Metabolite profiling of non-sterile rhizosphere soil

Rhizosphere chemistry is the sum of root exudation chemicals, their breakdown products and the microbial products of soil-derived chemicals. To date, most studies about root exudation chemistry are based on sterile cultivation systems, which limits the discovery of microbial breakdown products that act as semiochemicals and shape microbial rhizosphere communities. Here, we present a method for untargeted metabolic profiling of non-sterile rhizosphere soil. We have developed an experimental growth system that enables the collection and analysis of rhizosphere chemicals from different plant species. High-throughput sequencing of 16SrRNA genes demonstrated that plants in the growth system support a microbial rhizosphere effect. To collect a range of (a)polar chemicals from the system, we developed extraction methods that do not cause detectable damage to root cells or soil-inhabiting microbes, thus preventing contamination with cellular metabolites. Untargeted metabolite profiling by UPLC-Q-TOF mass spectrometry, followed by uni- and multivariate statistical analyses, identified a wide range of secondary metabolites that are enriched in plant-containing soil, compared with control soil without roots. We show that the method is suitable for profiling the rhizosphere chemistry of Zea mays (maize) in agricultural soil, thereby demonstrating the applicability to different plant-soil combinations. Our study provides a robust method for the comprehensive metabolite profiling of non-sterile rhizosphere soil, which represents a technical advance towards the establishment of causal relationships between the chemistry and microbial composition of the rhizosphere

The frequency of transforming growth factor-TGF-B gene polymorphisms in a normal southern Iranian population

Several single nucleotide polymorphisms (SNPs) of the transforming growth factor-β1 gene (TGFB1) have been reported. Determination of TGFB1 SNPs allele frequencies in different ethnic groups is useful for both population genetic analyses and association studies with immunological diseases. In this study, five SNPs of TGFB1 were determined in 325 individuals from a normal southern Iranian population using polymerase chain reaction-restriction fragment length polymorphism method. This population was in Hardy-Weinberg equilibrium for these SNPs. Of the 12 constructed haplotypes, GTCGC and GCTGC were the most frequent in the normal southern Iranian population. Comparison of genotype and allele frequencies of TGFB SNPs between Iranian and other populations (meta-analysis) showed significant differences, and in this case the southern Iranian population seems genetically similar to Caucasoid populations. However, neighbour-joining tree using Nei's genetic distances based on TGF-β1 allele frequencies showed that southern Iranians are genetically far from people from the USA, Germany, UK, Denmark and the Czech Republic. In conclusion, this is the first report of the distribution of TGFB1 SNPs in an Iranian population and the results of this investigation may provide useful information for both population genetic and disease studies. © 2008 The Authors

Metabolic regulation of the maize rhizobiome by benzoxazinoids

The rhizobiome is an important regulator of plant growth and health. Plants shape their rhizobiome communities through production and release of primary and secondary root metabolites. Benzoxazinoids (BXs) are common tryptophan-derived secondary metabolites in grasses that regulate belowground and aboveground biotic interactions. In addition to their biocidal activity, BXs can regulate plant–biotic interactions as semiochemicals or within-plant defence signals. However, the full extent and mechanisms by which BXs shape the root-associated microbiome has remained largely unexplored. Here, we have taken a global approach to examine the regulatory activity of BXs on the maize root metabolome and associated bacterial and fungal communities. Using untargeted mass spectrometry analysis in combination with prokaryotic and fungal amplicon sequencing, we compared the impacts of three genetic mutations in different steps in the BX pathway. We show that BXs regulate global root metabolism and concurrently influence the rhizobiome in a root type-dependent manner. Correlation analysis between BX-controlled root metabolites and bacterial taxa suggested a dominant role for BX-dependent metabolites, particularly flavonoids, in constraining a range of soil microbial taxa, while stimulating methylophilic bacteria. Our study supports a multilateral model by which BXs control root–microbe interactions via a global regulatory function in root secondary metabolism

Morphologies of Sol–Gel Derived Thin Films of ZnO Using Different Precursor Materials and their Nanostructures

We have shown that the morphological features of the sol–gel derived thin films of ZnO depend strongly on the choice of the precursor materials. In particular, we have used zinc nitrate and zinc acetate as the precursor materials. While the films using zinc acetate showed a smoother topography, those prepared by using zinc nitrate exhibited dendritic character. Both types of films were found to be crystalline in nature. The crystallite dimensions were confined to the nanoscale. The crystallite size of the nanograins in the zinc nitrate derived films has been found to be smaller than the films grown by using zinc acetate as the precursor material. Selected area electron diffraction patterns in the case of both the precursor material has shown the presence of different rings corresponding to different planes of hexagonal ZnO crystal structure. The results have been discussed in terms of the fundamental considerations and basic chemistry governing the growth kinetics of these sol–gel derived ZnO films with both the precursor materials

Does a gluten-free diet improve quality of life and sleep in patients with non-coeliac gluten/wheat sensitivity?

Introduction: The role of a gluten-free diet (GFD) in Non-Coeliac Gluten/Wheat Sensitivity (NCGWS) is unclear. We present the largest study comparing adherence to a GFD in patients with Coeliac Disease (CD) and NCGWS and assess its impact on quality of life (QoL) and sleep in patients with NCGWS. Methods: Patients with NCGWS at a tertiary centre completed the Coeliac Disease Adherence Test (CDAT), Coeliac Symptom Index (CSI) and Sleep Condition Indicator (SCI). Higher CDAT scores indicate worse adherence, higher CSI scores indicate poorer QoL, and higher SCI scores indicate better sleep. CDAT scores were correlated with CSI and SCI scores. A second group of patients with CD completed the CDAT questionnaire only. Results were compared with the CDAT responses from the NCGWS group. Results: For the NCGWS cohort (n = 125), the median CDAT score was 17/35, indicating poor adherence. The median CSI score was 44/80, with 40% of scores associated with a poor QoL. The median SCI score was 14/32, and DSM-V criteria for insomnia was met by 42% of patients. There was a positive correlation between CSI and CDAT scores (r = 0.59, p < 0.0001) and a negative correlation between SCI and CDAT scores (r = −0.37, p = 0.0002). In the CD cohort (n = 170), the median CDAT score was 13/35. Patients with NCGWS had poorer adherence compared to CD (CDAT: 17.0 vs. 13.0, respectively, p = 0.0001). Conclusion: Patients with NCGWS adhere to a GFD less than those with CD. Poorer adherence to a GFD in patients with NCGWS correlates with a worse QoL and sleep performance

The association of body mass index with long-term clinical outcomes after ticagrelor monotherapy following abbreviated dual antiplatelet therapy in patients undergoing percutaneous coronary intervention: a prespecified sub-analysis of the GLOBAL LEADERS Trial

Background: The efficacy of antiplatelet therapies following percutaneous coronary intervention (PCI) may be affected by body mass index (BMI). Methods and results: This is a prespecified subgroup analysis of the GLOBAL LEADERS trial, a prospective, multicenter, open-label, randomized controlled trial in an all-comer population undergoing PCI, comparing the experimental strategy (23-month ticagrelor monotherapy following 1-month dual antiplatelet therapy [DAPT]) with a reference regimen (12-month aspirin monotherapy following 12-month DAPT). A total of 15,968 patients were stratified by baseline BMI with prespecified threshold of 27 kg/m2. Of those, 6973 (43.7%) patients with a BMI < 27 kg/m2 had a higher risk of all-cause mortality at 2 years than those with BMI ≥ 27 kg/m2 (adjusted HR 1.24, 95% CI 1.02–1.49). At 2 years, the rates of the primary endpoint (all-cause mortality or new Q-wave myocardial infarction) were similar between treatment strategies in either BMI group (pinteraction = 0.51). In acute coronary syndrome, however, the experimental strategy was associated with significant reduction of the primary endpoint compared to the reference strategy in patients with BMI < 27 kg/m2 (HR 0.69, 95% CI 0.51–0.94), but not in the ones with BMI ≥ 27 kg/m2 (pinteraction = 0.047). In chronic coronary syndrome, there was no between-group difference in the efficacy and safety of the two antiplatelet strategies. This is a prespecified subgroup analysis of the GLOBAL LEADERS trial, a prospective, multicenter, open-label, randomized controlled trial in an all-comer population undergoing PCI, comparing the experimental strategy (23-month ticagrelor monotherapy following 1-month dual antiplatelet therapy [DAPT]) with a reference regimen (12-month aspirin monotherapy following 12-month DAPT). A total of 15,968 patients were stratified by baseline BMI with prespecified threshold of 27 kg/m2. Of those, 6973 (43.7%) patients with a BMI < 27 kg/m2 had a higher risk of all-cause mortality at 2 years than those with BMI ≥ 27 kg/m2 (adjusted HR 1.24, 95% CI 1.02–1.49). At 2 years, the rates of the primary endpoint (all-cause mortality or new Q-wave myocardial infarction) were similar between treatment strategies in either BMI group (pinteraction = 0.51). In acute coronary syndrome, however, the experimental strategy was associated with significant reduction of the primary endpoint compared to the reference strategy in patients with BMI < 27 kg/m2 (HR 0.69, 95% CI 0.51–0.94), but not in the ones with BMI ≥ 27 kg/m2 (pinteraction = 0.047). In chronic coronary syndrome, there was no between-group difference in the efficacy and safety of the two antiplatelet strategies. This is a prespecified subgroup analysis of the GLOBAL LEADERS trial, a prospective, multicenter, open-label, randomized controlled trial in an all-comer population undergoing PCI, comparing the experimental strategy (23-month ticagrelor monotherapy following 1-month dual antiplatelet therapy [DAPT]) with a reference regimen (12-month aspirin monotherapy following 12-month DAPT). A total of 15,968 patients were stratified by baseline BMI with prespecified threshold of 27 kg/m2. Of those, 6973 (43.7%) patients with a BMI < 27 kg/m2 had a higher risk of all-cause mortality at 2 years than those with BMI ≥ 27 kg/m2 (adjusted HR 1.24, 95% CI 1.02–1.49). At 2 years, the rates of the primary endpoint (a

Origin of the ring structures in Hercules A.: Sub-arcsecond 144 MHz to 7 GHz observations

Large scale structure and cosmologyGalaxie

A Global View on Star Formation: The GLOSTAR Galactic Plane Survey: II Supernova Remnants in the first quadrant of the Milky Way

Context. The properties of the population of the Galactic Supernova Remnants (SNRs) are essential to our understanding of the dynamics of the Milky Way’s interstellar medium (ISM). However, the completeness of the catalog of Galactic SNRs is expected to be only ∼30%, with on order 700 SNRs yet to be detected. Deep interferometric radio continuum surveys of the Galactic plane help in rectifying this apparent deficiency by identifying low surface brightness SNRs and compact SNRs that have not been detected in previous surveys. However, SNRs are routinely confused with H ii regions, which can have similar radio morphologies. Radio spectral index, polarization, and emission at mid-infrared (MIR) wavelengths can help distinguish between SNRs and H ii regions. Aims. We aim to identify SNR candidates using continuum emission from the Karl G. Jansky Very Large Array Global view of the Star formation in the Milky Way (GLOSTAR) survey. Methods. GLOSTAR is a C-band (4–8 GHz) radio wavelength survey of the Galactic plane covering 358◦ ≤ l ≤ 60◦, |b| ≤ 1◦. The continuum images from this survey that resulted from observations in the array’s most compact configuration have an angular resolution of 18″. We searched for SNRs in these images to identify known SNRs, previously-identified SNR candidates and new SNR candidates. We study these objects in MIR surveys and the GLOSTAR polarization data to classify their emission as thermal or nonthermal. Results. We identify 157 SNR candidates, out of which 80 are new. Polarization measurements provide evidence of nonthermal emission from 9 of these candidates. We find that two previously identified candidates are filaments. We also detect emission from 91 out of 94 known SNRs in the survey region. Four of these are reclassified as H ii regions following detection in MIR surveys. Conclusions. The better sensitivity and resolution of the GLOSTAR data have led to the identification of 157 SNR candidates, along with the reclassification of several misidentified objects. We show that the polarization measurements can identify nonthermal emission, despite the diffuse Galactic synchrotron emission. These results underscore the importance of higher resolution and higher sensitivity radio continuum data in identifying and confirming SNRs

GLOSTAR — Radio Source Catalog II: 28◦ < l < 36◦ and |b| < 1◦,VLA B-configuration

As part of the Global View on Star Formation (GLOSTAR) survey we have used the Karl G. Jansky Very Large Array (VLA) in its B-configuration to observe the part of the Galactic plane between longitudes of 28◦ and 36◦ and latitudes from −1◦ to +1◦ at the C-band (4–8 GHz). To reduce the contamination of extended sources that are not well recovered by our coverage of the (u, v)-plane we discarded short baselines that are sensitive to emission on angular scales < 4′′. The resulting radio continuum images have an angular resolution of 1.′′0, and a sensitivity of ∼ 60 μJy beam−1; making it the most sensitive radio survey covering a large area of the Galactic plane with this angular resolution. An automatic source extraction algorithm was used in combination with visual inspection to identify a total of 3325 radio sources. A total of 1457 radio sources are ≥ 7σ and comprise our highly reliable catalog; 72 of these are grouped as 22 fragmented sources, e.g., multiple components of an extended and resolved source. To explore the nature of the catalogued radio sources we searched for counterparts at millimeter and infrared wavelengths. Our classification attempts resulted in 93 H ii region candidates, 104 radio stars, 64 planetary nebulae, while most of the remaining radio sources are suggested to be extragalactic sources. We investigated the spectral indices (α, S ν ∝ να) of radio sources classified as H ii region candidates and found that many have negative values. This may imply that these radio sources represent young stellar objects that are members of the star clusters around the high mass stars that excite the H ii regions, but not these H ii regions themselves. By comparing the peak flux densities from the GLOSTAR and CORNISH surveys we have identified 49 variable radio sources, most of them with an unknown nature. Additionally, we provide the list of 1866 radio sources detected within 5 to 7σ levels

AD51B in Familial Breast Cancer

Common variation on 14q24.1, close to RAD51B, has been associated with breast cancer: rs999737 and rs2588809 with the risk of female breast cancer and rs1314913 with the risk of male breast cancer. The aim of this study was to investigate the role of RAD51B variants in breast cancer predisposition, particularly in the context of familial breast cancer in Finland. We sequenced the coding region of RAD51B in 168 Finnish breast cancer patients from the Helsinki region for identification of possible recurrent founder mutations. In addition, we studied the known rs999737, rs2588809, and rs1314913 SNPs and RAD51B haplotypes in 44,791 breast cancer cases and 43,583 controls from 40 studies participating in the Breast Cancer Association Consortium (BCAC) that were genotyped on a custom chip (iCOGS). We identified one putatively pathogenic missense mutation c.541C&gt;T among the Finnish cancer patients and subsequently genotyped the mutation in additional breast cancer cases (n = 5259) and population controls (n = 3586) from Finland and Belarus. No significant association with breast cancer risk was seen in the meta-analysis of the Finnish datasets or in the large BCAC dataset. The association with previously identified risk variants rs999737, rs2588809, and rs1314913 was replicated among all breast cancer cases and also among familial cases in the BCAC dataset. The most significant association was observed for the haplotype carrying the risk-alleles of all the three SNPs both among all cases (odds ratio (OR): 1.15, 95% confidence interval (CI): 1.11–1.19, P = 8.88 x 10−16) and among familial cases (OR: 1.24, 95% CI: 1.16–1.32, P = 6.19 x 10−11), compared to the haplotype with the respective protective alleles. Our results suggest that loss-of-function mutations in RAD51B are rare, but common variation at the RAD51B region is significantly associated with familial breast cancer risk