Improved detection and consistency of RNA-interacting proteomes using DIA SILAC.

The RNA-interacting proteome is commonly characterized by UV-crosslinking followed by RNA purification, with protein recovery quantified using SILAC labeling followed by data-dependent acquisition (DDA) of proteomic data. However, the low efficiency of UV-crosslinking, combined with limited sensitivity of the DDA approach often restricts detection to relatively abundant proteins, necessitating multiple mass spec injections of fractionated peptides for each biological sample. Here we report an application of data-independent acquisition (DIA) with SILAC in a total RNA-associated protein purification (TRAPP) UV-crosslinking experiment. This gave 15% greater protein detection and lower inter-replicate variation relative to the same biological materials analyzed using DDA, while allowing single-shot analysis of the sample. As proof of concept, we determined the effects of arsenite treatment on the RNA-bound proteome of HEK293T cells. The DIA dataset yielded similar GO term enrichment for RNA-binding proteins involved in cellular stress responses to the DDA dataset while detecting extra proteins unseen by DDA. Overall, the DIA SILAC approach improved detection of proteins over conventional DDA SILAC for generating RNA-interactome datasets, at a lower cost due to reduced machine time. Analyses are described for TRAPP data, but the approach is suitable for proteomic analyses following essentially any RNA-binding protein enrichment technique.

Impacts of metal mining on river systems: a global assessment.

An estimated 23 million people live on floodplains affected by potentially dangerous concentrations of toxic waste derived from past and present metal mining activity. We analyzed the global dimensions of this hazard, particularly in regard to lead, zinc, copper, and arsenic, using a georeferenced global database detailing all known metal mining sites and intact and failed tailings storage facilities. We then used process-based and empirically tested modeling to produce a global assessment of metal mining contamination in river systems and the numbers of human populations and livestock exposed. Worldwide, metal mines affect 479,200 kilometers of river channels and 164,000 square kilometers of floodplains. The number of people exposed to contamination sourced from long-term discharge of mining waste into rivers is almost 50 times greater than the number directly affected by tailings dam failures.

Bioaerosols are the dominant source of warm-temperature immersion-mode INPs and drive uncertainties in INP predictability.

Ice-nucleating particles (INPs) are rare atmospheric aerosols that initiate primary ice formation, but accurately simulating their concentrations and variability in large-scale climate models remains a challenge. Doing so requires both simulating major particle sources and parameterizing their ice nucleation (IN) efficiency. Validating and improving model predictions of INP concentrations requires measuring their concentrations delineated by particle type. We present a method to speciate INP concentrations into contributions from dust, sea spray aerosol (SSA), and bioaerosol. Field campaign data from Bodega Bay, California, showed that bioaerosols were the primary source of INPs between -12° and -20°C, while dust was a minor source and SSA had little impact. We found that recent parameterizations for dust and SSA accurately predicted ambient INP concentrations. However, the model did not skillfully simulate bioaerosol INPs, suggesting a need for further research to identify major factors controlling their emissions and INP efficiency for improved representation in models.

The minor chicken class I gene BF1 is deleted between short imperfect direct repeats in the B14 and typical B15 major histocompatibility complex (MHC) haplotypes.

The chicken major histocompatibility complex (MHC, also known as the BF-BL region of the B locus) is notably small and simple with few genes, most of which are involved in antigen processing and presentation. There are two classical class I genes, of which only BF2 is well and systemically expressed as the major ligand for cytotoxic T lymphocytes (CTLs). The other class I gene, BF1, is believed to be primarily a natural killer (NK) cell ligand. Among most standard chicken MHC haplotypes examined in detail, BF1 is expressed tenfold less than BF2 at the RNA level due to defects in the promoter or in a splice site. However, in the B14 and typical B15 haplotypes, BF1 RNA was not detected, and here, we show that a deletion between imperfect 32 nucleotide direct repeats has removed the BF1 gene entirely. The phenotypic effects of not having a BF1 gene (particularly on resistance to infectious pathogens) have not been systematically explored, but such deletions between short direct repeats are also found in some BF1 promoters and in the 5' untranslated region (5'UTR) of some BG genes found in the BG region of the B locus. Despite the opposite transcriptional orientation of homologous genes in the chicken MHC, which might prevent the loss of key genes from a minimal essential MHC, it appears that small direct repeats can still lead to deletion.

Persistence and Potential Atmospheric Ramifications of Ice-Nucleating Particles Released from Thawing Permafrost.

Permafrost underlies approximately a quarter of the Northern Hemisphere and is changing amidst a warming climate. Thawed permafrost can enter water bodies through top-down thaw, thermokarst erosion, and slumping. Recent work revealed that permafrost contains ice-nucleating particles (INPs) with concentrations comparable to midlatitude topsoil. These INPs may impact the surface energy budget of the Arctic by affecting mixed-phase clouds, if emitted into the atmosphere. In two 3-4-week experiments, we placed 30,000- and 1000-year-old ice-rich silt permafrost in a tank with artificial freshwater and monitored aerosol INP emissions and water INP concentrations as the water's salinity and temperature were varied to mimic aging and transport of thawed material into seawater. We also tracked aerosol and water INP composition through thermal treatments and peroxide digestions and bacterial community composition with DNA sequencing. We found that the older permafrost produced the highest and most stable airborne INP concentrations, with levels comparable to desert dust when normalized to particle surface area. Both samples showed that the transfer of INPs to air persisted during simulated transport to the ocean, demonstrating a potential to influence the Arctic INP budget. This suggests an urgent need for quantifying permafrost INP sources and airborne emission mechanisms in climate models.

Translation factor eIF5a is essential for IFNγ production and cell cycle regulation in primary CD8+ T lymphocytes.

Control of mRNA translation adjusts protein production rapidly and facilitates local cellular responses to environmental conditions. Traditionally initiation of translation is considered to be a major translational control point, however, control of peptide elongation is also important. Here we show that the function of the elongation factor, eIF5a, is regulated dynamically in naïve CD8+ T cells upon activation by post-translational modification, whereupon it facilitates translation of specific subsets of proteins. eIF5a is essential for long-term survival of effector CD8+ T cells and sequencing of nascent polypeptides indicates that the production of proteins which regulate proliferation and key effector functions, particularly the production of IFNγ and less acutely TNF production and cytotoxicity, is dependent on the presence of functional eIF5a. Control of translation in multiple immune cell lineages is required to co-ordinate immune responses and these data illustrate that translational elongation contributes to post-transcriptional regulons important for the control of inflammation.

Annual cycle observations of aerosols capable of ice formation in central Arctic clouds.

The Arctic is warming faster than anywhere else on Earth, prompting glacial melt, permafrost thaw, and sea ice decline. These severe consequences induce feedbacks that contribute to amplified warming, affecting weather and climate globally. Aerosols and clouds play a critical role in regulating radiation reaching the Arctic surface. However, the magnitude of their effects is not adequately quantified, especially in the central Arctic where they impact the energy balance over the sea ice. Specifically, aerosols called ice nucleating particles (INPs) remain understudied yet are necessary for cloud ice production and subsequent changes in cloud lifetime, radiative effects, and precipitation. Here, we report observations of INPs in the central Arctic over a full year, spanning the entire sea ice growth and decline cycle. Further, these observations are size-resolved, affording valuable information on INP sources. Our results reveal a strong seasonality of INPs, with lower concentrations in the winter and spring controlled by transport from lower latitudes, to enhanced concentrations of INPs during the summer melt, likely from marine biological production in local open waters. This comprehensive characterization of INPs will ultimately help inform cloud parameterizations in models of all scales.

Protein disulphide isomerase (PDI) is protective against amyotrophic lateral sclerosis (ALS)-related mutant Fused in Sarcoma (FUS) in in vitro models.

Mutations in Fused in Sarcoma (FUS) are present in familial and sporadic cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). FUS is localised in the nucleus where it has important functions in DNA repair. However, in ALS/FTD, mutant FUS mislocalises from the nucleus to the cytoplasm where it forms inclusions, a key pathological hallmark of neurodegeneration. Mutant FUS also inhibits protein import into the nucleus, resulting in defects in nucleocytoplasmic transport. Fragmentation of the neuronal Golgi apparatus, induction of endoplasmic reticulum (ER) stress, and inhibition of ER-Golgi trafficking are also associated with mutant FUS misfolding in ALS. Protein disulphide isomerase (PDI) is an ER chaperone previously shown to be protective against misfolding associated with mutant superoxide dismutase 1 (SOD1) and TAR DNA-binding protein-43 (TDP-43) in cellular and zebrafish models. However, a protective role against mutant FUS in ALS has not been previously described. In this study, we demonstrate that PDI is protective against mutant FUS. In neuronal cell line and primary cultures, PDI restores defects in nuclear import, prevents the formation of mutant FUS inclusions, inhibits Golgi fragmentation, ER stress, ER-Golgi transport defects, and apoptosis. These findings imply that PDI is a new therapeutic target in FUS-associated ALS.

Relating Structure and Ice Nucleation of Mixed Surfactant Systems Relevant to Sea Spray Aerosol.

Ice nucleating particles (INPs) influence weather and climate by their effect on cloud phase state. Fatty alcohols present within aerosol particles confer a potentially important source of ice nucleation activity to sea spray aerosol produced in oceanic regions. However, their interactions with other aerosol components and the influence on freezing were previously largely unknown. Here, we report quantitative measurements of fatty alcohols in model sea spray aerosol and examine the relationships between the composition and structure of the surfactants and subphase in the context of these measurements. Deposited mixtures of surfactants retain the ability to nucleate ice, even in fatty acid-dominant compositions. Strong refreezing effects are also observed, where previously frozen water-surfactant samples nucleate more efficiently. Structural sources of refreezing behavior are identified as either kinetically trapped film states or three-dimensional (3D) solid surfactant particles. Salt effects are especially important for surfactant INPs, where high salt concentrations suppress freezing. A simple water uptake model suggests that surfactant-containing aerosol requires either very low salt content or kinetic trapping as solid particles to act as INPs in the atmosphere. These types of INPs could be identified through comparison of different INP instrument responses.

Incorporating hydrology into climate suitability models changes projections of malaria transmission in Africa.

Continental-scale models of malaria climate suitability typically couple well-established temperature-response models with basic estimates of vector habitat availability using rainfall as a proxy. Here we show that across continental Africa, the estimated geographic range of climatic suitability for malaria transmission is more sensitive to the precipitation threshold than the thermal response curve applied. To address this problem we use downscaled daily climate predictions from seven GCMs to run a continental-scale hydrological model for a process-based representation of mosquito breeding habitat availability. A more complex pattern of malaria suitability emerges as water is routed through drainage networks and river corridors serve as year-round transmission foci. The estimated hydro-climatically suitable area for stable malaria transmission is smaller than previous models suggest and shows only a very small increase in state-of-the-art future climate scenarios. However, bigger geographical shifts are observed than with most rainfall threshold models and the pattern of that shift is very different when using a hydrological model to estimate surface water availability for vector breeding.

The contribution of black carbon to global ice nucleating particle concentrations relevant to mixed-phase clouds.

Black carbon (BC) aerosol plays an important role in the Earth's climate system because it absorbs solar radiation and therefore potentially warms the climate; however, BC can also act as a seed for cloud particles, which may offset much of its warming potential. If BC acts as an ice nucleating particle (INP), BC could affect the lifetime, albedo, and radiative properties of clouds containing both supercooled liquid water droplets and ice particles (mixed-phase clouds). Over 40% of global BC emissions are from biomass burning; however, the ability of biomass burning BC to act as an INP in mixed-phase cloud conditions is almost entirely unconstrained. To provide these observational constraints, we measured the contribution of BC to INP concentrations ([INP]) in real-world prescribed burns and wildfires. We found that BC contributes, at most, 10% to [INP] during these burns. From this, we developed a parameterization for biomass burning BC and combined it with a BC parameterization previously used for fossil fuel emissions. Applying these parameterizations to global model output, we find that the contribution of BC to potential [INP] relevant to mixed-phase clouds is ∼5% on a global average.

Airborne bacteria confirm the pristine nature of the Southern Ocean boundary layer.

Microorganisms are ubiquitous and highly diverse in the atmosphere. Despite the potential impacts of airborne bacteria found in the lower atmosphere over the Southern Ocean (SO) on the ecology of Antarctica and on marine cloud phase, no previous region-wide assessment of bioaerosols over the SO has been reported. We conducted bacterial profiling of boundary layer shipboard aerosol samples obtained during an Austral summer research voyage, spanning 42.8 to 66.5°S. Contrary to findings over global subtropical regions and the Northern Hemisphere, where transport of microorganisms from continents often controls airborne communities, the great majority of the bacteria detected in our samples were marine, based on taxonomy, back trajectories, and source tracking analysis. Further, the beta diversity of airborne bacterial communities varied with latitude and temperature, but not with other meteorological variables. Limited meridional airborne transport restricts southward community dispersal, isolating Antarctica and inhibiting microorganism and nutrient deposition from lower latitudes to these same regions. A consequence and implication for this region's marine boundary layer and the clouds that overtop it is that it is truly pristine, free from continental and anthropogenic influences, with the ocean as the dominant source controlling low-level concentrations of cloud condensation nuclei and ice nucleating particles.

Simultaneous or Staged Bilateral Total Hip Arthroplasty? An Analysis of Complications in 14,460 Patients Using National Data.

BACKGROUND: Simultaneous bilateral total hip arthroplasty (SimBTHA) is often performed in younger, fitter patients with bilateral hip disease. If patients are deemed not suitable for SimBTHA due to concurrent comorbidity, it may be more appropriate to perform staged bilateral total hip arthroplasties (StBTHAs) 3-6 months apart to minimize complications and morbidity. Complication rates following hip arthroplasty are low and large national datasets are helpful for assessing these rare events. We aimed at comparing SimBTHA vs StBTHA in order to determine any differences in morbidity and mortality. METHODS: Hospital Episode Statistics data for all patients who underwent bilateral THAs in the English National Health Service between April 2005 and July 2014 were obtained. Patients were grouped into SimBTHAs (same day) or staged, with the second THA occurring between 3 and 6 months after the first. Medical and surgical complications were compared and total length of stay was assessed. RESULTS: A total of 2507 underwent SimBTHAs and 9915 had StBTHAs. SimBTHA patients were significantly younger (60.6 vs 65.5 years, P < .001) and more likely to be male, but had similar Charlson comorbidity scores. Compared to StBTHAs, patients undergoing SimBTHAs had a greater risk of pulmonary embolism, myocardial infarction, renal failure, chest infection, and inhospital death. Patients undergoing SimBTHAs had a significantly shorter overall hospital stay (8.9 vs 10.4 days). Patients undergoing SimBTHA at high-volume units had a lower average Charlson score and subsequent complication rate than low-volume units. CONCLUSION: These findings highlight the greater risks of SimBTHA in patients with Charlson score greater than 0 performed at lower-volume centers in England.

Conventional Versus Highly Cross-Linked Polyethylene in Primary Total Knee Replacement: A Comparison of Revision Rates Using Data from the National Joint Registry for England, Wales, and Northern Ireland.

BACKGROUND: There is evidence to support the use of highly cross-linked polyethylene (HXLPE) in patients undergoing total hip arthroplasty. However, the benefits for those undergoing total knee arthroplasty are uncertain, with conflicting reports based on previous cohort analyses. The purpose of the present study was to compare the revision rates following primary total knee arthroplasty with use of HXLPE as compared with conventional polyethylene (CPE) using data from the National Joint Registry (NJR) for England, Wales and Northern Ireland. METHODS: We performed a retrospective analysis of primary total knee arthroplasties recorded in the NJR from 2003 to 2014. Cobalt-chromium (CoCr)-CPE and CoCr-HXLPE bearing surfaces were compared using all-cause revision, aseptic revision, and septic revision as end points. Survival analyses were conducted using rates per 100 years observed, Kaplan-Meier survival estimates, and Cox regression hazard ratios (HRs) adjusted for age, sex, American Society of Anesthesiologists (ASA) classification, body mass index (BMI), lead surgeon grade, and implant constraint. Secondary analyses compared the most commonly used HXLPEs (Zimmer Prolong, DePuy XLK, and Stryker X3) against CPE for the 3 most common total knee arthroplasty systems (NexGen, PFC Sigma, and Triathlon). RESULTS: In the present study of 550,658 total knee arthroplasties, the unadjusted aseptic revision rates were significantly lower following procedures performed with CPE (n = 513,744) as compared with those performed with HXLPE total knee replacements (n = 36,914) (0.29 [95% confidence interval (CI), 0.28 to 0.30] compared to 0.38 [95% CI, 0.35 to 0.42], p < 0.01). The 10-year HR associated with CPE was 0.4 (95% CI, 0.1 to 0.8, p = 0.03). There were no significant differences between the adjusted revision rates of HXPLE compared with CPE in individual analyses of the most common total knee arthroplasty systems. However, for the subset of patients who were both <60 years of age and had a BMI of >35 kg/m, the "second-generation" Stryker X3 HXLPE demonstrated significantly better survival than its respective CPE, with CPE having an HR of 2.6 (95% CI, 1.2 to 5.9) (p = 0.02). CONCLUSIONS: Alternative bearings are marketed as having improved wear properties over traditional CoCr-CPE. This registry-based analysis demonstrated no overall survival benefit of HXLPE after a maximum duration of follow-up of 12 years. Because of their increased cost, the routine use of HXLPE bearings may not be justified. However, they may have a role in specific "higher demand" groups such as patients <60 years of age and/or those with a BMI of >35 kg/m. LEVEL OF EVIDENCE: Therapeutic Level III. See Instructions for Authors for a complete list of levels of evidence.

Seasonal Changes of Airborne Bacterial Communities Over Tokyo and Influence of Local Meteorology.

In order to study airborne bacterial community dynamics over Tokyo, including fine-scale correlations between airborne microorganisms and meteorological conditions, and the influence of local versus long-range transport of microbes, air samples were collected on filters for periods ranging from 48 to 72 h. The diversity of the microbial community was assessed by next generation sequencing. Predicted source regions of airborne particles, from back trajectory analyses, changed abruptly from the Pacific Ocean to the Eurasian Continent in the beginning of October. However, the microbial community composition and the alpha and beta diversities were not affected by this shift in meteorological regime, suggesting that long-range transport from oceanic or continental sources was not the principal determinant controlling the local airborne microbiome. By contrast, we found a significant correlation between the local meteorology, especially relative humidity and wind speed, and both alpha diversity and beta diversity. Among four potential local source categories (soil, bay seawater, river, and pond), bay seawater and soil were identified as constant and predominant sources. Statistical analyses point toward humidity as the most influential meteorological factor, most likely because it is correlated with soil moisture and hence negatively correlated with the dispersal of particles from the land surface. In this study, we have demonstrated the benefits of fine-scale temporal analyses for understanding the sources and relationships with the meteorology of Tokyo's "aerobiome."

Ice nucleation by particles containing long-chain fatty acids of relevance to freezing by sea spray aerosols.

Heterogeneous ice nucleation in the atmosphere regulates cloud properties, such as phase (ice versus liquid) and lifetime. Aerosol particles of marine origin are relevant ice nucleating particle sources when marine aerosol layers are lifted over mountainous terrain and in higher latitude ocean boundary layers, distant from terrestrial aerosol sources. Among many particle compositions associated with ice nucleation by sea spray aerosols are highly saturated fatty acids. Previous studies have not demonstrated their ability to freeze dilute water droplets. This study investigates ice nucleation by monolayers at the surface of supercooled droplets and as crystalline particles at temperatures exceeding the threshold for homogeneous freezing. Results show the poor efficiency of long chain fatty acid (C16, C18) monolayers in templating freezing of pure water droplets and seawater subphase to temperatures of at least -30 °C, consistent with theory. This contrasts with freezing of fatty alcohols (C22 used here) at nearly 20 °C warmer. Evaporation of µL-sized droplets to promote structural compression of a C19 acid monolayer did not favor warmer ice formation of drops. Heterogeneous ice nucleation occurred for nL-sized droplets condensed on 5 to 100 µm crystalline particles of fatty acid (C12 to C20) at a range of temperatures below -28 °C. These experiments suggest that fatty acids nucleate ice at warmer than -36 °C only when the crystalline phase is present. Rough estimates of ice active site densities are consistent with those of marine aerosols, but require knowledge of the proportion of surface area comprised of fatty acids for application.

Terrestrial Origin for Abundant Riverine Nanoscale Ice-Nucleating Particles.

Ice-nucleating particles (INPs) associated with fresh waters are a neglected, but integral component of the water cycle. Abundant INPs were identified from surface waters of both the Maumee River and Lake Erie with ice nucleus spectra spanning a temperature range from -3 to -15 °C. The majority of river INPs were submicron in size and attributed to biogenic macromolecules, inferred from the denaturation of ice-nucleation activity by heat. In a watershed dominated by row-crop agriculture, higher concentrations of INPs were found in river samples compared to lake samples. Further, ice-nucleating temperatures differed between river and lake samples, which indicated different populations of INPs. Seasonal analysis of INPs that were active at warmer temperatures (≥-10 °C; INP-10) showed their concentration to correlate with river discharge, suggesting a watershed origin of these INPs. A terrestrial origin for INPs in the Maumee River was further supported by a correspondence between the ice-nucleation signatures of river INPs and INPs derived from the soil fungus Mortierella alpina. Aerosols derived from turbulence features in the river carry INP-10, although their potential influence on regional weather is unclear. INP-10 contained within aerosols generated from a weir spanning the river, ranged in concentration from 1 to 11 INP m-3, which represented a fold-change of 3.2 over average INP-10 concentrations sampled from aerosols at control locations.

Central obesity and the Mediterranean diet: A systematic review of intervention trials.

Central obesity is associated with chronic low-grade inflammation, and is a risk factor for cardiometabolic syndrome. The Mediterranean diet pattern has a convincing evidence-base for improving cardiometabolic health. This review investigated the impact of Mediterranean diet interventions on central obesity, specifically. A systematic literature search was conducted in the MEDLINE, CINAHL, EMBASE and Cochrane library databases. Search terms included: 'Mediterranean Diet', 'Mediterranean dietary pattern', 'central obesity' and 'visceral fat'. The search was limited to English language and humans ≥18 years. Eighteen articles met the eligibility criteria and reported at least one outcome measure of central obesity with Mediterranean diet intervention. Central obesity measures included waist circumference (16 studies), waist-hip ratio (5 studies) and visceral fat (2 studies). Thirteen (72%) of the studies, totaling 7186 subjects (5168 subjects assigned to a Mediterranean Diet), reported a significant reduction in central obesity with a Mediterranean-type diet. However, seven out of these 13 interventions employed energy restriction, and only three showed a statistically significant favorable effect of the Mediterranean diet relative to a control group. This systematic review highlights the potential for a Mediterranean diet intervention to reduce central obesity and in turn reduce obesity-related chronic disease risk and associated public health burden.

Suboptimal T-cell receptor signaling compromises protein translation, ribosome biogenesis, and proliferation of mouse CD8 T cells.

Global transcriptomic and proteomic analyses of T cells have been rich sources of unbiased data for understanding T-cell activation. Lack of full concordance of these datasets has illustrated that important facets of T-cell activation are controlled at the level of translation. We undertook translatome analysis of CD8 T-cell activation, combining polysome profiling and microarray analysis. We revealed that altering T-cell receptor stimulation influenced recruitment of mRNAs to heavy polysomes and translation of subsets of genes. A major pathway that was compromised, when TCR signaling was suboptimal, was linked to ribosome biogenesis, a rate-limiting factor in both cell growth and proliferation. Defective TCR signaling affected transcription and processing of ribosomal RNA precursors, as well as the translation of specific ribosomal proteins and translation factors. Mechanistically, IL-2 production was compromised in weakly stimulated T cells, affecting the abundance of Myc protein, a known regulator of ribosome biogenesis. Consequently, weakly activated T cells showed impaired production of ribosomes and a failure to maintain proliferative capacity after stimulation. We demonstrate that primary T cells respond to various environmental cues by regulating ribosome biogenesis and mRNA translation at multiple levels to sustain proliferation and differentiation.