Inter-model comparison of global hydroxyl radical (OH) distributions and their impact on atmospheric methane over the 2000–2016 period

The modeling study presented here aims to estimate how uncertainties in global hydroxyl radical (OH) distributions, variability, and trends may contribute to resolving discrepancies between simulated and observed methane (CH4) changes since 2000. A multi-model ensemble of 14 OH fields was analyzed and aggregated into 64 scenarios to force the offline atmospheric chemistry transport model LMDz (Laboratoire de Meteorologie Dynamique) with a standard CH4 emission scenario over the period 2000–2016. The multi-model simulated global volume-weighted tropospheric mean OH concentration ([OH]) averaged over 2000–2010 ranges between 8:7*10^5 and 12:8*10^5 molec cm-3. The inter-model differences in tropospheric OH burden and vertical distributions are mainly determined by the differences in the nitrogen oxide (NO) distributions, while the spatial discrepancies between OH fields are mostly due to differences in natural emissions and volatile organic compound (VOC) chemistry. From 2000 to 2010, most simulated OH fields show an increase of 0.1–0:3*10^5 molec cm-3 in the tropospheric mean [OH], with year-to-year variations much smaller than during the historical period 1960–2000. Once ingested into the LMDz model, these OH changes translated into a 5 to 15 ppbv reduction in the CH4 mixing ratio in 2010, which represents 7%–20% of the model-simulated CH4 increase due to surface emissions. Between 2010 and 2016, the ensemble of simulations showed that OH changes could lead to a CH4 mixing ratio uncertainty of > 30 ppbv. Over the full 2000–2016 time period, using a common stateof- the-art but nonoptimized emission scenario, the impact of [OH] changes tested here can explain up to 54% of the gap between model simulations and observations. This result emphasizes the importance of better representing OH abundance and variations in CH4 forward simulations and emission optimizations performed by atmospheric inversions

Novel gene expression responses in the ovine abomasal mucosa to infection with the gastric nematode Teladorsagia circumcincta

Infection of sheep with the gastric nematode Teladorsagia circumcincta results in distinct Th2-type changes in the mucosa, including mucous neck cell and mast cell hyperplasia, eosinophilia, recruitment of IgA/IgE producing cells and neutrophils, altered T-cell subsets and mucosal hypertrophy. To address the protective mechanisms generated in animals on previous exposure to this parasite, gene expression profiling was carried out using samples of abomasal mucosa collected pre- and post- challenge from animals of differing immune status, using an experimental model of T. circumcincta infection. Recently developed ovine cDNA arrays were used to compare the abomasal responses of sheep immunised by trickle infection with worm-naïve sheep, following a single oral challenge of 50 000 T. circumcincta L3. Key changes were validated using qRT-PCR techniques. Immune animals demonstrated highly significant increases in levels of transcripts normally associated with cytotoxicity such as granulysin and granzymes A, B and H, as well as mucous-cell derived transcripts, predominantly calcium-activated chloride channel 1 (CLCA1). Challenge infection also induced up-regulation of transcripts potentially involved in initiating or modulating the immune response, such as heat shock proteins, complement factors and the chemokine CCL2. In contrast, there was marked infection-associated down-regulation of gene expression of members of the gastric lysozyme family. The changes in gene expression levels described here may reflect roles in direct anti-parasitic effects, immuno-modulation or tissue repair. (Funding; DEFRA/SHEFC (VT0102) and the BBSRC (BB/E01867X/1))

Novel gene expression responses in the ovine abomasal mucosa to infection with the gastric nematode Teladorsagia circumcincta

Infection of sheep with the gastric nematode Teladorsagia circumcincta results in distinct Th2-type changes in the mucosa, including mucous neck cell and mast cell hyperplasia, eosinophilia, recruitment of IgA/IgE producing cells and neutrophils, altered T-cell subsets and mucosal hypertrophy. To address the protective mechanisms generated in animals on previous exposure to this parasite, gene expression profiling was carried out using samples of abomasal mucosa collected pre- and post- challenge from animals of differing immune status, using an experimental model of T. circumcincta infection. Recently developed ovine cDNA arrays were used to compare the abomasal responses of sheep immunised by trickle infection with worm-naïve sheep, following a single oral challenge of 50 000 T. circumcincta L3. Key changes were validated using qRT-PCR techniques. Immune animals demonstrated highly significant increases in levels of transcripts normally associated with cytotoxicity such as granulysin and granzymes A, B and H, as well as mucous-cell derived transcripts, predominantly calcium-activated chloride channel 1 (CLCA1). Challenge infection also induced up-regulation of transcripts potentially involved in initiating or modulating the immune response, such as heat shock proteins, complement factors and the chemokine CCL2. In contrast, there was marked infection-associated down-regulation of gene expression of members of the gastric lysozyme family. The changes in gene expression levels described here may reflect roles in direct anti-parasitic effects, immuno-modulation or tissue repair. (Funding; DEFRA/SHEFC (VT0102) and the BBSRC (BB/E01867X/1))

Stem cell-derived porcine macrophages as a new platform for studying host-pathogen interactions

BACKGROUND: Infectious diseases of farmed and wild animals pose a recurrent threat to food security and human health. The macrophage, a key component of the innate immune system, is the first line of defence against many infectious agents and plays a major role in shaping the adaptive immune response. However, this phagocyte is a target and host for many pathogens. Understanding the molecular basis of interactions between macrophages and pathogens is therefore crucial for the development of effective strategies to combat important infectious diseases. RESULTS: We explored how porcine pluripotent stem cells (PSCs) can provide a limitless in vitro supply of genetically and experimentally tractable macrophages. Porcine PSC-derived macrophages (PSCdMs) exhibited molecular and functional characteristics of ex vivo primary macrophages and were productively infected by pig pathogens, including porcine reproductive and respiratory syndrome virus (PRRSV) and African swine fever virus (ASFV), two of the most economically important and devastating viruses in pig farming. Moreover, porcine PSCdMs were readily amenable to genetic modification by CRISPR/Cas9 gene editing applied either in parental stem cells or directly in the macrophages by lentiviral vector transduction. CONCLUSIONS: We show that porcine PSCdMs exhibit key macrophage characteristics, including infection by a range of commercially relevant pig pathogens. In addition, genetic engineering of PSCs and PSCdMs affords new opportunities for functional analysis of macrophage biology in an important livestock species. PSCs and differentiated derivatives should therefore represent a useful and ethical experimental platform to investigate the genetic and molecular basis of host-pathogen interactions in pigs, and also have wider applications in livestock. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-021-01217-8

The osteology of ‘Periptychus carinidens’: a robust, ungulate-like placental mammal (Mammalia: Periptychidae) from the Paleocene of North America

Periptychus is the archetypal genus of Periptychidae, a clade of prolific Paleocene 'condylarth' mammals from North America that were among the first placental mammals to radiate after the end-Cretaceous extinction, remarkable for their distinctive dental anatomy. A comprehensive understanding of the anatomy of Periptychus has been hindered by a lack of cranial and postcranial material and only cursory description of existing material. We comprehensively describe the cranial, dental and postcranial anatomy of Periptychus carinidens based on new fossil material from the early Paleocene (Torrejonian) of New Mexico, USA. The cranial anatomy of Periptychus is broadly concurrent with the inferred plesiomorphic eutherian condition, albeit more robust in overall construction. The rostrum is moderately elongate with no constriction, the facial region is broad, and the braincase is small with a well-exposed mastoid on the posterolateral corner and tall sagittal and nuchal crests. The dentition of Periptychus is characterized by strongly crenulated enamel, enlarged upper and lower premolars with a tall centralised paracone/protoconid. The postcranial skeleton of Periptychus is that of a robust, medium-sized (~20 Kg) stout-limbed animal that was incipiently mediportal and adopted a plantigrade stance. The structure of the fore- and hindlimb of Periptychus corresponds to that of a typically terrestrial mammal, while morphological features of the forelimb such as the low tubercles of the humerus, long and prominent deltopectoral crest, pronounced medial epicondyle, and hemispherical capitulum indicate some scansorial and/or fossorial ability. Most striking is the strongly dorsoplantarly compressed astragalus of Periptychus, which in combination with the distal crus and calcaneal morphology indicates a moderately mobile cruropedal joint. The anatomy of Periptychus is unique and lacks any extant analogue; it combines a basic early placental body plan with numerous unique specializations in its dental, cranial and postcranial anatomy that exemplify the ability of mammals to adapt and evolve following catastrophic environmental upheaval

Molecular composition of organic aerosols in central Amazonia: An ultra-high-resolution mass spectrometry study

The Amazon Basin plays key role in atmospheric chemistry, biodiversity and climate change. In this study we applied nanoelectrospray (nanoESI) ultra-high-resolution mass spectrometry (UHRMS) for the analysis of the organic fraction of PM2.5 aerosol samples collected during dry and wet seasons at a site in central Amazonia receiving background air masses, biomass burning and urban pollution. Comprehensive mass spectral data evaluation methods (e.g. Kendrick mass defect, Van Krevelen diagrams, carbon oxidation state and aromaticity equivalent) were used to identify compound classes and mass distributions of the detected species. Nitrogen-and/or sulfur-containing organic species contributed up to 60% of the total identified number of formulae. A large number of molecular formulae in organic aerosol (OA) were attributed to later-generation nitrogen-and sulfur-containing oxidation products, suggesting that OA composition is affected by biomass burning and other, potentially anthropogenic, sources. Isoprene-derived organosulfate (IEPOX-OS) was found to be the most dominant ion in most of the analysed samples and strongly followed the concentration trends of the gas-phase anthropogenic tracers confirming its mixed anthropogenic-biogenic origin. The presence of oxidised aromatic and nitro-aromatic compounds in the samples suggested a strong influence from biomass burning especially during the dry period. Aerosol samples from the dry period and under enhanced biomass burning conditions contained a large number of molecules with high carbon oxidation state and an increased number of aromatic compounds compared to that from the wet period. The results of this work demonstrate that the studied site is influenced not only by biogenic emissions from the forest but also by biomass burning and potentially other anthropogenic emissions from the neighbouring urban environments. © 2016 Author(s)

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing

International audienceCurrent sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans

The NANOGrav 15-year Data Set: Search for Anisotropy in the Gravitational-Wave Background

The North American Nanohertz Observatory for Gravitational Waves (NANOGrav) has reported evidence for the presence of an isotropic nanohertz gravitational wave background (GWB) in its 15 yr dataset. However, if the GWB is produced by a population of inspiraling supermassive black hole binary (SMBHB) systems, then the background is predicted to be anisotropic, depending on the distribution of these systems in the local Universe and the statistical properties of the SMBHB population. In this work, we search for anisotropy in the GWB using multiple methods and bases to describe the distribution of the GWB power on the sky. We do not find significant evidence of anisotropy, and place a Bayesian $95\%$ upper limit on the level of broadband anisotropy such that $(C_{l>0} / C_{l=0}) < 20\%$. We also derive conservative estimates on the anisotropy expected from a random distribution of SMBHB systems using astrophysical simulations conditioned on the isotropic GWB inferred in the 15-yr dataset, and show that this dataset has sufficient sensitivity to probe a large fraction of the predicted level of anisotropy. We end by highlighting the opportunities and challenges in searching for anisotropy in pulsar timing array data.Comment: 19 pages, 11 figures; submitted to Astrophysical Journal Letters as part of Focus on NANOGrav's 15-year Data Set and the Gravitational Wave Background. For questions or comments, please email [email protected]

The NANOGrav 15-Year Data Set: Detector Characterization and Noise Budget

Pulsar timing arrays (PTAs) are galactic-scale gravitational wave detectors. Each individual arm, composed of a millisecond pulsar, a radio telescope, and a kiloparsecs-long path, differs in its properties but, in aggregate, can be used to extract low-frequency gravitational wave (GW) signals. We present a noise and sensitivity analysis to accompany the NANOGrav 15-year data release and associated papers, along with an in-depth introduction to PTA noise models. As a first step in our analysis, we characterize each individual pulsar data set with three types of white noise parameters and two red noise parameters. These parameters, along with the timing model and, particularly, a piecewise-constant model for the time-variable dispersion measure, determine the sensitivity curve over the low-frequency GW band we are searching. We tabulate information for all of the pulsars in this data release and present some representative sensitivity curves. We then combine the individual pulsar sensitivities using a signal-to-noise-ratio statistic to calculate the global sensitivity of the PTA to a stochastic background of GWs, obtaining a minimum noise characteristic strain of $7\times 10^{-15}$ at 5 nHz. A power law-integrated analysis shows rough agreement with the amplitudes recovered in NANOGrav's 15-year GW background analysis. While our phenomenological noise model does not model all known physical effects explicitly, it provides an accurate characterization of the noise in the data while preserving sensitivity to multiple classes of GW signals.Comment: 67 pages, 73 figures, 3 tables; published in Astrophysical Journal Letters as part of Focus on NANOGrav's 15-year Data Set and the Gravitational Wave Background. For questions or comments, please email [email protected]