Assessing the potential economic benefits to farmers from various GM crops becoming available in the European Union by 2025: results from an expert survey

This paper reports on a study that identified a range of crop-trait combinations that are: agronomically suited to the EU; provide advantages to arable farmers and consumers; and are either already available in international markets, or advancing along the development pipeline and likely to become available by 2025. An expert stakeholder panel was recruited and asked for their views, using the Delphi approach, on the impact of these crop-traits on enterprise competitiveness, through changes to yields, production costs and product prices. In terms of input traits, there was consensus that traits such as herbicide tolerant/insect resistant (HT/IR) maize, HT sugar beet and HT soya bean would provide positive benefits for farmers. Output-side traits such as winter-sown rape with reduced saturated fats, were seen as offering benefits to consumers, but were either likely to be restricted to niche markets, or offer relatively modest price premia to farmers growing them. Our analysis of the financial impact of the adoption of GM crops more widely in the EU, showed that the competitiveness of the agricultural sector could well be improved by this. However, such improvements would be relatively small-scale in that large-scale national natural advantages from either economic or environmental conditions is unlikely to be overturned

Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome

Background: Little is known regarding the pool of mobile genetic elements associated with the human gut microbiome. In this study we employed the culture independent TRACA system to isolate novel plasmids from the human gut microbiota, and a comparative metagenomic analysis to investigate the distribution and relative abundance of functions encoded by these plasmids in the human gut microbiome. Results: Novel plasmids were acquired from the human gut microbiome, and homologous nucleotide sequences with high identity (>90%) to two plasmids (pTRACA10 and pTRACA22) were identified in the multiple human gut microbiomes analysed here. However, no homologous nucleotide sequences to these plasmids were identified in the murine gut or environmental metagenomes. Functions encoded by the plasmids pTRACA10 and pTRACA22 were found to be more prevalent in the human gut microbiome when compared to microbial communities from other environments. Among the most prevalent functions identified was a putative RelBE toxin-antitoxin (TA) addiction module, and subsequent analysis revealed that this was most closely related to putative TA modules from gut associated bacteria belonging to the Firmicutes. A broad phylogenetic distribution of RelE toxin genes was observed in gut associated bacterial species (Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria), but no RelE homologues were identified in gut associated archaeal species. We also provide indirect evidence for the horizontal transfer of these genes between bacterial species belonging to disparate phylogenetic divisions, namely Gram negative Proteobacteria and Gram positive species from the Firmicutes division. Conclusions: The application of a culture independent system to capture novel plasmids from the human gut mobile metagenome, coupled with subsequent comparative metagenomic analysis, highlighted the unexpected prevalence of plasmid encoded functions in the gut microbial ecosystem. In particular the increased relative abundance and broad phylogenetic distribution was identified for a putative RelBE toxin/antitoxin addiction module, a putative phosphohydrolase/phosphoesterase, and an ORF of unknown function. Our analysis also indicates that some plasmids or plasmid families are present in the gut microbiomes of geographically isolated human hosts with a broad global distribution (America, Japan and Europe), and are potentially unique to the human gut microbiome. Further investigation of the plasmid population associated with the human gut is likely to provide important insights into the development, functioning and evolution of the human gut microbiota

Driven Morse Oscillator: Model for Multi-photon Dissociation of Nitrogen Oxide

Within a one-dimensional semi-classical model with a Morse potential the possibility of infrared multi-photon dissociation of vibrationally excited nitrogen oxide was studied. The dissociation thresholds of typical driving forces and couplings were found to be similar, which indicates that the results were robust to variations of the potential and of the definition of dissociation rate. PACS: 42.50.Hz, 33.80.WzComment: old paper, 8 pages 6 eps file

Identifying GM crops for future cultivation in the EU through a Delphi forecasting exercise

This paper reports on a Delphi forecasting exercise carried out to identify crop traits that could feasibly be introduced to the advantage of arable farmers, and for the general benefit of the public, in EU member states. An expert stakeholder panel was recruited and asked for opinions on scenarios concerning the availability of GM events, and also scenarios that envisage novel crops developed using advanced technology not classified as GM. In a second round of consultation, panel members commented anonymously on opinions elicited in the first phase. Results indicate that crops with input traits most likely to become available in the EU before 2025 are HTIR maize, HT sugarbeet and HT soybean; these are already widely adopted outside Europe. The crops with output traits most likely to become available and offering benefits to consumers are winter-sown varieties of rape with reduced saturated fats, spring varieties of which are already available outside EU (notably Canadian Canola)

The effect of Si species released from bioactive glasses on cell behaviour: A quantitative review

Despite over 50 years of silicate bioactive glass (SBG) research, commercial success, and 6000+ published articles, there remains a lack of understanding of how soluble silicate (Si) species released from SBGs influences cellular responses. Using a systematic approach, this article quantitatively compares the in vitro responses of cells to SBG dissolution products reported in the literature and determines if there is a Si concentration ([Si]) dependent effect on cell behaviour. Cell behavioural responses to SBGs [Si] in dissolution products included metabolic activity (reported in 52 % of articles), cell number (24 %), protein production (22 %), gene expression (22 %) and biomineralization (24 %). There was a difference in the [Si] reported to cause increased (desirable) cellular responses (median = 30.2 ppm) compared to the [Si] reported to cause decreased (undesirable) cellular responses (median = 52.0 ppm) (P ≤ 0.001). The frequency of undesirable outcomes increased with increasing [Si], with ∼3 times more negative outcomes reported above 52 ppm. We also investigated the effect of [Si] on specific cellular outcomes (e.g., metabolic activity, angiogenesis, osteogenesis),if cell type/species influenced these responses and the impact of other ions (Ca, P, Na) within the SBG dissolution media on cell behaviour. This review has, for the first time, quantitatively compared the cellular responses to SBGs from the literature, providing a quantitative overview of SBG in vitro practices and presents evidence of a range of [Si] where desirable cellular responses may be more likely (30-52 ppm). This review also demonstrates the need for greater standardisation of in vitro methodological approaches and recommends some minimum reporting standards

The dual PI3K/mTOR inhibitor GSK2126458 is effective for treating solid renal tumours in Tsc2+/- mice through suppression of cell proliferation and induction of apoptosis

Tuberous sclerosis (TSC) is an inherited tumour syndrome caused by mutations in TSC1 or TSC2 that lead to aberrant activation of mTOR. Tumour responses in TSC patients to rapamycin, an allosteric inhibitor of mTOR, or its analogs are partial and reversible probably due to feedback activation of Akt. In this study, we examined the efficacy of GSK2126458, an ATP-competitive dual inhibitor of PI3K/mTOR, in comparison to rapamycin for treatment of renal tumours in genetically engineered Tsc2+/- mice. We found that both GSK2126458 and rapamycin caused significant reduction in number and size of solid renal tumours. GSK2126458 also significantly reduced the number and size of all lesions (cystic, papillary and solid) although to a lesser extent compared to rapamycin. GSK2126458 inhibited both PI3K and mTOR while rapamycin exerted stronger inhibitory effect on mTORC1 in renal tumours. Furthermore, GSK2126458 and rapamycin suppressed proliferation of tumour cells. Importantly, GSK2126458 increased apoptosis of solid tumours but rapamycin did not. Further investigations are therefore needed to test whether rapamycin in combination with GSK2126458 could promote apoptosis and thus improve therapy of TSC-associated renal tumours

Bioactivity in silica/poly(γ-glutamic acid) sol–gel hybrids through calcium chelation

Bioactive glasses and inorganic/organic hybrids have great potential as biomedical implant materials. Sol–gel hybrids with interpenetrating networks of silica and biodegradable polymers can combine the bioactive properties of a glass with the toughness of a polymer. However, traditional calcium sources such as calcium nitrate and calcium chloride are unsuitable for hybrids. In this study calcium was incorporated by chelation to the polymer component. The calcium salt form of poly(γ-glutamic acid) (γCaPGA) was synthesized for use as both a calcium source and as the biodegradable toughening component of the hybrids. Hybrids of 40 wt.% γCaPGA were successfully formed and had fine scale integration of Ca and Si ions, according to secondary ion mass spectrometry imaging, indicating a homogeneous distribution of organic and inorganic components. 29Si magic angle spinning nuclear magnetic resonance data demonstrated that the network connectivity was unaltered with changing polymer molecular weight, as there was no perturbation to the overall Si speciation and silica network formation. Upon immersion in simulated body fluid a hydroxycarbonate apatite surface layer formed on the hybrids within 1 week. The polymer molecular weight (Mw 30–120 kDa) affected the mechanical properties of the resulting hybrids, but all hybrids had large strains to failure, >26%, and compressive strengths, in excess of 300 MPa. The large strain to failure values showed that γCaPGA hybrids exhibited non-brittle behaviour whilst also incorporating calcium. Thus calcium incorporation by chelation to the polymer component is justified as a novel approach in hybrids for biomedical materials

Acoustic streaming in a soft tissue microenvironment

We demonstrated that sound can push fluid through a tissue-mimicking material. Although acousticstreaming in tissue has been proposed as a mechanism for biomedical ultrasound applications, such as neuromodu-lation and enhanced drug penetration, streaming in tissue or acoustic phantoms has not been directly observed. Wedeveloped a material that mimics the porous structure of tissue and used a dye and a video camera to track fluidmovement. When applied above an acoustic intensity threshold, a continuous focused ultrasound beam (spatialpeak time average intensity: 238 W/cm2, centre frequency: 5 MHz) was found to push the dye axially, that is, in thedirection of wave propagation and in the radial direction. Dye clearance increased with ultrasound intensity andwas modelled using an adapted version of Eckart’s acoustic streaming velocity equation. No microstructuralchanges were observed in the sonicated region when assessed using scanning electron microscopy. Our study indi-cates that acoustic streaming can occur in soft porous materials and provides a mechanistic basis for future use ofstreaming for therapeutic or diagnostic purposes.WOS:000451607300022Scopus - Affiliation ID: 60105072PMID: 30336964Science Citation Index ExpandedQ1 - Q2ArticleUluslararası işbirliği ile yapılan - EVETOcak2019YÖK - 2018-1

Functional characterization of two human MutY homolog (hMYH) missense mutations (R227W and V232F) that lie within the putative hMSH6 binding domain and are associated with hMYH polyposis

The base excision repair DNA glycosylase MutY homolog (MYH) is responsible for removing adenines misincorporated into DNA opposite guanine or 7,8-dihydro-8-oxo-guanine (8-oxoG), thereby preventing G:C to T:A mutations. Biallelic germline mutations in the human MYH gene predispose individuals to multiple colorectal adenomas and carcinoma. We have recently demonstrated that hMYH interacts with the mismatch repair protein hMSH6, and that the hMSH2/hMSH6 (hMutSα) heterodimer stimulates hMYH activity. Here, we characterize the functional effect of two missense mutations (R227W and V232F) associated with hMYH polyposis that lie within, or adjacent to, the putative hMSH6 binding domain. Neither missense mutation affects the physical interaction between hMYH and hMSH6. However, hMYH(R227W) has a severe defect in A/8-oxoG binding and glycosylase activities, while hMYH(V232F) has reduced A/8-oxoG binding and glycosylase activities. The glycosylase activity of the V232F mutant can be partially stimulated by hMutSα but cannot be restored to the wild-type level. Both mutants also fail to complement mutY-deficiency in Escherichia coli. These data define the pathogenic mechanisms underlying two further hMYH polyposis-associated mutations

The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential.

Three strains of fungus-associated Burkholderiales bacteria with antagonistic activity against Gram-negative plant pathogens were genome sequenced to investigate their taxonomic placement and potential for antimicrobial specialized metabolite production. The selected strains were identified as novel taxa belonging to the genus Paraburkholderia and carry multiple biosynthetic gene clusters