF-kappaB associated with thrombosis.     

Effects of Predator and Prey Dispersal on Success or Failure of Biological Control

Biological control, defined as the reduction of pest populations by natural enemies, is often a component of integrated pest management strategies. Augmentation of natural enemy numbers by planned releases is a common biological control method, the successes and failures of which have been extensively reviewed. The effectiveness of biological control is influenced by how populations of predators and prey (or hosts and parasitoids) disperse in patchy environments. Here, we address the question of whether such dispersal leads to beneficial or detrimental pest control outcomes by developing a simple predator-prey model with constant releases of natural enemies in a two-patch environment. Theoretical and numerical results for all possible cases indicate that population dispersal has significant effects on the persistence of pests. For some ranges of dispersal rates or parameter space, dispersal is beneficial for pest control measures but this is not so for other ranges when it is detrimental. Therefore, knowledge of pest and natural enemy dispersal is crucial for understanding the effectiveness of biological control in a patchy environment. Finally, the model is generalised for multi-patch systems.     

Identification of two antagonists of the scavenger receptor CD36 using a high-throughput screening model

CD36, a class B scavenger receptor, is an integral membrane protein that mediates the endocytosis of modified lipoproteins. The functions of CD36 are complex and have been associated with atherosclerosis. In the current study, we developed a high-throughput screening (HTS) assay to identify small molecule antagonists by expressing human CD36 using a Bac-to-Bac baculovirus expression system in Spodoptera frugiperda (Sf9) cells. Uptake of 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate-labeled acetylated low-density lipoprotein (DiI-AcLDL) revealed that the IC₅₀ values for the CD36 ligands oxidatively modified LDL (Ox-LDL), Ac-LDL, and high-density lipoprotein (HDL) were 0.039, 0.019, and 0.010 μg/ml, respectively. Using the HTS assay, two novel compounds, 2016481B and 2038751B, were found to inhibit DiI-AcLDL uptake in insect cells and exhibited IC₅₀ values of 17.4 and 23.7 μM, respectively. These two novel compounds also inhibited DiI-AcLDL uptake in cultured Chinese hamster ovary (CHO) cells permanently expressing human CD36. Furthermore, these two compounds inhibited lipid accumulation in RAW 264.7 murine macrophage cells in foam cell assays. This HTS assay represents a potential method for identifying more effective macrophage scavenger receptor antagonists, which may serve as starting points for the development of novel anti-atherosclerotic agents.     

Natural endophytic association between Rhizobium leguminosarum bv. trifolii and rice roots and assessment of its potential to promote rice growth

For over 7 centuries, production of rice (Oryza sativa L.) in Egypt has benefited from rotation with Egyptian berseem clover (Trifolium alexandrinum). The nitrogen supplied by this rotation replaces 25- 33% of the recommended rate of fertilizer-N application for rice production. This benefit to the rice cannot be explained solely by an increased availability of fixed N through mineralization of N- rich clover crop residues. Since rice normally supports a diverse microbial community of internal root colonists, we have examined the possibility that the clover symbiont, Rhizobium leguminosarum bv. trifolii colonizes rice roots endophytically in fields where these crops are rotated, and if so, whether this novel plant-microbe association benefits rice growth. MPN plant infection studies were performed on macerates of surface-sterilized rice roots inoculated on T. alexandrinum as the legume trap host. The results indicated that the root interior of rice grown in fields rotated with clover in the Nile Delta contained 10⁶ clover-nodulating rhizobial endophytes g fresh weight of root. Plant tests plus microscopical, cultural, biochemical, and molecular structure studies indicated that the numerically dominant isolates of clover-nodulating rice endophytes represent 3 – 4 authentic strains of R. leguminosarum bv. trifolii that were Nod Fix on berseem clover. Pure cultures of selected strains were able to colonize the interior of rice roots grown under gnotobiotic conditions. These rice endophytes were reisolated from surface-sterilized roots and shown by molecular methods to be the same as the original inoculant strains, thus verifying Koch's postulates. Two endophytic strains of R. leguminosarum bv. trifolii significantly increased shoot and root growth of rice in growth chamber experiments, and grain yield plus agronomic fertilizer N-use efficiency of Giza-175 hybrid rice in a field inoculation experiment conducted in the Nile Delta. Thus, fields where rice has been grown in rotation with clover since antiquity contain Fix strains of R. leguminosarum bv. trifolii that naturally colonize the rice root interior, and these true rhizobial endophytes have the potential to promote rice growth and productivity under laboratory and field conditions.     

Response of symbiotic interrelationship between soybean and the indigenous or inoculated microsymbiont,Bradyrhizobium japonicum,to soil application of manganese and molybdenum

Soybean nodulation was induced indigenously by three strains ofBradyrhizobium japonicum inoculated in each of the two previous seasons. The same strains were applied, as a peat-based inoculum in similar cell density as the indigenous ones, to a rhizobia-free soll from the same field. Inoculation was tested under soll application of 10 or 20 ppm Mn and/or 2 or 4 ppm Mo. Inoculation with the peat-based inoculum significantly increased nodule numbers and weight, dry weight, N content and mg N/g of the 50-day-old plants, number of pods and seeds per plant, seed yield, seed N content and percentage, and mg N/g of the empty pods. Increasing the application of Mn and Mo fed to further increases. There was a complex response of nodulation, vegetative growth and yield to the applications of Mn and Mo.

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Résumé La nodulation chez le soja a été induite de manière indigène par trois souches deBradyrhizobium japonicum, inoculées pendant chacune des deux saisons précédentes. Les mêmes souches ont été appliquées dans un inoculum à base de tourbe de densité similaire aux inocula indigènes, à un sol exempt de rhizobia dans le même champ. L'inoculation a été testée sous des applications au sol de 10 ou 20 ppm de Mn et/ou de 2 ou 4 ppm de Mo. L'inoculation avec l'inoculum à base de tourbe a augmenté de manière significative le nombre et le poids des nodules, leur contenu en azote et en mg d'N par g de plants âgés de 50 jours, le nombre de cosses et de grains par plant, le rendement en graines, leur contenu en azote ainsi que le pourcentage et le rapport mg d'N par g de cosses vides. L'augmentation de l'application de Mn et du Mo a conduit à un nouvel accroissment. La réponse de la nodulation, de la croissance végétative et du rendement aux applications de Mn et Mo s'est révèlée complexe.

     

Ascending Migration of Endophytic Rhizobia, from Roots to Leaves, inside Rice Plants and Assessment of Benefits to Rice Growth Physiology

Rhizobia, the root-nodule endosymbionts of leguminous plants, also form natural endophytic associations with roots of important cereal plants. Despite its widespread occurrence, much remains unknown about colonization of cereals by rhizobia. We examined the infection, dissemination, and colonization of healthy rice plant tissues by four species of gfp-tagged rhizobia and their influence on the growth physiology of rice. The results indicated a dynamic infection process beginning with surface colonization of the rhizoplane (especially at lateral root emergence), followed by endophytic colonization within roots, and then ascending endophytic migration into the stem base, leaf sheath, and leaves where they developed high populations. In situ CMEIAS image analysis indicated local endophytic population densities reaching as high as 9 × 10¹⁰ rhizobia per cm³ of infected host tissues, whereas plating experiments indicated rapid, transient or persistent growth depending on the rhizobial strain and rice tissue examined. Rice plants inoculated with certain test strains of gfp-tagged rhizobia produced significantly higher root and shoot biomass; increased their photosynthetic rate, stomatal conductance, transpiration velocity, water utilization efficiency, and flag leaf area (considered to possess the highest photosynthetic activity); and accumulated higher levels of indoleacetic acid and gibberellin growth-regulating phytohormones. Considered collectively, the results indicate that this endophytic plant-bacterium association is far more inclusive, invasive, and dynamic than previously thought, including dissemination in both below-ground and above-ground tissues and enhancement of growth physiology by several rhizobial species, therefore heightening its interest and potential value as a biofertilizer strategy for sustainable agriculture to produce the world's most important cereal crops.