Dynamic range and mass accuracy of wide-scan direct infusion nanoelectrospray fourier transform ion cyclotron resonance mass spectrometry-based metabolomics increased by the spectral stitching method

Direct infusion nanoelectrospray Fourier transform ion cyclotron resonance mass spectrometry (DI nESI FT-ICR MS)offers high mass accuracy and resolution for analyzing complex metabolite mixtures. High dynamic range across a wide mass range, however, can only be achieved at the expense of mass accuracy, since the large numbers of ions entering the ICR detector induce adverse spacecharge effects. Here we report an optimized strategy for wide-scan DI nESI FT-ICR MS that increases dynamic range but maintains high mass accuracy. It comprises the collection if multiple adjacent selected ion monitoring (SIM) windows that are stitched together using novel algorithms. The final SIM-stitching method, derived from several optimization experiments, comprises 21 adjoining SIM windows each of width m/z 30 (from m/z 70 to 500; adjacent windows overlap by m/z 10) with an automated gain control (AGC) target of 1 105 charges. SIMstitching and wide-scan range (WSR; Thermo Electron)were compared using a defined standard to assess mass accuracy and a liver extract to assess peak count and dynamic range. SIM-stitching decreased the maximum mass error by 1.3- and 4.3-fold, and increased the peak count by 5.3- and 1.8-fold, versus WSR (AGC targets of 1 x 105 and 5 x 105, respectively). SIM-stitching achieved an rms mass error of 0.18 ppm and detected over 3000 peaks in liver extract. This novel approach increases metabolome coverage, has very high mass accuracy, and at 5.5 min/sample is conducive for high- throughput metabolomics

An infrared study of modern and paleo-filamentous bacteria from Rio Tinto, Spain

The Rio Tinto River Basin in southwestern Spain is a natural acidic (pH ~2.3) drainage system that supports a diversity of acid tolerant bacteria and eukaryotes with iron and sulfur- oxidizing prokaryotes performing chemolithotrophy and supporting anaerobic respiration [1, 2]. River terrace deposits formed over the past 2 Myr have preserved remnants of this unique biosphere, particularly microbial filaments, which provide templates for iron sulphate and iron oxide precipitation [1, 2]. This process of permineralization causes organic material to become trapped within a mineral matrix and preserved over geological time. This study analysed cultured filamentous bacteria, modern biofilms and sediments, and river terrace deposits spanning 2.1 Myr to assess the preservation of organics in this extreme environment over time, and the ability to correlate them with a contemporary culture. Filamentous bacteria are preserved within optically translucent nanophase to crystalline jarosite and goethite within all samples. The cultures contained 1 μm diameter filaments, some partially encrusted with iron oxides with visible cell walls, and others completely free of iron oxides, that are morphologically comparable to those preserved in the Rio Tinto rock record. Organic compounds (e.g. aliphatic hydrocarbons, amides and carboxylic acids) were detected at various levels within the culture and river terraces using mid-IR spectroscopy. Rio Tinto is a natural laboratory allowing living cells to be studied and correlated to morphological and biomolecular fossils in the geological record. These deposits will provide predictive tools for biomarker studies that may be extended to analogous environments on ancient Earth or even Mars. [1] Fernández-Remolar et al. (2005) Earth Planet Sci Lett 240,149-167. [2] Fernández-Remolar & Knoll (2008) Icarus 194,72-85

‘Imposter participants’ in online qualitative research, a new and increasing threat to data integrity?

Letter to the Editor: Health Expectation

Biogeochemical cycling of silver in acidic, weathering environments

Under acidic, weathering conditions, silver (Ag) is considered to be highly mobile and can be dispersed within near-surface environments. In this study, a range of regolith materials were sampled from three abandoned open pit mines located in the Iberian Pyrite Belt, Spain. Samples were analyzed for Ag mineralogy, content, and distribution using micro-analytical techniques and high-resolution electron microscopy. While Ag concentrations were variable within these materials, elevated Ag concentrations occurred in gossans. The detection of Ag within younger regolith materials, i.e., terrace iron formations and mine soils, indicated that Ag cycling was a continuous process. Microbial microfossils were observed within crevices of gossan and their presence highlights the preservation of mineralized cells and the potential for biogeochemical processes contributing to metal mobility in the rock record. An acidophilic, iron-oxidizing microbial consortium was enriched from terrace iron formations. When the microbial consortium was exposed to dissolved Ag, more than 90% of Ag precipitated out of solution as argentojarosite. In terms of biogeochemical Ag cycling, this demonstrates that Ag re-precipitation processes may occur rapidly in comparison to Ag dissolution processes. The kinetics of Ag mobility was estimated for each type of regolith material. Gossans represented 0.6–146.7 years of biogeochemical Ag cycling while terrace iron formation and mine soils represented 1.9–42.7 years and 0.7–1.6 years of Ag biogeochemical cycling, respectively. Biogeochemical processes were interpreted from the chemical and structural characterization of regolith material and demonstrated that Ag can be highly dispersed throughout an acidic, weathering environment.Jeremiah Shuster, Frank Reith, Matthew R. M. Izawa, Roberta L. Flemming, Neil R. Banerjee and Gordon Southa

Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants?

AIMS/HYPOTHESIS: According to the thrifty genotype hypothesis, the high prevalence of type 2 diabetes and obesity is a consequence of genetic variants that have undergone positive selection during historical periods of erratic food supply. The recent expansion in the number of validated type 2 diabetes- and obesity-susceptibility loci, coupled with access to empirical data, enables us to look for evidence in support (or otherwise) of the thrifty genotype hypothesis using proven loci. METHODS: We employed a range of tests to obtain complementary views of the evidence for selection: we determined whether the risk allele at associated 'index' single-nucleotide polymorphisms is derived or ancestral, calculated the integrated haplotype score (iHS) and assessed the population differentiation statistic fixation index (F (ST)) for 17 type 2 diabetes and 13 obesity loci. RESULTS: We found no evidence for significant differences for the derived/ancestral allele test. None of the studied loci showed strong evidence for selection based on the iHS score. We find a high F (ST) for rs7901695 at TCF7L2, the largest type 2 diabetes effect size found to date. CONCLUSIONS/INTERPRETATION: Our results provide some evidence for selection at specific loci, but there are no consistent patterns of selection that provide conclusive confirmation of the thrifty genotype hypothesis. Discovery of more signals and more causal variants for type 2 diabetes and obesity is likely to allow more detailed examination of these issues

Metabolomics Reveals Target and Off-Target Toxicities of a Model Organophosphate Pesticide to Roach (Rutilus rutilus): Implications for Biomonitoring

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Primary osteoarthritis chondrocyte map of chromatin conformation reveals novel candidate effector genes

Objectives: Osteoarthritis is a complex disease with a huge public health burden. Genome-wide association studies (GWAS) have identified hundreds of osteoarthritis-associated sequence variants, but the effector genes underpinning these signals remain largely elusive. Understanding chromosome organisation in three-dimensional (3D) space is essential for identifying long-range contacts between distant genomic features (e.g., between genes and regulatory elements), in a tissue-specific manner. Here, we generate the first whole genome chromosome conformation analysis (Hi-C) map of primary osteoarthritis chondrocytes and identify novel candidate effector genes for the disease. Methods: Primary chondrocytes collected from 8 patients with knee osteoarthritis underwent Hi-C analysis to link chromosomal structure to genomic sequence. The identified loops were then combined with osteoarthritis GWAS results and epigenomic data from primary knee osteoarthritis chondrocytes to identify variants involved in gene regulation via enhancer-promoter interactions. Results: We identified 345 genetic variants residing within chromatin loop anchors that are associated with 77 osteoarthritis GWAS signals. Ten of these variants reside directly in enhancer regions of 10 newly described active enhancer-promoter loops, identified with multiomics analysis of publicly available chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) data from primary knee chondrocyte cells, pointing to two new candidate effector genes SPRY4 and PAPPA (pregnancy-associated plasma protein A) as well as further support for the gene SLC44A2 known to be involved in osteoarthritis. For example, PAPPA is directly associated with the turnover of insulin-like growth factor 1 (IGF-1) proteins, and IGF-1 is an important factor in the repair of damaged chondrocytes. Conclusions: We have constructed the first Hi-C map of primary human chondrocytes and have made it available as a resource for the scientific community. By integrating 3D genomics with large-scale genetic association and epigenetic data, we identify novel candidate effector genes for osteoarthritis, which enhance our understanding of disease and can serve as putative high-value novel drug targets

Whole-genome sequencing analysis of the cardiometabolic proteome.

The human proteome is a crucial intermediate between complex diseases and their genetic and environmental components, and an important source of drug development targets and biomarkers. Here, we comprehensively assess the genetic architecture of 257 circulating protein biomarkers of cardiometabolic relevance through high-depth (22.5×) whole-genome sequencing (WGS) in 1328 individuals. We discover 131 independent sequence variant associations (P < 7.45 × 10-11) across the allele frequency spectrum, all of which replicate in an independent cohort (n = 1605, 18.4x WGS). We identify for the first time replicating evidence for rare-variant cis-acting protein quantitative trait loci for five genes, involving both coding and noncoding variation. We construct and validate polygenic scores that explain up to 45% of protein level variation. We find causal links between protein levels and disease risk, identifying high-value biomarkers and drug development targets