DNA Barcoding Simplifies Environmental Risk Assessment of Genetically Modified Crops in Biodiverse Regions

Transgenes encoding for insecticidal crystal (Cry) proteins from the soil-dwelling bacterium Bacillus Thuringiensis have been widely introduced into Genetically Modified (GM) crops to confer protection against insect pests. Concern that these transgenes may also harm beneficial or otherwise valued insects (so-called Non Target Organisms, NTOs) represents a major element of the Environmental Risk Assessments (ERAs) used by all countries prior to commercial release. Compiling a comprehensive list of potentially susceptible NTOs is therefore a necessary part of an ERA for any Cry toxin-containing GM crop. In partly-characterised and biodiverse countries, NTO identification is slowed by the need for taxonomic expertise and time to enable morphological identifications. This limitation represents a potentially serious barrier to timely adoption of GM technology in some developing countries. We consider Bt Cry1A cowpea (Vigna unguiculata) in Nigeria as an exemplar to demonstrate how COI barcoding can provide a simple and cost-effective means of addressing this problem. Over a period of eight weeks, we collected 163 insects from cowpea flowers across the agroecological and geographic range of the crop in Nigeria. These individuals included 32 Operational Taxonomic Units (OTUs) spanning four Orders and that could mostly be assigned to genus or species level. They included 12 Lepidopterans and two Coleopterans (both potentially sensitive to different groups of Cry proteins). Thus, barcode-assisted diagnoses were highly harmonised across groups (typically to genus or species level) and so were insensitive to expertise or knowledge gaps. Decisively, the entire study was completed within four months at a cost of less than 10,000 US$. The broader implications of the findings for food security and the capacity for safe adoption of GM technology are briefly explored

GM Risk Assessment:Pollen carriage from Brassica napus to B. rapa varies widely between pollinators

© 2017 Gesellschaft für Ökologie Characterizing insect pollen carriage between closely related plant species is especially challenging where source species possess morphologically identical pollen and share many pollinators in common. Here, we use an SNP-based assay using the plant DNA barcoding locus matK to characterize pollen carriage between cultivated Brassica napus and wild Brassica rapa in three sites across southern England. The assay differentiated B. napus and B. rapa pollen carried by honey bees (Apis melifera), bumblebees (Bombus spp.), mining bees (Andrena spp.) and hoverflies (Syrphidae) captured on B. napus plants 1–2 m from wild B. rapa, and on B. rapa plants at various distances from the crop. Apis individuals foraging on B. rapa and carrying B. napus pollen were rarely found beyond 10 m from the crop. However, Bombus and Andrena individuals captured on B. rapa occasionally carried crop pollen up to 300 m from the source field. Hoverflies carried less pollen overall but featured high proportions of B. napus pollen even at the most distant capture points. We predict that different pollinator species will evoke markedly different patterns of interspecific hybrid formation. We conclude that more exhaustive surveys of this kind will help parameterize future mechanistic models to predict the distribution of hybrids between Genetically Modified B. napus and B. rapa on a landscape scale

Tumor angiogenesis revisited: Regulators and clinical implications

Since Judah Folkman hypothesized in 1971 that angiogenesis is required for solid tumor growth, numerous studies have been conducted to unravel the angiogenesis process, analyze its role in primary tumor growth, metastasis and angiogenic diseases, and to develop inhibitors of proangiogenic factors. These studies have led in 2004 to the approval of the first antiangiogenic agent (bevacizumab, a humanized antibody targeting vascular endothelial growth factor) for the treatment of patients with metastatic colorectal cancer. This approval launched great expectations for the use of antiangiogenic therapy for malignant diseases. However, these expectations have not been met and, as knowledge of blood vessel formation accumulates, many of the original paradigms no longer hold. Therefore, the regulators and clinical implications of angiogenesis need to be revisited. In this review, we discuss recently identified angiogenesis mediators and pathways, new concepts that have emerged over the past 10 years, tumor resistance and toxicity associated with the use of currently available antiangiogenic treatment and potentially new targets and/or approaches for malignant and nonmalignant neovascular diseases

The value of twinned pollinator-pollen metabarcoding: Bumblebee pollination service is weakly partitioned within a UK grassland community

Predicting ecological impact of declining bumblebee (Bombus) populations requires better understanding of interactions between pollinator partitioning of floral resources and plant partitioning of pollinator resources. Here, we combine Cytochrome Oxidase 1 (CO1) barcoding for bumblebee identification and rbcL metabarcoding of pollen carried by bees in three species-rich UK pastures. CO1 barcoding assigned 272 bees to eight species, with 33 individuals belonging to the cryptic Bombus lucorumcomplex (16 B. lucorum and 17 B. cryptarum). Seasonal bias in capture rates varied by species, with B. pratorum found exclusively in June/July and B. pascuorum moreabundant in August. Pollen metabarcoding coupled with PERMANOVA and NMDS analyses revealed all bees carried several local pollen species and evidence of pollen resource partitioning between some species pairings, with Bombus pratorum carrying the most divergent pollen load. There was no evidence of resource partitioning between the two cryptic species present, but significantly divergent capture rates concorded with previous suggestions of separation on the basis of foraging behaviour being shaped by local/temporal differences in climatic conditions. Considering the bee carriage profile of pollen species revealed no significant difference between the ninemost widely carried plant species. However, there was a sharp, tipping point change in community pollen carriage across all three sites occurred during the transition between late July and early August. This transition resulted in a strong divergence in community pollen carriage between the two seasonal periods in both years. We conclude that the combined use of pollen and bee barcoding offers several benefits for further study of plant-pollinator interactions at the landscape scale

The gut microbiomes of two Pachysoma MacLeay desert dung beetle species (Coleoptera: Scarabaeidae: Scarabaeinae) feeding on different diets

Micro-organisms inhabiting animal guts benefit from a protected and nutrient-rich environment while assisting the host with digestion and nutrition. In this study we compare, for the first time, the bacterial and fungal gut communities of two species of the small desert dung beetle genus Pachysoma feeding on different diets: the detritivorous P. endroedyi and the dry-dung-feeding P. striatum. Whole-gut microbial communities from 5 individuals of each species were assessed using 454 pyrosequencing of the bacterial 16S rRNA gene and fungal ITS gene regions. The two bacterial communities were significantly different, with only 3.7% of operational taxonomic units shared, and displayed intra-specific variation. The number of bacterial phyla present within the guts of P. endroedyi and P. striatum individuals ranged from 6–11 and 4–7, respectively. Fungal phylotypes could only be detected within the gut of P. striatum. Although the role of host phylogeny in Pachysoma microbiome assembly remains unknown, evidence presented in this study suggests that host diet may be a deterministic factor.S1 Fig. Rarefactions curves showing gut microbial community richness of all Pachysoma individuals for bacterial 16S rRNA gene amplicon data of: a) P. endroedyi, b) P. striatum; and c) fungal ITS gene region amplicon data of P. striatum.S2 Fig. Photographs of P. endroedyi (a) and P. striatum (b) in their natural environment before collection (courtesy of Hennie de Klerk).http://www.plosone.orgam2016Genetic

DNA barcoding the native flowering plants and conifers of Wales

We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification

Inferring the behaviour of pollinators by molecular characterisation of pollen carriage at the population, community and landscape scales

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Tumor angiogenesis revisited: Regulators and clinical implications

Since Judah Folkman hypothesized in 1971 that angiogenesis is required for solid tumor growth, numerous studies have been conducted to unravel the angiogenesis process, analyze its role in primary tumor growth, metastasis and angiogenic diseases, and to develop inhibitors of proangiogenic factors. These studies have led in 2004 to the approval of the first antiangiogenic agent (bevacizumab, a humanized antibody targeting vascular endothelial growth factor) for the treatment of patients with metastatic colorectal cancer. This approval launched great expectations for the use of antiangiogenic therapy for malignant diseases. However, these expectations have not been met and, as knowledge of blood vessel formation accumulates, many of the original paradigms no longer hold. Therefore, the regulators and clinical implications of angiogenesis need to be revisited. In this review, we discuss recently identified angiogenesis mediators and pathways, new concepts that have emerged over the past 10 years, tumor resistance and toxicity associated with the use of currently available antiangiogenic treatment and potentially new targets and/or approaches for malignant and nonmalignant neovascular diseases.status: publishe

Cuckoo leaf-cutter bee clade collected from cowpea flowers in Nigeria.

<p>Neighbour Joining tree representing COI barcodes for individuals clustering in the <i>Coelioxys</i> clade. The tree is based on Kimura two-parameter distances (K2P). The five OTUs (presumed species) of <i>Coelioxys</i> collected in Nigeria are highlighted. Individuals specified using site code and sample number (e.g. MA-1 was collected MA: Mbano site A and 1 is the sample ID) see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035929#pone.0035929.s002" target="_blank">Table S1</a> for site code. Reference sequences have been downloaded from ncbi and CBOL and they indicate species name plus entry ID.</p