Improved Mass Accuracy and Isotope Confirmation through Alignment of Ultrahigh-Resolution Mass Spectra of Complex Natural Mixtures

Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is one of the state-of-the-art methods to analyze complex natural organic mixtures. The precision of detected masses is crucial for molecular formula attribution. Random errors can be reduced by averaging multiple measurements of the same mass, but because of limited availability of ultrahigh-resolution mass spectrometers, most studies cannot afford analyzing each sample multiple times. Here we show that random errors can be eliminated also by averaging mass spectral data from independent environmental samples. By averaging the spectra of 30 samples analyzed on our 15 T instrument we reach a mass precision comparable to a single spectrum of a 21 T instrument. We also show that it is possible to accurately and reproducibly determine isotope ratios with FT-ICR-MS. Intensity ratios of isotopologues were improved to a degree that measured deviations were within the range of natural isotope fractionation effects. In analogy to δ13C in environmental studies, we propose Δ13C as an analytical measure for isotope ratio deviances instead of widely employed C deviances. In conclusion, here we present a simple tool, extensible to Orbitrap-based mass spectrometers, for postdetection data processing that significantly improves mass accuracy and the precision of intensity ratios of isotopologues at no extra cost

Dissolved organic matter signatures in urban surface waters: spatio-temporal patterns and drivers

Advances in analytical chemistry have facilitated the characterization of dissolved organic matter (DOM), which has improved understanding of DOM sources and transformations in surface waters. For urban waters, however, where DOM diversity is likely to be high, the interpretation of DOM signatures is hampered by a lack of information on the influence of land cover and anthropogenic factors such as nutrient enrichment and release of organic contaminants. Here we explored the spatio-temporal variation in DOM composition in contrasting urban water bodies, based on spectrophotometry and fluorometry, size-exclusion chromatography, and ultrahigh-resolution mass spectrometry, to identify linkages between DOM signatures and potential drivers. The highly diverse DOM we observed distinguished lakes and ponds, which are characterized by a high proportion of autochthonous DOM, from rivers and streams where allochthonous DOM is more prevalent. Seasonal variation in DOM composition was apparent in all types of water bodies, apparently due to interactions between phenology and urban influences, such as nutrient supply, the percentage of green space surrounding the water bodies and point source pollution. Optical DOM properties also revealed the influence of effluents from wastewater treatment plants, suggesting that simple optical measurements can be useful in water quality assessment and monitoring, providing information about processes both within water bodies and in their catchments.</p

Use of high throughput sequencing to observe genome dynamics at a single cell level

With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions. Here, we sequenced several genomes of Escherichia coli from colonies obtained after chemical mutagenesis and observed a strikingly nonrandom distribution of the induced mutations. These include long stretches of exclusively G to A or C to T transitions along the genome and orders of magnitude intra- and inter-genomic differences in mutation density. Whereas most of these observations can be explained by the known features of enzymatic processes, the others could reflect stochasticity in the molecular processes at the single-cell level. Our results demonstrate how analysis of the molecular records left in the genomes of the descendants of an individual mutagenized cell allows for genome-scale observations of fixation and segregation of mutations, as well as recombination events, in the single genome of their progenitor.Comment: 22 pages, 9 figures (including 5 supplementary), one tabl

Methane emissions from contrasting urban freshwaters: Rates, drivers, and a whole‐city footprint

Global urbanization trends impose major alterations on surface waters. This includes impacts on ecosystem functioning that can involve feedbacks on climate through changes in rates of greenhouse gas emissions. The combination of high nutrient supply and shallow depth typical of urban freshwaters is particularly conducive to high rates of methane (CH4) production and emission, suggesting a potentially important role in the global CH4 cycle. However, there is a lack of comprehensive flux data from diverse urban water bodies, of information on the underlying drivers, and of estimates for whole cities. Based on measurements over four seasons in a total of 32 water bodies in the city of Berlin, Germany, we calculate the total CH4 emission from various types of surface waters of a large city in temperate climate at 2.6 ± 1.7 Gg CH4/year. The average total emission was 219 ± 490 mg CH4 m−2 day−1. Water chemical variables were surprisingly poor predictors of total CH4 emissions, and proxies of productivity and oxygen conditions had low explanatory power as well, suggesting a complex combination of factors governing CH4 fluxes from urban surface waters. However, small water bodies (area <1 ha) typically located in urban green spaces were identified as emission hotspots. These results help constrain assessments of CH4 emissions from freshwaters in the world's growing cities, facilitating extrapolation of urban emissions to large areas, including at the global scale.DFG, 248198858, GRK 2032: Grenzzonen in urbanen Wassersysteme

Frontline Science: Rapid adipose tissue expansion triggers unique proliferation and lipid accumulation profiles in adipose tissue macrophages

Obesityâ related changes in adipose tissue leukocytes, in particular adipose tissue macrophages (ATMs) and dendritic cells (ATDCs), are implicated in metabolic inflammation, insulin resistance, and altered regulation of adipocyte function. We evaluated stromal cell and white adipose tissue (WAT) expansion dynamics with high fat diet (HFD) feeding for 3â 56 days, quantifying ATMs, ATDCs, endothelial cells (ECs), and preadipocytes (PAs) in visceral epididymal WAT and subcutaneous inguinal WAT. To better understand mechanisms of the early response to obesity, we evaluated ATM proliferation and lipid accumulation. ATMs, ATDCs, and ECs increased with rapid WAT expansion, with ATMs derived primarily from a CCR2â independent resident population. WAT expansion stimulated proliferation in resident ATMs and ECs, but not CD11c+ ATMs or ATDCs. ATM proliferation was unperturbed in Csf2â and Rag1â deficient mice with WAT expansion. Additionally, ATM apoptosis decreased with WAT expansion, and proliferation and apoptosis reverted to baseline with weight loss. Adipocytes reached maximal hypertrophy at 28 days of HFD, coinciding with a plateau in resident ATM accumulation and the appearance of lipidâ laden CD11c+ ATMs in visceral epididymal WAT. ATM increases were proportional to tissue expansion and adipocyte hypertrophy, supporting adipocyteâ mediated regulation of resident ATMs. The appearance of lipidâ laden CD11c+ ATMs at peak adipocyte size supports a role in responding to ectopic lipid accumulation within adipose tissue. In contrast, ATDCs increase independently of proliferation and may be derived from circulating precursors. These changes precede and establish the setting in which largeâ scale adipose tissue infiltration of CD11c+ ATMs, inflammation, and adipose tissue dysfunction contributes to insulin resistance.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142947/1/jlb10097_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142947/2/jlb10097.pd

Weight Regain in Formerly Obese Mice Hastens Development of Hepatic Steatosis Due to Impaired Adipose Tissue Function

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155467/1/oby22788-sup-0001-Supinfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155467/2/oby22788_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155467/3/oby22788.pd

Ecosystem respiration increases with biofilm growth and bed forms: Flume measurements with resazurin

In a set of streamside mesocosms, stream ecosystem respiration (ER) increased with biofilm biomass and flow heterogeneity (turbulence) generated by impermeable bed forms, even though those bed forms had no hyporheic exchange. Two streamside flumes with gravel beds (single layer of gravel) were operated in parallel. The first flume had no bed forms, and the second flume had 10 cm high dune-shaped bed forms with a wavelength of 1.0 m. Ecosystem respiration was measured via resazurin reduction to resorufin in each flume at three different biomass stages during biofilm growth. Results support the hypothesis that ER increases with flow heterogeneity generated by bed forms across all biofilm biomass stages. For the same biofilm biomass, ER was up to 1.9 times larger for a flume with 10 cm high impermeable bed forms than for a flume without the bed forms. Further, the amount of increase in ER associated with impermeable bed forms was itself increased as biofilms grew. Regardless of bed forms, biofilms increased transient storage by a factor of approximately 4.Keywords: bed forms, respiration, transient storage, biofilm, metabolism, resazuri

Salerno's model of DNA reanalysed: could solitons have biological significance?

We investigate the sequence-dependent behaviour of localised excitations in a toy, nonlinear model of DNA base-pair opening originally proposed by Salerno. Specifically we ask whether ``breather'' solitons could play a role in the facilitated location of promoters by RNA polymerase. In an effective potential formalism, we find excellent correlation between potential minima and {\em Escherichia coli} promoter recognition sites in the T7 bacteriophage genome. Evidence for a similar relationship between phage promoters and downstream coding regions is found and alternative reasons for links between AT richness and transcriptionally-significant sites are discussed. Consideration of the soliton energy of translocation provides a novel dynamical picture of sliding: steep potential gradients correspond to deterministic motion, while ``flat'' regions, corresponding to homogeneous AT or GC content, are governed by random, thermal motion. Finally we demonstrate an interesting equivalence between planar, breather solitons and the helical motion of a sliding protein ``particle'' about a bent DNA axis.Comment: Latex file 20 pages, 5 figures. Manuscript of paper to appear in J. Biol. Phys., accepted 02/09/0

Scientific Opportunities with an X-ray Free-Electron Laser Oscillator

An X-ray free-electron laser oscillator (XFELO) is a new type of hard X-ray source that would produce fully coherent pulses with meV bandwidth and stable intensity. The XFELO complements existing sources based on self-amplified spontaneous emission (SASE) from high-gain X-ray free-electron lasers (XFEL) that produce ultra-short pulses with broad-band chaotic spectra. This report is based on discussions of scientific opportunities enabled by an XFELO during a workshop held at SLAC on June 29 - July 1, 2016Comment: 21 pages, 12 figure

Fluvial network organization imprints on microbial co-occurrence networks

Recent studies highlight linkages among the architecture of ecological networks, their persistence facing environmental disturbance, and the related patterns of biodiversity. A hitherto unresolved question is whether the structure of the landscape inhabited by organisms leaves an imprint on their ecological networks. We analyzed, based on pyrosequencing profiling of the biofilm communities in 114 streams, how features inherent to fluvial networks affect the co-occurrence networks that the microorganisms form in these biofilms. Our findings suggest that hydrology and metacommunity dynamics, both changing predictably across fluvial networks, affect the fragmentation of the microbial co-occurrence networks throughout the fluvial network. The loss of taxa from co-occurrence networks demonstrates that the removal of gatekeepers disproportionately contributed to network fragmentation, which has potential implications for the functions biofilms fulfill in stream ecosystems. Our findings are critical because of increased anthropogenic pressures deteriorating stream ecosystem integrity and biodiversity