We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an α-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.

SummaryWe present genome‐wide gene expression patterns as a time series through the infection cycle of the fungal pine needle blight pathogen, Dothistroma septosporum, as it invades its gymnosperm host, Pinus radiata. We determined the molecular changes at three stages of the disease cycle: epiphytic/biotrophic (early), initial necrosis (mid) and mature sporulating lesion (late). Over 1.7 billion combined plant and fungal reads were sequenced to obtain 3.2 million fungal‐specific reads, which comprised as little as 0.1% of the sample reads early in infection. This enriched dataset shows that the initial biotrophic stage is characterized by the up‐regulation of genes encoding fungal cell wall‐modifying enzymes and signalling proteins. Later necrotrophic stages show the up‐regulation of genes for secondary metabolism, putative effectors, oxidoreductases, transporters and starch degradation. This in‐depth through‐time transcriptomic study provides our first snapshot of the gene expression dynamics that characterize infection by this fungal pathogen in its gymnosperm host.

The first stereospecific synthesis of polyneuridine aldehyde (6), 16-epi-vellosimine (7), (+)-polyneuridine (8), and (+)-macusine A (9) has been accomplished from commercially available D-(+)-tryptophan methyl ester. D-(+)-Tryptophan has served here both as the chiral auxiliary and the starting material for the synthesis of the common intermediate, (+)-vellosimine (13). This alkaloid was available in enantiospecific fashion in seven reaction vessels in 27% overall yield from D-(+)-trytophan methyl ester (14) via a combination of the asymmetric Pictet-Spengler reaction, Dieckmann cyclization, and a stereocontrolled intramolecular enolate-driven palladium-mediated cross-coupling reaction. A new process for this stereocontrolled intramolecular cross-coupling has been developed via a copper-mediated process. The initial results of this investigation indicated that an enolate driven palladium-mediated cross-coupling reaction can be accomplished by a copper-mediated process which is less expensive and much easier to work-up. An enantiospecific total synthesis of (+)-polyneuridine aldehyde (6), which has been proposed as an important biogenetic intermediate in the biosynthesis of quebrachidine (2), was then accomplished in an overall yield of 14.1% in 13 reaction vessels from D-(+)-tryptophan methyl ester (14). Aldehyde 13 was protected as the Na-Boc aldehyde 32 and then converted into the prochiral C (16)-quaternary diol 12 via the practical Tollens’ reaction and deprotection. The DDQ-mediated oxidative cyclization and TFA/Et3SiH reductive cleavage served as protection/deprotection steps to provide a versatile entry into the three alkaloids, polyneuridine aldehyde (6), polyneuridine (8) and macusine A (9) from the quarternary diol 12. The oxidation of the 16-hydroxymethyl group present in the axial position was achieved with the Corey-Kim reagent to provide the desired β-axial aldehydes, polyneuridine aldehyde (6) and 16-epi-vellosimine (7) with 100% diastereoselectivity.

BackgroundGene regulatory network is an abstract mapping of gene regulations in living cells that can help to predict the system behavior of living organisms. Such prediction capability can potentially lead to the development of improved diagnostic tests and therapeutics. DNA microarrays, which measure the expression level of thousands of genes in parallel, constitute the numeric seed for the inference of gene regulatory networks. In this paper, we have proposed a new approach for inferring gene regulatory networks from time-series gene expression data using linear time-variant model. Here, Self-Adaptive Differential Evolution, a versatile and robust Evolutionary Algorithm, is used as the learning paradigm.ResultsTo assess the potency of the proposed work, a well known nonlinear synthetic network has been used. The reconstruction method has inferred this synthetic network topology and the associated regulatory parameters with high accuracy from both the noise-free and noisy time-series data. For validation purposes, the proposed approach is also applied to the simulated expression dataset of cAMP oscillations in Dictyostelium discoideum and has proved it's strength in finding the correct regulations. The strength of this work has also been verified by analyzing the real expression dataset of SOS DNA repair system in Escherichia coli and it has succeeded in finding more correct and reasonable regulations as compared to various existing works.ConclusionBy the proposed approach, the gene interaction networks have been inferred in an efficient manner from both the synthetic, simulated cAMP oscillation expression data and real expression data. The computational time of this approach is also considerably smaller, which makes it to be more suitable for larger network reconstruction. Thus the proposed approach can serve as an initiate for the future researches regarding the associated area.

2-Pyridin-2-yl-1H-benzoimidazole L3 is presented as a new, efficient, and versatile bidentate N-donor ligand suitable for the copper-catalyzed formation of vinyl C-N and C-O bonds. This inexpensive and easily prepared ligand facilitates copper-catalyzed cross-coupling reactions of alkenyl bromides and iodides with N-heterocycles and phenols to afford the desired cross-coupled products in good to excellent yields with full retention of stereochemistry. This method is particularly noteworthy given its efficiency i.e., mild reaction conditions, low catalyst loading, simplicity, versatility, and exceptional level of functional group tolerance.