Validation of a microarrays protocol for detection and genotyping isolates of Plum pox virus

A genomic strategy for PPV identification has been recently developed (Pasquini et al., 2008). The method is based on using a 70-mer oligonucleotide DNA microarray chip capable of simultaneously detecting and genotyping PPV strains. Universal and specific probes have been identified and used with a sensitive protocol of hybridization using an indirect fluorescent labelling of cDNA product with cyanine able to enhance the sensitivity of the virus detection avoiding the use of the PCR amplification step. In order to evaluate the protocol fitness for diagnostic use, about 30 samples belonging to a PPV isolates collection, including M, D, EA and C strains, have been used for its validation, that was determined, estimating the performance criteria that include the following parameters: diagnostic sensitivity (D-SN), diagnostic specificity (D-SP) and diagnostic accuracy (D-AC). Keywords: oligonucleotides chip, PPV, sensitivity, specificity, accuracy, performance criteri

Molecular characterization of a Moroccan isolate of Tomato yellow leaf curl Sardinia virus and differentiation of the Tomato yellow leaf curl virus complex by the polymerase chain reaction

The polymerase chain reaction (PCR) was used to identify an isolate of Tomato yellow leaf curl Sardinia virus (TYLCSV) from southwestern Morocco and to detect the members of the Tomato yellow leaf curl virus (TYLCV) complex. Thirty-five tomato samples with typical TYLCV symptoms were collected from infected tomato fields in the Souss-Massa region. PCR was performed with a general primer pair based on the coat protein (Cp) gene of the TYLCV complex, as well as with specific primer pairs for TYLCV and TYLCSV. Of the 35 samples tested, 29 generated a viral DNA product with the general primer pair, 29 samples gave a viral DNA product with the TYLCV-specific primers, and of these, 9 also gave a product with the TYLCSV primer pair; 6 samples did not give any PCR product with either primer pair. The full-length genome of TYLCSV was amplified with overlapping primers at the unique NcoI site in the TYLCSV genome (GenBank accession number X61153). The full-length genome of the TYLCSV isolate from Morocco is 2,777 nucleotides long (accession number AY702650) and is almost identical (97% nucleotide identity) to a TYLCSV isolate from Murcia, Spain (accession number Z25751). A PCR-based diagnostic method was developed to distinguish between TYLCV and TYLCSV in Morocco. To diagnose the TYLCV/TYLCSV complex a general primer pair was designed that anneals to a conserved region of the Cp gene. To diagnose TYLCSV exclusively, two primer pairs were designed to anneal specifically to the replication-associated protein gene (Rep) of TYLCSV from Morocco. To detect TYLCV exclusively, a primer pair previously described to amplify the intergenic region (IR) of TYLCV was used. The PCR primers were tested for their effectiveness using DNA clones of the TYLCSV from Morocco and of the TYLCV from the Dominican Republic. PCR using these primers offers a rapid means to detect the TYLCV complex and to distinguish between the two TYLCV species present in Morocco

Genetic identification of members of the Bemisia tabaci cryptic species complex from South Africa reveals native and introduced haplotypes

The whitefly Bemisia tabaci cryptic species complex contains some important agricultural pest and virus vectors. Members of the complex have become serious pests in South Africa (SA) because of their feeding habit and their ability to transmit begomovirus species. Despite their economic importance, studies on the biology and distribution of B. tabaci in SA are limited. To this end, a survey was made to investigate the diversity and distribution of B. tabaci cryptic species in eight geographical locations (provinces) in SA, between 2002 and 2009, using the mitochondrial cytochrome oxidase I (mtCOI) sequences. Phylogenetic analysis revealed the presence of members from two endemic sub-Saharan Africa (SSAF) subclades coexisting with two introduced putative species. The SSAF-1 subclade includes cassava host-adapted B. tabaci populations, whereas the whiteflies collected from cassava and non-cassava hosts formed a distinct subclade, referred to as SSAF-5, and represent a new subclade among previously recognized southern Africa clades. Two introduced cryptic species, belonging to the Mediterranean and Middle East–Asia minor 1 clades, were identified and include the B and Q types. The B type showed the widest distribution, being present in five of the eight provinces explored in SA, infesting several host plants and predominating over the indigenous haplotypes. This is the first report of the occurrence of the exotic Q type in SA alongside the more widely distributed B type. Furthermore, mtCOI PCR-RFLP was developed for the SA context to allow rapid discrimination between the B, Q and SSAF putative species. The capacity to manage pests and disease effectively relies on knowledge of the identity of the agents causing the damage. Therefore, this study contributes to the understanding of South African B. tabaci species diversity, information needed for the development of knowledge- based disease management practices.National Research Foundation (NRF), South Africa.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1439-0418hb2013ab201

Identification of Host Genes Involved in Geminivirus Infection Using a Reverse Genetics Approach

Geminiviruses, like all viruses, rely on the host cell machinery to establish a successful infection, but the identity and function of these required host proteins remain largely unknown. Tomato yellow leaf curl Sardinia virus (TYLCSV), a monopartite geminivirus, is one of the causal agents of the devastating Tomato yellow leaf curl disease (TYLCD). The transgenic 2IRGFP N. benthamiana plants, used in combination with Virus Induced Gene Silencing (VIGS), entail an important potential as a tool in reverse genetics studies to identify host factors involved in TYLCSV infection. Using these transgenic plants, we have made an accurate description of the evolution of TYLCSV replication in the host in both space and time. Moreover, we have determined that TYLCSV and Tobacco rattle virus (TRV) do not dramatically influence each other when co-infected in N. benthamiana, what makes the use of TRV-induced gene silencing in combination with TYLCSV for reverse genetic studies feasible. Finally, we have tested the effect of silencing candidate host genes on TYLCSV infection, identifying eighteen genes potentially involved in this process, fifteen of which had never been implicated in geminiviral infections before. Seven of the analyzed genes have a potential anti-viral effect, whereas the expression of the other eleven is required for a full infection. Interestingly, almost half of the genes altering TYLCSV infection play a role in postranslational modifications. Therefore, our results provide new insights into the molecular mechanisms underlying geminivirus infections, and at the same time reveal the 2IRGFP/VIGS system as a powerful tool for functional reverse genetics studies

The Spread of Tomato Yellow Leaf Curl Virus from the Middle East to the World

The ongoing global spread of Tomato yellow leaf curl virus (TYLCV; Genus Begomovirus, Family Geminiviridae) represents a serious looming threat to tomato production in all temperate parts of the world. Whereas determining where and when TYLCV movements have occurred could help curtail its spread and prevent future movements of related viruses, determining the consequences of past TYLCV movements could reveal the ecological and economic risks associated with similar viral invasions. Towards this end we applied Bayesian phylogeographic inference and recombination analyses to available TYLCV sequences (including those of 15 new Iranian full TYLCV genomes) and reconstructed a plausible history of TYLCV's diversification and movements throughout the world. In agreement with historical accounts, our results suggest that the first TYLCVs most probably arose somewhere in the Middle East between the 1930s and 1950s (with 95% highest probability density intervals 1905–1972) and that the global spread of TYLCV only began in the 1980s after the evolution of the TYLCV-Mld and -IL strains. Despite the global distribution of TYLCV we found no convincing evidence anywhere other than the Middle East and the Western Mediterranean of epidemiologically relevant TYLCV variants arising through recombination. Although the region around Iran is both the center of present day TYLCV diversity and the site of the most intensive ongoing TYLCV evolution, the evidence indicates that the region is epidemiologically isolated, which suggests that novel TYLCV variants found there are probably not direct global threats. We instead identify the Mediterranean basin as the main launch-pad of global TYLCV movements

Transcriptome analysis and comparison reveal divergence between two invasive whitefly cryptic species

<p>Abstract</p> <p>Background</p> <p>Invasive species are valuable model systems for examining the evolutionary processes and molecular mechanisms associated with their specific characteristics by comparison with closely related species. Over the past 20 years, two species of the whitefly <it>Bemisia tabaci </it>species complex, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), have both spread from their origin Middle East/Mediterranean to many countries despite their apparent differences in many life history parameters. Previously, we have sequenced the transcriptome of MED. In this study, we sequenced the transcriptome of MEAM1 and took a comparative genomic approach to investigate the transcriptome evolution and the genetic factors underlying the differences between MEAM1 and MED.</p> <p>Results</p> <p>Using Illumina sequencing technology, we generated 17 million sequencing reads for MEAM1. These reads were assembled into 57,741 unique sequences and 15,922 sequences were annotated with an E-value above 10^-5. Compared with the MED transcriptome, we identified 3,585 pairs of high quality orthologous genes and inferred their sequence divergences. The average differences in coding, 5' untranslated and 3' untranslated region were 0.83%, 1.66% and 1.43%, respectively. The level of sequence divergence provides additional support to the proposition that MEAM1 and MED are two species. Based on the ratio of nonsynonymous and synonymous substitutions, we identified 24 sequences that have evolved in response to positive selection. Many of those genes are predicted to be involved in metabolism and insecticide resistance which might contribute to the divergence of the two whitefly species.</p> <p>Conclusions</p> <p>Our data present a comprehensive sequence comparison between the two invasive whitefly species. This study will provide a road map for future investigations on the molecular mechanisms underlying their biological differences.</p

Protein synthesis and transport in the regenerating goldfish visual system

The nature of the proteins synthesized in the goldfish retina and axonally transported to the tectum during optic nerve regeneration has been examined. Electrophoretic analysis of labeled soluble retinal proteins by fluorography verified our previous observation of a greatly enhanced synthesis of the microtubule subunits. In addition, labeling of a tubulin-like protein in the retinal particulate fraction was also increased during regeneration. Like soluble tubulin, the particulate material had an apparent MW of 53–55K and could be tyrosylated in the presence of cycloheximide and [ 3 H]tyrosine. Comparison of post-crush and normal retinal proteins by two-dimensional gel electrophoresis also revealed a marked enhancement in the labeling of two acidic 68–70K proteins. Analysis of proteins slowly transported to the optic tectum revealed changes following nerve crush similar to those observed in the retina, with enhanced labeling of both soluble and particulate tubulin and of 68–70K polypeptides. The most striking change in the profile of rapidly transported protein was the appearance of a labeled 45K protein which was barely detectable in control fish.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45430/1/11064_2004_Article_BF00965529.pd