Quantification of African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV-UG) in single and mixed infected Cassava (Manihot esculenta Crantz) using quantitative PCR.

The quantity of genomic DNA-A and DNA-B of African cassava mosaic virus (ACMV) and East African cassava mosaic virus Uganda (Uganda variant, EACMV-UG) was analysed using quantitative PCR to assess virus concentrations in plants from susceptible and tolerant cultivars. The concentrations of genome components in absolute and relative quantification experiments in single and mixed viral infections were determined. Virus concentration was much higher in symptomatic leaf tissues compared to non-symptomatic leaves and corresponded with the severity of disease symptoms. In general, higher titres were recorded for EACMV-UG Ca055 compared to ACMV DRC6. The quantitative assessment also showed that the distribution of both viruses in the moderately resistant cassava cv. TMS 30572 was not different from the highly susceptible cv. TME 117. Natural mixed infections with both viruses gave severe disease symptoms. Relative quantification of virus genomes in mixed infections showed higher concentrations of EACMV-UG DNA-A compared to ACMV DNA-A, but a marked reduction of EACMV-UG DNA-B. The higher concentrations of EACMV-UG DNA-B compared to EACMV DNA-A accumulation in single infections were consistent. Since DNA-B is implicated in virus cell-to-cell spread and systemic movement, the abundance of the EACMV-UG DNA-B may be an important factor driving cassava mosaic disease epidemic.

Characterization of bacteriophage vB_AbaP_PD-AB9 infecting Acinetobacter baumannii with broad host range / 中华检验医学杂志

Objective To isolate bacteriophages against extensively-drug resistant Acinetobacter baumannii from hospital sewage and analyze their biological characteristics.Methods Extensively-drug resistant Acinetobacter baumannii isolated from several hospitals in Shanghai during December, 2013 to July, 2014 were used as host bacteria, adopting double-layer agar method to isolate bacteriophages from raw sewage of these hospitals.The phage with broad host range was selected for further study, including observation of electron microscopic morphology, examination of thermal stability, pH stability and the optimal MOI, drawing of the adsorption, one-step-growth and infection curves, as well as sequencing of the phage genome DNA. Results An extensively-drug resistant Acinetobacter baumannii bacteriophage vB_AbaP_PD-AB9 ( PD-AB9 for short) with broad host range was isolated, and electron microscopy revealed it belonged to Podoviridae family.The optimal MOI of PD-AB9 was 0.001.PD-AB9 remained stable among 4 ℃to 50 ℃and pH 4 to 11.In the adsorption experiment, the adsorption rate of PD-AB9 reached above 95%within 5 min.PD-AB9 had a latent period of 4 min and a burst size of 213.PD-AB9 could obviously restrain the host growth, with faster effect at the higher MOIs (MOI=1, 0.1, 0.01) than at the lower ones (MOI=0.001, 0.000 1).Furthermore, genome of PD-AB9 proved to be a double-stranded linear DNA with size of 40 938 bp and GC content of 39.34%.Conclusions PD-AB9 exhibits good thermal stability, wide pH tolerance range, very fast adsorption, a short latent period, a large burst size and it could quickly cause effective host lysis after infection.Therefore, PD-AB9 is promised to act as a new antimicrobial agent to control drug-resistant Acinetobacter baumannii infections and its bio information remains to be further studied.

A bioinformatics approach to reanalyze the genome annotation of kinetoplastid protozoan parasite Leishmania donovani.

Leishmania donovani is a kinetoplastid protozoan parasite which causes the fatal disease visceral leishmaniasis in humans. Genome sequencing of L. donovani revealed information about the arrangement of genes and genome architecture. After curation of the genome sequence, many genes in L. donovani were assigned as truncated or "partial" genes by the genome sequencing group. In the present study, we have carried out an extensive analysis and attempted to improve the gene models of these partial genes. Our analysis resulted in the identification of 308 partial genes in L. donovani, which were further categorized as C-terminal extensions, joining of genes, tandemly repeated paralogs and wrong chromosomal assignments. We have analyzed each of these genes from these categories and have improved the annotation of existing gene models in L. donovani. Some of these corrections have been confirmed by mass spectrometry derived peptide data from our previous comparative proteogenomics study in L. donovani.

[Nanoviruses, small plant viruses: similarities and differences with geminiviruses]. / Les nanovirus, petits virus de plantes : similitudes et différences avec les géminivirus.

Nanoviridae family comprises genus Nanovirus (viruses infecting legume plants) and Babuvirus (viruses infecting banana plants). Nanovirus genomes consist of multiple circular single-stranded DNAs of about 1 kb each. They are encapsidated individually in small icosahedral particles. Each DNA molecule encodes only one protein. Nanoviruses replicate in the nucleus of infected plants by a rolling-circle replication mechanism initiated by viral Rep protein. Multiple DNAs encoding similar but clearly distinct Rep proteins have been described for each nanovirus. All Rep proteins of a given nanovirus are functional and each initiates replication of the DNA by which it is encoded (auto-replication). Only the Master Rep protein is able to initiate replication of other genome components (trans-replication). Induction of nanovirus disease by cloned genome components was established only for Faba bean necrotic yellows virus.