Erratum:

This corrects the article DOI: 10.1103/PhysRevLett.123.033201.

Animal safety of a tall fescue endophyte (Epichloë sp.) in a perennial ryegrass (Lolium perenne) host.

AIMS: To assess animal health and production in sheep grazing perennial ryegrass (Lolium perenne) infected with a tall fescue endophyte (Epichloë sp.). METHODS: Three replicates of pure perennial ryegrass pastures infected with AR501 tall fescue endophyte (AR501 HE), AR1, AR37 or standard endophyte (STD) (all >85% infection) and a low endophyte control (AR501 LE) were grazed by 10 lambs for 7 weeks during late summer/early autumn, 2017. AR501 HE and AR501 LE were in the same tetraploid cultivar and the remaining treatments were in the same diploid cultivar. Lambs were weighed on Days 0, 19, 37 and 48 and assessed for ryegrass staggers on a 0-4 tremor scale nine times from Day 13. On Days 14 and 20, rectal temperatures and respiration rates were measured in lambs grazing AR501 HE, AR501 LE and STD under heat load. Pasture samples from each treatment were taken regularly (8 times) for analysis of known endophyte secondary metabolites. RESULTS: Peak mean ryegrass staggers scores for lambs grazing STD and AR37 treatments were 3.9 and 2.7, respectively, indicating environmental conditions were conducive to toxicity. Lambs grazing AR501 HE showed no ryegrass staggers at any date. The liveweight of STD lambs was up to 6.6 kg less than some or all other treatments on Days 19, 34 and 48, but there was no evidence of a difference between the liveweight of AR501 HE lambs and AR501 LE, AR37 or AR1 lambs on any date. Rectal temperatures and respiration rates of STD lambs were higher than AR501 HE lambs by 0.2°C and 26 breaths/minute, respectively. Apart from lower rectal temperature of AR501 HE lambs on Day 14, there was no evidence of differences between the AR501 HE and AR501 LE lambs. N-Formylloline was the only loline present in AR501 HE herbage (350-860 mg/kg). Peramine in AR501 HE herbage (42-77 mg/kg) was greater than that in STD and AR1 herbage on five and seven of the eight sampling dates, respectively. CONCLUSION: Lambs grazing AR501 HE showed no ryegrass staggers, exacerbated heat stress or suppressed liveweight gain compared with lambs grazing AR501 LE in a season when endophyte-induced toxicity was evident in STD and AR37 pastures. This suggests AR501 tall fescue endophyte does not produce toxic concentrations of secondary metabolites. CLINICAL RELEVANCE: This study suggests that there are no secondary metabolites produced by the tall fescue AR501 endophyte-perennial ryegrass association which affect animal health or production.

Using regulatory variants to detect gene-gene interactions identifies networks of genes linked to cell immortalisation.

The extent to which the impact of regulatory genetic variants may depend on other factors, such as the expression levels of upstream transcription factors, remains poorly understood. Here we report a framework in which regulatory variants are first aggregated into sets, and using these as estimates of the total cis-genetic effects on a gene we model their non-additive interactions with the expression of other genes in the genome. Using 1220 lymphoblastoid cell lines across platforms and independent datasets we identify 74 genes where the impact of their regulatory variant-set is linked to the expression levels of networks of distal genes. We show that these networks are predominantly associated with tumourigenesis pathways, through which immortalised cells are able to rapidly proliferate. We consequently present an approach to define gene interaction networks underlying important cellular pathways such as cell immortalisation.

Systematic uncertainty due to background-gas collisions in trapped-ion optical clocks.

We describe a framework for calculating the frequency shift and uncertainty of trapped-ion optical atomic clocks caused by background-gas collisions, and apply this framework to an 27Al+ clock to enable a total fractional systematic uncertainty below 10-18. For this clock, with 38(19) nPa of room-temperature H2 background gas, we find that collisional heating generates a non-thermal distribution of motional states with a mean time-dilation shift of order 10-16 at the end of a 150 ms probe, which is not detected by sideband thermometry energy measurements. However, the contribution of collisional heating to the spectroscopy signal is highly suppressed and we calculate the BGC shift to be -0.6(2.4) × 10-19, where the shift is due to collisional heating time dilation and the uncertainty is dominated by the worst case ±π/2 bound used for collisional phase shift of the 27Al+ superposition state. We experimentally validate the framework and determine the background-gas pressure in situ using measurements of the rate of collisions that cause reordering of mixed-species ion pairs.

Environmentally enriched pigs have transcriptional profiles consistent with neuroprotective effects and reduced microglial activity.

Environmental enrichment (EE) is widely used to study the effects of external factors on brain development, function and health in rodent models, but very little is known of the effects of EE on the brain in a large animal model such as the pig. Twenty-four young pigs (aged 5 weeks at start of study, 1:1 male: female ratio) were housed in environmentally enriched (EE) pens and provided with additional enrichment stimulation (a bag filled with straw) once daily. Litter, weight and sex matched controls n= (24) were housed in barren (B) conditions. Behaviour was recorded on alternate days from study day 10. After 21 days, RNA-sequencing of the frontal cortex of male piglets culled one hour after the enrichment stimulation, but not those at 4 h after stimulation, showed upregulation of genes involved in neuronal activity and synaptic plasticity in the EE compared to the B condition. This result is mirrored in the behavioural response to the stimulation which showed a peak in activity around the 1 h time-point. By contrast, EE piglets displayed a signature consistent with a relative decrease in microglial activity compared to those in the B condition. These results confirm those from rodents, suggesting that EE may also confer neuronal health benefits in large mammal models, through a potential relative reduction in neuroinflammatory process and increase in neuroprotection driven by an enrichment-induced increase in behavioural activity.

An update on equine post-operative ileus: Definitions, pathophysiology and management.

Post-operative ileus (POI) is a serious condition which any horse undergoing abdominal surgery is at risk of developing, leading to increased hospitalisation time and resulting costs. Advances in the understanding of the development of equine POI are mainly based on human and rodent literature, where manipulation-induced inflammation has been identified as a trigger, with activation of resident muscularis externa macrophages playing a crucial role in the pathophysiology. Despite many pharmacological trials in all species, there is no single completely successful treatment for POI, highlighting that the condition is multifactorial in cause and requires a multimodal approach to minimise its incidence.

The genomic architecture of mastitis resistance in dairy sheep.

BACKGROUND: Mastitis is the most prevalent disease in dairy sheep with major economic, hygienic and welfare implications. The disease persists in all dairy sheep production systems despite the implementation of improved management practises. Selective breeding for enhanced mastitis resistance may provide the means to further control the disease. In the present study, we investigated the genetic architecture of four mastitis traits in dairy sheep. Individual animal records for clinical mastitis occurrence and three mastitis indicator traits (milk somatic cell count, total viable bacterial count in milk and the California mastitis test) were collected monthly throughout lactation for 609 ewes of the Greek Chios breed. All animals were genotyped with a custom-made 960-single nucleotide polymorphism (SNP) DNA array based on markers located in quantitative trait loci (QTL) regions for mastitis resistance previously detected in three other distinct dairy sheep populations. RESULTS: Heritable variation and strong positive genetic correlations were estimated for clinical mastitis occurrence and the three mastitis indicator traits. SNP markers significantly associated with these mastitis traits were confirmed on chromosomes 2, 3, 5, 16 and 19. We identified pathways, molecular interaction networks and functional gene clusters for mastitis resistance. Candidate genes within the detected regions were identified based upon analysis of an ovine transcriptional atlas and transcriptome data derived from milk somatic cells. Relevant candidate genes implicated in innate immunity included SOCS2, CTLA4, C6, C7, C9, PTGER4, DAB2, CARD6, OSMR, PLXNC1, IDH1, ICOS, FYB, and LYFR. CONCLUSIONS: The results confirmed the presence of animal genetic variability in mastitis resistance and identified genomic regions associated with specific mastitis traits in the Chios sheep. The conserved genetic architecture of mastitis resistance between distinct dairy sheep breeds suggests that across-breed selection programmes would be feasible.

Enhanced insulin sensitivity in successful, long-term weight loss maintainers compared with matched controls with no weight loss history.

BACKGROUND: Weight gain is associated with deterioration in metabolic health, whereas weight loss improves insulin sensitivity. This study assesses the impact of long-term, successfully maintained weight loss and weight-loss relapse on measures of insulin sensitivity and identifies factors that explain variability in insulin sensitivity. METHODS: Women (20-45 years) were recruited into four groups: reduced-overweight/obese (RED, n=15); body mass index (BMI)-matched controls (stable low-weight, n=19), BMI⩽27 kg m-2; relapsed-overweight/obese subjects (REL, n=11); and BMI-matched controls (obese stable weight, n=11), BMI⩾27 kg m-2. A 75 g oral glucose tolerance test determined fasting and 2 h plasma glucose and insulin. Homeostatic Model Assessment (HOMA-IR) and insulin sensitivity index (ISI(0,120)) assessed insulin sensitivity. Anthropometric measurements, fasting resting metabolic rate (RMR) and respiratory quotient (RQ) were measured. Questionnaires and dietary intake were recorded, and physical activity was measured using accelerometers. RESULTS: RED were more insulin sensitive, characterised by lower fasting (P=0.001) and 2 h insulin (P=0.003) levels compared with all other groups. There were no significant differences in dietary intake, sedentary, light and moderate activity, RMR or RQ in the RED compared with the other three groups. % Body weight (BW) lost (P<0.001), % BW regained (P<0.05), body fat %, light activity (P<0.05, only log HOMA), vigorous activity (P<0.05) and RQ (P<0.01) predicted 61.4% and 59.7% of variability in log HOMA and log ISI(0,120), respectively, in multiple linear regression models. CONCLUSION: This study showed sustained enhanced insulin sensitivity in successful weight loss maintainers compared with BMI-matched controls with no weight loss history. Weight-loss-relapsed individuals were indistinguishable from controls. Weight loss itself was the strongest predictor of improved insulin sensitivity, whereas weight regain significantly predicted reduced insulin sensitivity. Weight-loss maintenance programs are essential to retaining metabolic benefits acquired through weight loss. Being physically active, reducing sedentary behaviour and, in particular, including small amounts of vigorous physical activity significantly predicted improved insulin sensitivity.

The occurrence of ryegrass staggers and heat stress in sheep grazing ryegrass-endophyte associations with diverse alkaloid profiles.

AIMS: To compare ryegrass pastures infected with endophytes producing diverse alkaloids for their ability to cause ryegrass staggers in grazing lambs; to compare respiration rates and rectal temperatures of these lambs after exposure to heat stress, and to compare liveweight gains during the study period. METHODS: Ryegrass pastures of cultivar Trojan infected with NEA endophytes, branded NEA2 (T-NEA2), endophyte-free Trojan (T-NIL), Samson infected with standard endophyte (S-STD), Samson infected with AR37 endophyte (S-AR37) and endophyte-free Samson (S-NIL), were grazed by lambs (n=30 per cultivar) for up to 48 days in February and March of 2012 and 2013. Pasture samples were analysed for alkaloid concentrations and lambs were scored for ryegrass staggers at intervals during the study period. Liveweight was recorded at the start (Day 0) and end of the study, and rectal temperatures and respiratory rates were measured in lambs exposed to heat stress on Days 23 and 26, in 2012 and 2013, respectively. RESULTS: Concentrations of alkaloids were lower in 2012 than 2013, associated with warmer and drier conditions in 2013, and the prevalence of ryegrass staggers was low in 2012. In 2013, concentrations of ergovaline were similar in T-NEA2 and S-STD, but concentrations of lolitrem B were lower in T-NEA2 than S-STD. S-AR37 produced epoxy-janthitrems but no lolitrem B or ergovaline. In 2013, by Day 20, 9/30 (30%) sheep grazing S-STD had severe staggers (score ≥4), and by Day 47 all sheep had been removed from this cultivar due to severe staggers. By Day 47, 18/30 (60%), 4/30 (13%) and 0/30 (0%) sheep grazing S-AR37, T-NEA2 and T-NIL pastures, respectively, had severe staggers. There were no differences in mean daily weight gain of lambs between cultivars in either year. In both years, mean rectal temperature and respiration rate following exposure to heat stress were highest in sheep grazing S-STD and T-NEA2, and lowest in sheep grazing T-NIL. CONCLUSIONS: In lambs grazing different ryegrass pastures infected with endophytes, ryegrass staggers was most severe on S-STD, less severe on S-AR37 and least on T-NEA2. When under heat stress, lambs grazing ergovaline-producing S-STD and T-NEA2 pastures had increased respiration rates and rectal temperatures compared with lambs grazing T-NIL. CLINICAL RELEVANCE: If ambient temperatures are suitable, NEA2-branded endophytes have the potential to express concentrations of ergovaline sufficient to induce heat stress in grazing sheep.

Sympathetic Ground State Cooling and Time-Dilation Shifts in an

We report on Raman sideband cooling of ^{25}Mg^{+} to sympathetically cool the secular modes of motion in a ^{25}Mg^{+}-^{27}Al^{+} two-ion pair to near the three-dimensional (3D) ground state. The evolution of the Fock-state distribution during the cooling process is studied using a rate-equation simulation, and various heating sources that limit the efficiency of 3D sideband cooling in our system are discussed. We characterize the residual energy and heating rates of all of the secular modes of motion and estimate a secular motion time-dilation shift of -(1.9±0.1)×10^{-18} for an ^{27}Al^{+} clock at a typical clock probe duration of 150 ms. This is a 50-fold reduction in the secular motion time-dilation shift uncertainty in comparison with previous ^{27}Al^{+} clocks.

Comparative transcriptome analysis of equine alveolar macrophages.

REASONS FOR PERFORMING STUDY: Alveolar macrophages (AMs) are the first line of defence against pathogens in the lungs of all mammalian species and thus may constitute appropriate therapeutic target cells in the treatment and prevention of opportunistic airway infections. Therefore, acquiring a better understanding of equine macrophage biology is of paramount importance in addressing this issue in relation to the horse. OBJECTIVES: To compare the transcriptome of equine AMs with that of equine peritoneal macrophages (PMs) and to investigate the effect of lipopolysaccharide (LPS) on equine AM. STUDY DESIGN: Gene expression study of equine AMs. METHODS: Cells from both bronchoalveolar and peritoneal lavage fluid were isolated from systemically healthy horses that had been submitted to euthanasia. Cells were cryopreserved. RNA was extracted and comparative microarray analyses were performed in AMs and PMs, and in AMs treated and untreated with LPS. Comparisons with published data derived from human AM studies were made, with particular focus on LPS-induced inflammatory status. RESULTS: The comparison between AMs and PMs revealed the differential basal expression of 451 genes. Gene expression analysis revealed an alternative (M2) macrophage polarisation profile in AMs and a hybrid macrophage activation profile in PMs, a phenomenon potentially attributable to a degree of induced endotoxin tolerance. The gene expression profile of equine AMs following LPS stimulation revealed significant changes in the expression of 240 genes, including well-known upregulated inflammatory genes. This LPS-induced gene expression profile of equine AMs more closely resembles that of human rather than murine macrophages. CONCLUSIONS: This study improves current understanding of equine macrophage biology. These data suggest that the horse may represent a suitable animal model for the study of human macrophage-associated lung inflammation and data derived from human macrophage studies may have significant relevance to the horse.

The genomic architecture of resistance to Campylobacter jejuni intestinal colonisation in chickens.

BACKGROUND: Campylobacter is the leading cause of foodborne diarrhoeal illness in humans and is mostly acquired from consumption or handling of contaminated poultry meat. In the absence of effective licensed vaccines and inhibitors, selection for chickens with increased resistance to Campylobacter could potentially reduce its subsequent entry into the food chain. Campylobacter intestinal colonisation levels are influenced by the host genetics of the chicken. In the present study, two chicken populations were used to investigate the genetic architecture of avian resistance to colonisation: (i) a back-cross of two White Leghorn derived inbred lines [(61 x N) x N] known to differ in resistance to Campylobacter colonisation and (ii) a 9(th) generation advanced intercross (61 x N) line. RESULTS: The level of colonisation with Campylobacter jejuni following experimental infection was found to be a quantitative trait. A back-cross experiment using 1,243 fully informative single nucleotide polymorphism (SNP) markers revealed quantitative trait loci (QTL) on chromosomes 7, 11 and 14. In the advanced intercross line study, the location of the QTL on chromosome 14 was confirmed and refined and two new QTLs were identified located on chromosomes 4 and 16. Pathway and re-sequencing data analysis of the genes located in the QTL candidate regions identified potential pathways, networks and candidate resistance genes. Finally, gene expression analyses were performed for some of the candidate resistance genes to support the results. CONCLUSION: Campylobacter resistance in chickens is a complex trait, possibly involving the Major Histocompatibility Complex, innate and adaptive immune responses, cadherins and other factors. Two of the QTLs for Campylobacter resistance are co-located with Salmonella resistance loci, indicating that it may be possible to breed simultaneously for enhanced resistance to both zoonoses.

Scalable spin squeezing for quantum-enhanced magnetometry with Bose-Einstein condensates.

A major challenge in quantum metrology is the generation of entangled states with a macroscopic atom number. Here, we demonstrate experimentally that atomic squeezing generated via nonlinear dynamics in Bose-Einstein condensates, combined with suitable trap geometries, allows scaling to large ensemble sizes. We achieve a suppression of fluctuations by 5.3(5) dB for 12,300 particles, from which we infer that similar squeezing can be obtained for more than 10(7) atoms. With this resource, we demonstrate quantum-enhanced magnetometry by swapping the squeezed state to magnetically sensitive hyperfine levels that have negligible nonlinearity. We find a quantum-enhanced single-shot sensitivity of 310(47) pT for static magnetic fields in a probe volume as small as 90 µm3.

Development and characterisation of monoclonal antibodies reactive with porcine CSF1R (CD115).

Macrophage colony-stimulating factor (CSF1) controls the proliferation and differentiation of cells of the mononuclear phagocyte system. CSF1, alongside a second ligand, interleukin-34 (IL-34), acts by binding to a cell surface receptor (CSF1R). We previously cloned and expressed pig CSF1 and IL-34. Here we produced a pig CSF1R-Ig+pFUSE Fc fusion protein and used it as an immunogen to produce three monoclonal antibodies (ROS8G11, ROS3A5 and ROS3B10) targeted against porcine CSF1R. Specific binding of each monoclonal antibody was confirmed by ELISA, Western blot, flow cytometry and immunocytochemistry. The antibodies did not block CSF1 signalling. The surface expression of CSF1R in pig peripheral blood was restricted to CD14-positive monocytes and was also detected on lung macrophages. These antibodies provided an opportunity to investigate the increase of available CSF1R during pig BMDM differentiation. The new monoclonal antibodies provide useful reagents to support the study of monocyte and macrophage biology in the pig.

Forages and pastures symposium: fungal endophytes of tall fescue and perennial ryegrass: pasture friend or foe?

Tall fescue [Lolium arundinaceum (Schreb.) Darbysh. syn. Festuca arundinacea Schreb.] and perennial ryegrass (Lolium perenne L.) are important perennial forage grasses utilized throughout the moderate- to high-rainfall temperate zones of the world. These grasses have coevolved with symbiotic fungal endophytes (Epichloë/Neotyphodium spp.) that can impart bioactive properties and environmental stress tolerance to the grass compared with endophyte-free individuals. These endophytes have proven to be very important in pastoral agriculture in the United States, New Zealand, and Australia, where forage grasses are the principal feed for grazing ruminants. In this review, we describe the biology of these grass-endophyte associations and implications for the livestock industries that are dependent on these forages. Endophyte alkaloid production is put in context with endophyte diversity, and we illustrate how this has facilitated utilization of grasses infected with different endophyte strains that reduce livestock toxicity issues. Utilization of tall fescue and use of perennial ryegrass in the United States, New Zealand, and Australia are compared, and management strategies focused predominantly on the success of endophyte-infected perennial ryegrass in New Zealand and Australia are discussed. In addition, we consider the impact of grass-endophyte associations on the sustainability of pasture ecosystems and their likely response to future changes in climate.

Accurate atom counting in mesoscopic ensembles.

Many cold atom experiments rely on precise atom number detection, especially in the context of quantum-enhanced metrology where effects at the single particle level are important. Here, we investigate the limits of atom number counting via resonant fluorescence detection for mesoscopic samples of trapped atoms. We characterize the precision of these fluorescence measurements beginning from the single-atom level up to more than one thousand. By investigating the primary noise sources, we obtain single-atom resolution for atom numbers as high as 1200. This capability is an essential prerequisite for future experiments with highly entangled states of mesoscopic atomic ensembles.

Quantum coherence between two atoms beyond Q=10(15).

We place two atoms in quantum superposition states and observe coherent phase evolution for 3.4×10(15) cycles. Correlation signals from the two atoms yield information about their relative phase even after the probe radiation has decohered. This technique allowed a frequency comparison of two (27)Al(+) ions with fractional uncertainty 3.7(-0.8)(+1.0)×10(-16)/√[τ/s]. Two measures of the Q factor are reported: The Q factor derived from quantum coherence is 3.4(-1.1)(+2.4)×10(16), and the spectroscopic Q factor for a Ramsey time of 3 s is 6.7×10(15). We demonstrate a method to detect the individual quantum states of two Al(+) ions in a Mg(+)-Al(+)-Al(+) linear ion chain without spatially resolving the ions.

Trapped-ion state detection through coherent motion.

We demonstrate a general method for state detection of trapped ions that can be applied to a large class of atomic and molecular species. We couple a spectroscopy ion (27Al+) to a control ion (25Mg+) in the same trap and perform state detection through off-resonant laser excitation of the spectroscopy ion that induces coherent motion. The motional amplitude, dependent on the spectroscopy ion state, is measured either by time-resolved photon counting or by resolved sideband excitations on the control ion. The first method provides a simplified way to distinguish clock states in 27Al+, which avoids ground-state cooling and sideband transitions. The second method reduces spontaneous emission and optical pumping on the spectroscopy ion, which we demonstrate by nondestructively distinguishing Zeeman sublevels in the (1)S0 ground state of 27Al+.

Optical clocks and relativity.

Observers in relative motion or at different gravitational potentials measure disparate clock rates. These predictions of relativity have previously been observed with atomic clocks at high velocities and with large changes in elevation. We observed time dilation from relative speeds of less than 10 meters per second by comparing two optical atomic clocks connected by a 75-meter length of optical fiber. We can now also detect time dilation due to a change in height near Earth's surface of less than 1 meter. This technique may be extended to the field of geodesy, with applications in geophysics and hydrology as well as in space-based tests of fundamental physics.