Discrimination of conventional and organic white cabbage from a long-term field trial study using untargeted LC-MS-based metabolomics

The influence of organic and conventional farming practices on the content of single nutrients in plants is disputed in the scientific literature. Here, large-scale untargeted LC-MS-based metabolomics was used to compare the composition of white cabbage from organic and conventional agriculture, measuring 1,600 compounds. Cabbage was sampled in 2 years from one conventional and two organic farming systems in a rigidly controlled long-term field trial in Denmark. Using Orthogonal Projection to Latent Structures-Discriminant Analysis (OPLS-DA), we found that the production system leaves a significant (p = 0.013) imprint in the white cabbage metabolome that is retained between production years. We externally validated this finding by predicting the production system of samples from one year using a classification model built on samples from the other year, with a correct classification in 83% of cases. Thus, it was concluded that the investigated conventional and organic management practices have a systematic impact on the metabolome of white cabbage. This emphasizes the potential of untargeted metabolomics for authenticity testing of organic plant products

Delineation of Culicoides species by morphology and barcode exemplified by three new species of the subgenus Culicoides (Diptera: Ceratopogonidae) from Scandinavia

BACKGROUND: Culicoides biting midges (Diptera: Ceratopogonidae) cause biting nuisance to livestock and humans and are vectors of a range of pathogens of medical and veterinary importance. Despite their economic significance, the delineation and identification of species where only morphology is considered, as well as the evolutionary relationships between species within this genus remains problematic. In recent years molecular barcoding has assisted substantially in the identification of biting midges in the multiple entomological survey projects which were initiated in many European countries following the bluetongue outbreak in 2006–2009. These studies revealed potentially new species and “species-complexes” with large genetic and morphological variability. Here we use molecular barcoding, together with morphological analysis, to study subgenus Culicoides Latreille from Scandinavia with focus on three potentially new species. METHODS: Biting midges were collected at various sites in Denmark and Sweden. Culicoides specimens were described by variation of a fragment of their cytochrome c oxidase subunit 1 (COI) gene sequence and wing, palp and antennal characters. RESULTS: It is shown that three new species initially separated by DNA barcoding with mitochondrial COI can be distinguished by morphological characters. In this context a key to Scandinavian subgenus Culicoides using wing and maxillary palp characters is presented. The key is including the three new species Culicoides boyi, Culicoides selandicus and Culicoides kalix. CONCLUSION: Three new species of Culicoides biting midges were identified and could be identified by both molecular and morphological differences. Evaluation of differences between and within taxa of biting midges using COI barcode yielded a rough estimate of species delineation; interspecies differences across Culicoides subgenera approaches 20%, whereas intraspecies differences are below 4% and in most cases below 1%. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13071-015-0750-4) contains supplementary material, which is available to authorized users

The global aerosol synthesis and science project (GASSP): Measurements and modeling to reduce uncertainty

This is the final version of the article. Available from American Meteorological Society via the DOI in this record.The largest uncertainty in the historical radiative forcing of climate is caused by changes in aerosol particles due to anthropogenic activity. Sophisticated aerosol microphysics processes have been included in many climate models in an effort to reduce the uncertainty. However, the models are very challenging to evaluate and constrain because they require extensive in situ measurements of the particle size distribution, number concentration, and chemical composition that are not available from global satellite observations. The Global Aerosol Synthesis and Science Project (GASSP) aims to improve the robustness of global aerosol models by combining new methodologies for quantifying model uncertainty, to create an extensive global dataset of aerosol in situ microphysical and chemical measurements, and to develop new ways to assess the uncertainty associated with comparing sparse point measurements with low-resolution models. GASSP has assembled over 45,000 hours of measurements from ships and aircraft as well as data from over 350 ground stations. The measurements have been harmonized into a standardized format that is easily used by modelers and nonspecialist users. Available measurements are extensive, but they are biased to polluted regions of the Northern Hemisphere, leaving large pristine regions and many continental areas poorly sampled. The aerosol radiative forcing uncertainty can be reduced using a rigorous model–data synthesis approach. Nevertheless, our research highlights significant remaining challenges because of the difficulty of constraining many interwoven model uncertainties simultaneously. Although the physical realism of global aerosol models still needs to be improved, the uncertainty in aerosol radiative forcing will be reduced most effectively by systematically and rigorously constraining the models using extensive syntheses of measurements.GASSP was funded by the Natural Environment Research Council (NERC) under Grants NE/J024252/1, NE/J022624/1, and NE/J023515/1; ACID-PRUF under Grants NE/I020059/1 and NE/I020148/1; the European Union BACCHUS project under Grant 603445-BACCHUS; ACTRIS under Grants 262254 and 654109; and by the UK–China Research and Innovation Partnership Fund through the Met Office Climate Science for Service Partnership (CSSP) China as part of the Newton Fund. We made use of the N8 HPC facility funded from the N8 consortium and an Engineering and Physical Sciences Research Council Grant to use ARCHER (EP/K000225/1) and the JASMIN facility (www.jasmin.ac.uk/) via the Centre for Environmental Data Analysis funded by NERC and the UK Space Agency and delivered by the Science and Technology Facilities Council. We acknowledge the following additional funding: the Royal Society Wolfson Merit Award (Carslaw); a doctoral training grant from the Natural Environment Research Council and a CASE studentship with the Met Office Hadley Centre (Regayre); the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement FP7-280025 (Stier); the Department of Energy under DE-SC0007178 (Zhang); the U.S. National Science Foundation under ATM-745986 (Snider); the NOAA Global Change Program (Nenes); NASA Global Tropospheric Experiment Program, the NASA Tropospheric Composition Program, the NASA Radiation Sciences Program, and the NASA Earth Venture Suborbital Project (Anderson); the NOAA Climate Program Office (Quinn); NSF Atmospheric Chemistry Program, the NASA Global Tropospheric Experiment, and NASA Earth Science Project Office (Clarke); German Federal Ministry of Education and Research (BMBF) CLOUD12 project Grant 01LK1222B (Kristensen); Swedish Research Council (VR), the Knut and Alice Wallenberg Foundation and the Swedish Polar Research Secretariat (SPRS) for access to the icebreaker Oden and logistical support (Leck); the Department of Energy (DE-SC0007178) and the Max Planck Society (Andreae, Poeschl); the global environment research fund of the Ministry of the Environment in Japan (2-1403), the Arctic Challenge for Sustainability (ArCS) project of the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) in Japan, and the Japan Society for the Promotion of Science (JSPS) KAKENHI (Grants JP16H01770, JP26701004, and JP26241003) (Kondo, Oshima); Lufthansa for enabling CARIBIC and the German Federal Ministry of Education and Research (BMBF) for financing the CARIBIC instruments operation as part of the Joint Project IAGOS-D (Hermann); the Collaborative Innovation Center of Climate Change supported by the Jiangsu provincial government and the JirLATEST supported by the Ministry of Education, China (Ding and Chi); the Max Planck Institute for Chemistry, Mainz, Germany (Schmale); the NOAA Atmospheric Composition and Climate Program, the NASA Radiation Sciences Program, and the NASA Upper Atmosphere Research Program supporting the NOAA SP2 BC data acquisition and analysis (Schwarz); DOE (BER/ASR) DE-SC0016559 and EPA STAR 83587701-0 (the EPA has not reviewed this manuscript and no endorsement should be inferred) (Jimenez); and Environment and Climate Change Canada (Leaitch)

The courage to change: Patient perceptions of 12-Step fellowships

<p>Abstract</p> <p>Background</p> <p>From a health services perspective, peer-based resources merit special attention. Participation in self-help fellowships, like the Twelve Step Groups (TSGs), have been shown to improve outcomes of patients with substance use disorder (SUD) and they represent a valuable adjunct to the SUD treatment system. This study investigated the relationship between patient perceptions of TSGs and the intent to participate in TSGs after receiving detoxification treatment.</p> <p>Methods</p> <p>We included 139 patients that entered a detoxification unit (detox) in Kristiansand, Norway. We analyzed factors associated with the intention to participate in TSGs post-discharge with contingency tables and ordinal regression analysis.</p> <p>Results</p> <p>Forty-eight percent of patients had participated in TSGs before entering detox. Respondents saw more advantages than disadvantages in TSG participation, but only 40% of patients showed high intentions of participating in TSGs post-discharge. A high intention to participate in TSGs was most strongly correlated with the notion that participation in TSGs could instill the courage to change. In a multivariate analysis, the perception that TSGs were beneficial was the strongest factor related to a high intention of TSG participation after treatment.</p> <p>Conclusions</p> <p>Our findings increased the understanding of factors most likely to influence decisions to attend TSGs in SUD treatment contexts with uncommon TSG participation. Our results suggested that the majority of patients may be sufficiently influenced by highlighting the potential gains of TSG participation. Treatment programs that do not focus on self-help group attendance during and after treatment should consider implementing facilitative measures to enhance utilization of these fellowships.</p

An epidemiological study of respiratory syncytial virus associated hospitalizations in Denmark

Respiratory syncytial virus (RSV) is the most common viral pathogen that causes lower respiratory tract infections in infants. Studies have implicated severe RSV infections early in life as a risk factor for subsequent development of reactive airway disease. We are conducting a study to validate RSV-associated diagnoses in the Danish National Patient Registry, to assess whether the incidence of severe RSV infection is increasing in Denmark, to identify predisposing and protective factors for RSV-associated hospitalization in Denmark, and to examine the association of severe RSV infection with reactive airway disease. The influence of various biological, social and environmental factors on hospitalization for RSV infection will be studied through several population-based registers, including the Danish National Birth Cohort: 'Better health for mothers and children'. The RSV hospitalization cases will be compared with control individuals selected within the same population groups on a case–control or a cohort basis in order to produce estimates of age-adjusted and sex-adjusted relative risks (odds ratio and relative risk) for hospitalization associated with various risk factors. Using register linkage and unique registration of exposures collected through interviews and blood samples from the Danish National Birth Cohort, we will be able to resolve the issues referred to above in a very large sample of Danish children

Analysis of Polymorphisms and Haplotype Structure of the Human Thymidylate Synthase Genetic Region: A Tool for Pharmacogenetic Studies

5-fluorouracil (5FU), a widely used chemotherapeutic drug, inhibits the DNA replicative enzyme, thymidylate synthase (Tyms). Prior studies implicated a VNTR (variable numbers of tandem repeats) polymorphism in the 5′-untranslated region (5′-UTR) of the TYMS gene as a determinant of Tyms expression in tumors and normal tissues and proposed that these VNTR genotypes could help decide fluoropyrimidine dosing. Clinical associations between 5FU-related toxicity and the TYMS VNTR were reported, however, results were inconsistent, suggesting that additional genetic variation in the TYMS gene might influence Tyms expression. We thus conducted a detailed genetic analysis of this region, defining new polymorphisms in this gene including mononucleotide (poly A:T) repeats and novel single nucleotide polymorphisms (SNPs) flanking the VNTR in the TYMS genetic region. Our haplotype analysis of this region used data from both established and novel genetic variants and found nine SNP haplotypes accounting for more than 90% of the studied population. We observed non-exclusive relationships between the VNTR and adjacent SNP haplotypes, such that each type of VNTR commonly occurred on several haplotype backgrounds. Our results confirmed the expectation that the VNTR alleles exhibit homoplasy and lack the common ancestry required for a reliable marker of a linked adjacent locus that might govern toxicity. We propose that it may be necessary in a clinical trial to assay multiple types of genetic polymorphisms in the TYMS region to meaningfully model linkage of genetic markers to 5FU-related toxicity. The presence of multiple long (up to 26 nt), polymorphic monothymidine repeats in the promoter region of the sole human thymidylate synthetic enzyme is intriguing

Sub region-specific modulation of synchronous neuronal burst firing after a kainic acid insult in organotypic hippocampal cultures

<p>Abstract</p> <p>Background</p> <p>Excitotoxicity occurs in a number of pathogenic states including stroke and epilepsy. The adaptations of neuronal circuits in response to such insults may be expected to play an underlying role in pathogenesis. Synchronous neuronal firing can be induced in isolated hippocampal slices and involves all regions of this structure, thereby providing a measure of circuit activity. The effect of an excitotoxic insult (kainic acid, KA) on Mg²⁺-free-induced synchronized neuronal firing was tested in organotypic hippocampal culture by measuring extracellular field activity in CA1 and CA3.</p> <p>Results</p> <p>Within 24 hrs of the insult regional specific changes in neuronal firing patterns were evident as: (i) a dramatic <it>reduction </it>in the ability of CA3 to generate firing; and (ii) a contrasting <it>increase </it>in the frequency and duration of synchronized neuronal firing events in CA1. Two distinct processes underlie the increased propensity of CA1 to generate synchronized burst firing; a lack of ability of the CA3 region to 'pace' CA1 resulting in an increased frequency of synchronized events; and a change in the 'intrinsic' properties limited to the CA1 region, which is responsible for increased event duration. Neuronal quantification using NeuN immunoflurescent staining and stereological confocal microscopy revealed no significant cell loss in hippocampal sub regions, suggesting that changes in the properties of neurons within this region were responsible for the KA-mediated excitability changes.</p> <p>Conclusion</p> <p>These results provide novel insight into adaptation of hippocampal circuits following excitotoxic injury. KA-mediated disruption of the interplay between CA3 and CA1 clearly increases the propensity to synchronized firing in CA1.</p

Genotypes and haplotypes in the insulin-like growth factors, their receptors and binding proteins in relation to plasma metabolic levels and mammographic density

<p>Abstract</p> <p>Background</p> <p>Increased mammographic density is one of the strongest independent risk factors for breast cancer. It is believed that one third of breast cancers are derived from breasts with more than 50% density. Mammographic density is affected by age, BMI, parity, and genetic predisposition. It is also greatly influenced by hormonal and growth factor changes in a woman's life cycle, spanning from puberty through adult to menopause. Genetic variations in genes coding for hormones and growth factors involved in development of the breast are therefore of great interest. The associations between genetic polymorphisms in genes from the IGF pathway on mammographic density and circulating levels of IGF1, its binding protein IGFBP3, and their ratio in postmenopausal women are reported here.</p> <p>Methods</p> <p>Samples from 964 postmenopausal Norwegian women aged 55-71 years were collected as a part of the Tromsø Mammography and Breast Cancer Study. All samples were genotyped for 25 SNPs in IGF1, IGF2, IGF1R, IGF2R, IGFALS and IGFBP3 using Taqman (ABI). The main statistical analyses were conducted with the PROC HAPLOTYPE procedure within SAS/GENETICS™ (SAS 9.1.3).</p> <p>Results</p> <p>The haplotype analysis revealed six haploblocks within the studied genes. Of those, four had significant associations with circulating levels of IGF1 or IGFBP3 and/or mammographic density. One haplotype variant in the IGF1 gene was found to be associated with mammographic density. Within the IGF2 gene one haplotype variant was associated with levels of both IGF1 and IGFBP3. Two haplotype variants in the IGF2R were associated with the level of IGF1. Both variants of the IGFBP3 haplotype were associated with the IGFBP3 level and indicate regulation in cis.</p> <p>Conclusion</p> <p>Polymorphisms within the IGF1 gene and related genes were associated with plasma levels of IGF1, IGFBP3 and mammographic density in this study of postmenopausal women.</p

Ibuprofen results in alterations of human fetal testis development

International audienceAmong pregnant women ibuprofen is one of the most frequently used pharmaceutical compounds with up to 28% reporting use. Regardless of this, it remains unknown whether ibuprofen could act as an endocrine disruptor as reported for fellow analgesics paracetamol and aspirin. To investigate this, we exposed human fetal testes (7-17 gestational weeks (GW)) to ibuprofen using ex vivo culture and xenograft systems. Ibuprofen suppressed testosterone and Leydig cell hormone INSL3 during culture of 8-9 GW fetal testes with concomitant reduction in expression of the steroidogenic enzymes CYP11A1, CYP17A1 and HSD17B3, and of INSL3. Testosterone was not suppressed in testes from fetuses younger than 8 GW, older than 10-12 GW, or in second trimester xenografted testes (14-17 GW). Ex vivo, ibuprofen also affected Sertoli cell by suppressing AMH production and mRNA expression of AMH, SOX9, DHH, and COL2A1. While PGE2 production was suppressed by ibuprofen, PGD2 production was not. Germ cell transcripts POU5F1, TFAP2C, LIN28A, ALPP and KIT were also reduced by ibuprofen. We conclude that, at concentrations relevant to human exposure and within a particular narrow 'early window' of sensitivity within first trimester, ibuprofen causes direct endocrine disturbances in the human fetal testis and alteration of the germ cell biology