Timely and accurate biodiversity analysis poses an ongoing challenge for the success of biomonitoring programs. Morphology-based identification of bioindicator taxa is time consuming, and rarely supports species-level resolution especially for immature life stages. Much work has been done in the past decade to develop alternative approaches for biodiversity analysis using DNA sequence-based approaches such as molecular phylogenetics and DNA barcoding. On-going assembly of DNA barcode reference libraries will provide the basis for a DNA-based identification system. The use of recently introduced next-generation sequencing (NGS) approaches in biodiversity science has the potential to further extend the application of DNA information for routine biomonitoring applications to an unprecedented scale. Here we demonstrate the feasibility of using 454 massively parallel pyrosequencing for species-level analysis of freshwater benthic macroinvertebrate taxa commonly used for biomonitoring. We designed our experiments in order to directly compare morphology-based, Sanger sequencing DNA barcoding, and next-generation environmental barcoding approaches. Our results show the ability of 454 pyrosequencing of mini-barcodes to accurately identify all species with more than 1% abundance in the pooled mixture. Although the approach failed to identify 6 rare species in the mixture, the presence of sequences from 9 species that were not represented by individuals in the mixture provides evidence that DNA based analysis may yet provide a valuable approach in finding rare species in bulk environmental samples. We further demonstrate the application of the environmental barcoding approach by comparing benthic macroinvertebrates from an urban region to those obtained from a conservation area. Although considerable effort will be required to robustly optimize NGS tools to identify species from bulk environmental samples, our results indicate the potential of an environmental barcoding approach for biomonitoring programs.
Reverse genetics systems have been established for all major groups of plant DNA and positive-strand RNA viruses, and our understanding of their infection cycles and pathogenesis has benefitted enormously from use of these approaches. However, technical difficulties have heretofore hampered applications of reverse genetics to plant negative-strand RNA (NSR) viruses. Here, we report recovery of infectious virus from cloned cDNAs of a model plant NSR, Sonchus yellow net rhabdovirus (SYNV). The procedure involves Agrobacterium-mediated transcription of full-length SYNV antigenomic RNA and co-expression of the nucleoprotein (N), phosphoprotein (P), large polymerase core proteins and viral suppressors of RNA silencing in Nicotiana benthamiana plants. Optimization of core protein expression resulted in up to 26% recombinant SYNV (rSYNV) infections of agroinfiltrated plants. A reporter virus, rSYNV-GFP, engineered by inserting a green fluorescence protein (GFP) gene between the N and P genes was able to express GFP during systemic infections and after repeated plant-to-plant mechanical passages. Deletion analyses with rSYNV-GFP demonstrated that SYNV cell-to-cell movement requires the sc4 protein and suggested that uncoiled nucleocapsids are infectious movement entities. Deletion analyses also showed that the glycoprotein is not required for systemic infection, although the glycoprotein mutant was defective in virion morphogenesis. Taken together, we have developed a robust reverse genetics system for SYNV that provides key insights into morphogenesis and movement of an enveloped plant virus. Our study also provides a template for developing analogous systems for reverse genetic analysis of other plant NSR viruses.
Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region.
BackgroundTraditional Chinese medicine (TCM) has been widely applied for cancer care in China. There have been a large number of controlled clinical studies published in Chinese literature, yet no systematic searching and analysis has been done. This study summarizes the current evidence of controlled clinical studies of TCM for cancer.MethodsWe searched all the controlled clinical studies of TCM therapies for all kinds of cancers published in Chinese in four main Chinese electronic databases from their inception to November 2011. We bibliometrically analyzed the included studies and assessed the reporting quality.ResultsA total of 2964 reports (involving 253,434 cancer patients) including 2385 randomized controlled trials and 579 non-randomized controlled studies were included. The top seven cancer types treated were lung cancer, liver cancer, stomach cancer, breast cancer, esophagus cancer, colorectal cancer and nasopharyngeal cancer by both study numbers and case numbers. The majority of studies (72%) applied TCM therapy combined with conventional treatment, whilst fewer (28%) applied only TCM therapy in the experimental groups. Herbal medicine was the most frequently applied TCM therapy (2677 studies, 90.32%). The most frequently reported outcome was clinical symptom improvement (1667 studies, 56.24%) followed by biomarker indices (1270 studies, 42.85%), quality of life (1129 studies, 38.09%), chemo/radiotherapy induced side effects (1094 studies, 36.91%), tumor size (869 studies, 29.32%) and safety (547 studies, 18.45%). Completeness and adequacy of reporting appeared to improve with time.ConclusionsData from controlled clinical studies of TCM therapies in cancer treatment is substantial, and different therapies are applied either as monotherapy or in combination with conventional medicine. Reporting of controlled clinical studies should be improved based on the CONSORT and TREND Statements in future. Further studies should address the most frequently used TCM therapy for common cancers and outcome measures should address survival, relapse/metastasis and quality of life.
The utility of hydropsychid (Trichoptera:Hydropsychidae) caddisfly larvae for freshwater biomonitoring has been demonstrated, but the major impediment to its implementation has been the lack of species-level larval descriptions and illustrations. A rapid and reliable molecular protocol that also uses morphology is proposed because conventional approaches to associating undescribed larvae with adults have been slow and problematic. Male adults were identified before DNA sequence analyses were used. These identifications established morphospecies boundaries that were mapped on phylograms constructed from 2 independent gene fragments: mitochondrial cytochrome c oxidase subunit I (COI) and large subunit (28S) nuclear ribosomal DNA expansion fragment D2 (D2). Species boundaries were confirmed if they were monophyletic on both molecular phylograms. Larval associations were made with reference to the phylogenetic analyses under 2 criteria: sequence identity across both genes or nested placement within a reference species boundary. A total of 133 individuals belonging to Chinese Hydropsyche sensu lato group (including Hydropsyche [Hydropsyche], Hydropsyche [Occutanspsyche], Ceratopsyche, Mexipsyche, Hydatomanicus, and Herbertorossia) were included in our study to test the new protocol. D2 sequences (all individuals) and COI sequences (101 individuals) were obtained, and 2 independent phylograms were constructed using neighbor joining. Both fragments provided enough nucleotide changes to differentiate independently most Hydropsyche sensu lato species, with ambiguity in only a few species that eventually could be resolved with additional sequences and specimens. COI diverges significantly within some species, suggesting a need for caution when applying typical genetic divergence thresholds in species diagnoses. The study enabled us to establish a procedure for delimiting species boundaries and associating larvae and adults using DNA sequences and morphological evidence. Ideal sampling strategies for larval-adult association are suggested. Associating larvae and adults of hydropsychids using DNA sequences appears to be promising in terms of both reliability and speed.
Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world's terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists. With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind.
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