Haplotype variation and phylogeography of Rhizoctonia solani AG1-IA strains based on rDNA5.8S-ITS and ß-actin gene sequence analyses

The haplotype variation and phylogeography of Rhizoctonia solani AG1-IA strains were estimated using rDNA5.8S-ITS and ß-actin gene sequences. Two haplotypes of ITS sequences were revealed, designated as ITSa and ITSb. Thirty-four SNPs from the ß-actin gene, which displayed more allele discriminations than rDNA-ITS, were identified. The SNPs were used to classify R. solani into 12 haplotypes, designated as H1–H12. Most SNPs occurred at the third codon position and resulted as silent mutations. Three SNPs occurred at the first codon position and one SNP occurred at the second position, which these four SNPs causing non-synonymous mutations. According to the translational amino acid sequences, the 12 nucleotide-inferred haplotypes were further classified into 5 groups, designated as ITRL, VARI, VARL, VTRI, and VAMI. Analysis of the geographical distribution of 12 haplotypes, showed that H1 and H9 were widely distributed in all studied locations and existed simultaneously in the strains collected in most areas. The results lead to the speculation that H1 and H9 could be the founder haplotypes of ß-actin gene, and other haplotypes might be derived from them.     

MicroRNA miR-320a and miR-140 inhibit mink enteritis virus infection by repression of its receptor,feline transferrin receptor

Mink enteritis virus (MEV) is one of the most important pathogens in the mink industry. Recent studies have shed light into the role of microRNAs (miRNAs), small noncoding RNAs of length ranging from 18–23 nucleotides (nt), as critical modulators in the host-pathogen interaction networks. We previously showed that miRNA miR-181b can inhibit MEV replication by repression of viral non-structural protein 1 expression. Here, we report that two other miRNAs (miR-320a and miR-140) inhibit MEV entry into feline kidney (F81) cells by downregulating its receptor, transferrin receptor (TfR), by targeting the 3′ untranslated region (UTR) of TfR mRNA, while being themselves upregulated.     

Erratum to: Maize grain concentrations and above-ground shoot acquisition of micronutrients as affected by intercropping with turnip,faba bean,chickpea, and soybean

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Sensitization enhancement of europium in ZnSe/ZnS core/shell quantum dots induced by efficient energy transfer

Eu‐doped ZnSe:/ZnS quantum dots (formed as ZnSe:Eu/ZnS QDs) were successfully synthesized by a two‐step wet chemical method: nucleation doping and epitaxial shell growing. The sensitization characteristics of Eu‐doped ZnSe and ZnSe/ZnS core/shell QD are studied in detail using photoluminescence (PL), PL excitation spectra (PLE) and time‐resolved PL spectroscopy. The emission intensity of Eu ions is enhanced and that of ZnSe QDs is decreased, implying that energy was transferred from the excited ZnSe host materials (the donor) to the doped Eu ions (the acceptor). PLE reveals that the ZnSe QDs act as an antenna for the sensitization of Eu ions through an energy transfer process. The dynamics of ZnSe:Eu/ZnS core/shell quantum dots with different shell thicknesses and doping concentrations are studied via PL spectra and fluorescence lifetime spectra. The maximum phosphorescence efficiency is obtained when the doping concentration of Eu is approximately 6% and the sample showed strong white light under ultraviolet lamp illumination. By surface modification with ZnS shell layer, the intensity of Eu‐related PL emission is increased approximately three times compared with that of pure ZnSe:Eu QDs. The emission intensity and wavelength of ZnSe:Eu/ZnS core/shell quantum dots can be modulated by different shell thickness and doping concentration. The results provide a valuable insight into the doping control for practical applications in laser, light‐emitting diodes and in the field of biotechnology. Copyright © 2014 John Wiley & Sons, Ltd.     

Pathological Mechanism for Delayed Hyperenhancement of Chronic Scarred Myocardium in Contrast Agent Enhanced Magnetic Resonance Imaging

Objectives

To evaluate possible mechanism for delayed hyperenhancement of scarred myocardium by investigating the relationship of contrast agent (CA) first pass and delayed enhancement patterns with histopathological changes.

Materials and Methods

Eighteen pigs underwent 4 weeks ligation of 1 or 2 diagonal coronary arteries to induce chronic infarction. The hearts were then removed and perfused in a Langendorff apparatus. The hearts firstly experienced phosphorus 31 MR spectroscopy. The hearts in group I (n = 9) and II (n = 9) then received the bolus injection of Gadolinium diethylenetriamine pentaacetic acid (0.05 mmol/kg) and gadolinium-based macromolecular agent (P792, 15 µmol/kg), respectively. First pass T₂ ^* MRI was acquired using a gradient echo sequence. Delayed enhanced T₁ MRI was acquired with an inversion recovery sequence. Masson''s trichrome and anti- von Willebrand Factor (vWF) staining were performed for infarct characterization.

Results

Wash-in of both kinds of CA caused the sharp and dramatic T₂ ^* signal decrease of scarred myocardium similar to that of normal myocardium. Myocardial blood flow and microvessel density were significantly recovered in 4-week-old scar tissue. Steady state distribution volume (ΔR₁ relaxation rate) of Gd-DTPA was markedly higher in scarred myocardium than in normal myocardium, whereas ΔR₁ relaxation rate of P792 did not differ significantly between scarred and normal myocardium. The ratio of extracellular volume to the total water volume was significantly greater in scarred myocardium than in normal myocardium. Scarred myocardium contained massive residual capillaries and dilated vessels. Histological stains indicated the extensively discrete matrix deposition and lack of cellular structure in scarred myocardium.

Conclusions

Collateral circulation formation and residual vessel effectively delivered CA into scarred myocardium. However, residual vessel without abnormal hyperpermeability allowed Gd-DTPA rather than P792 to penetrate into extravascular compartment. Discrete collagen fiber meshwork and loss of cellularity enlarged extracellular space accessible to Gd-DTPA, resulting in the delayed hyper-enhanced scar.     

Tissue Culture-Induced Heritable Genomic Variation in Rice,and Their Phenotypic Implications

Background

Somaclonal variation generally occurs in plants regenerated from tissue culture. However, fundamental issues regarding molecular characteristics, mutation rates and mutation spectra of plant somatic variation as well as their phenotypic relevance have been addressed only recently. Moreover, these studies have reported highly discrepant results in different plant species and even in the same plant genotype.

Methodology/principal findings

We investigated heritable genomic variation induced by tissue culture in rice by whole genome re-sequencing of an extensively selfed somaclonal line (TC-reg-2008) and its wild type (WT) donor (cv. Hitomebore). We computed the overall mutation rate, single nucleotide polymorphisms (SNPs), small scale insertions/deletions (Indels) and mobilization of transposable elements (TEs). We assessed chromosomal distribution of the various types of genomic variations, tested correlations between SNPs and Indels, and examined concomitancy between TE activity and its cytosine methylation states. We also performed gene ontology (GO) analysis of genes containing nonsynonymous mutations and large-effect mutations, and assayed effects of the genomic variations on phenotypes under both normal growing condition and several abiotic stresses. We found that heritable somaclonal genomic variation occurred extensively in rice. The genomic variations distributed non-randomly across each of the 12 rice chromosomes, and affected a large number of functional genes. The phenotypic penetrance of the genomic variations was condition-dependent.

Conclusions/significance

Tissue culture is a potent means to generate heritable genetic variations in rice, which bear distinct difference at least in space (chromosomal distribution) from those occurred under natural settings. Our findings have provided new information regarding the mutation rate and spectrum as well as chromosomal distribution pattern of somaclonal variation in rice. Our data also suggest that rice possesses a strong capacity to canalize genetic variations under normal growing conditions to maintain phenotypic robustness, which however can be released by certain abiotic stresses to generate variable phenotypes.     

Species Associations in a Species-Rich Subtropical Forest Were Not Well-Explained by Stochastic Geometry of Biodiversity

The stochastic dilution hypothesis has been proposed to explain species coexistence in species-rich communities. The relative importance of the stochastic dilution effects with respect to other effects such as competition and habitat filtering required to be tested. In this study, using data from a 25-ha species-rich subtropical forest plot with a strong topographic structure at Badagongshan in central China, we analyzed overall species associations and fine-scale species interactions between 2,550 species pairs. The result showed that: (1) the proportion of segregation in overall species association analysis at 2 m neighborhood in this plot followed the prediction of the stochastic dilution hypothesis that segregations should decrease with species richness but that at 10 m neighborhood was higher than the prediction. (2) The proportion of no association type was lower than the expectation of stochastic dilution hypothesis. (3) Fine-scale species interaction analyses using Heterogeneous Poisson processes as null models revealed a high proportion (47%) of significant species effects. However, the assumption of separation of scale of this method was not fully met in this plot with a strong fine-scale topographic structure. We also found that for species within the same families, fine-scale positive species interactions occurred more frequently and negative ones occurred less frequently than expected by chance. These results suggested effects of environmental filtering other than species interaction in this forest. (4) We also found that arbor species showed a much higher proportion of significant fine-scale species interactions (66%) than shrub species (18%). We concluded that the stochastic dilution hypothesis only be partly supported and environmental filtering left discernible spatial signals in the spatial associations between species in this species-rich subtropical forest with a strong topographic structure.     

GMEnzy: A Genetically Modified Enzybiotic Database

GMEs are genetically modified enzybiotics created through molecular engineering approaches to deal with the increasing problem of antibiotic resistance prevalence. We present a fully manually curated database, GMEnzy, which focuses on GMEs and their design strategies, production and purification methods, and biological activity data. GMEnzy collects and integrates all available GMEs and their related information into one web based database. Currently GMEnzy holds 186 GMEs from published literature. The GMEnzy interface is easy to use, and allows users to rapidly retrieve data according to desired search criteria. GMEnzy’s construction will increase the efficiency and convenience of improving these bioactive proteins for specific requirements, and will expand the arsenal available for researches to control drug-resistant pathogens. This database will prove valuable for researchers interested in genetically modified enzybiotics studies. GMEnzy is freely available on the Web at http://biotechlab.fudan.edu.cn/database/gmenzy/.