Improving Néel Domain Walls Dynamics and Skyrmion Stability Using He Ion Irradiation.

Ion irradiation with light ions is an appealing way to finely tune the magnetic properties of thin magnetic films and in particular the perpendicular magnetic anisotropy (PMA). In this work, the effect of He+ irradiation on the magnetization reversal and on the domain wall dynamics  of Pt/Co/AlOx trilayers is illustrated. Fluences up to 1.5 × 1015 ions cm-2 strongly decrease the PMA, without affecting neither the spontaneous magnetization nor the strength of the interfacial Dzyaloshinskii-Moriya interaction (DMI). This confirms experimentally the robustness of the DMI interaction against interfacial chemical intermixing, already predicted by theory. In parallel with the decrease of the PMA, a strong decrease of the domain wall depinning field is observed after irradiation. This allows the domain walls to reach large maximum velocities with a lower magnetic field compared to that needed for the pristine films. Decoupling PMA from DMI can, therefore, be beneficial for the design of low energy devices based on domain wall dynamics. When the samples are irradiated with larger He+ fluences, the magnetization gets close to the out-of-plane/in-plane reorientation transition, where ≈100nm size magnetic skyrmions are stabilized. It is observed that as the He+ fluence increases, the skyrmion size decreases while these magnetic textures become more stable against the application of an external magnetic field, as predicted by theoretical models developed for ultrathin films with labyrinthine domains.

Discovery of chromene compounds as inhibitors of PvdQ acylase of Pseudomonas aeruginosa.

The acquisition of iron is a crucial mechanism for the survival of pathogenic bacteria such as Pseudomonas aeruginosa in eukaryotic hosts. The key iron chelator in this organism is the siderophore pyoverdine, which was shown to be crucial for iron homeostasis. Pyoverdine is a non-ribosomal peptide with several maturation steps in the cytoplasm and others in the periplasmatic space. A key enzyme for its maturation is the acylase PvdQ. The inhibition of PvdQ stops the maturation of pyoverdine causing a significant imbalance in the iron homeostasis and hence can negatively influence the survival of P. aeruginosa. In this work, we successfully synthesized chromene-derived inhibitory molecules targeting PvdQ in a low micromolar range. In silico modeling as well as kinetic evaluations of the inhibitors suggest a competitive inhibition of the PvdQ function. Further, we evaluated the inhibitor in vivo on P. aeruginosa cells and report a dose-dependent reduction of pyoverdine formation. The compound also showed a protecting effect in a Galleria mellonella infection model.

A whole genome sequencing study of moderate to severe asthma identifies a lung function locus associated with asthma risk.

Genome-wide association studies (GWAS) have identified many common variant loci associated with asthma susceptibility, but few studies investigate the genetics underlying moderate-to-severe asthma risk. Here, we present a whole-genome sequencing study comparing 3181 moderate-to-severe asthma patients to 3590 non-asthma controls. We demonstrate that asthma risk is genetically correlated with lung function measures and that this component of asthma risk is orthogonal to the eosinophil genetics that also contribute to disease susceptibility. We find that polygenic scores for reduced lung function are associated with younger asthma age of onset. Genome-wide, seven previously reported common asthma variant loci and one previously reported lung function locus, near THSD4, reach significance. We replicate association of the lung function locus in a recently published GWAS of moderate-to-severe asthma patients. We additionally replicate the association of a previously reported rare (minor allele frequency < 1%) coding variant in IL33 and show significant enrichment of rare variant burden in genes from common variant allergic disease loci. Our findings highlight the contribution of lung function genetics to moderate-to-severe asthma risk, and provide initial rare variant support for associations with moderate-to-severe asthma risk at several candidate genes from common variant loci.

Fighting Acinetobacter baumannii infections with the acylase PvdQ.

Acinetobacter baumannii is an opportunistic Gram-negative bacterial pathogen that poses a threat for frail patients worldwide. The high ability to withstand environmental stresses as well as its resistance towards a broad range of antibiotics make A. baumannii an effective hard-to-eradicate pathogen. One of the key mechanisms mediating tolerance against antibiotic treatment is the formation of biofilms, a process that is controlled by a multitude of different regulatory mechanisms. A key factor with major impact on biofilm formation is cell-to-cell communication by quorum-sensing, which in A. baumannii is mediated by acyl homoserine lactone signaling molecules. Here we show that the Ntn-Hydrolase PvdQ from Pseudomonas aeruginosa can reduce biofilm formation by the A. baumannii ATCC 17978 type strain and several clinical isolates on abiotic surfaces. Further, our study shows that a combination treatment of PvdQ-mediated quorum-quenching with the antibiotic gentamicin has a synergistic effect on the clearance of A. baumannii biofilms and possible biofilm dispersal. Moreover, we demonstrate in a Galleria mellonella larval infection model that PvdQ administration significantly prolongs survival of the larvae. Altogether, we conclude that the acylase-mediated irreversible cleavage of quorum-sensing signaling molecules as exemplified with PvdQ can set a profound limit to the progression of A. baumannii infections.

Enzyme-Mediated Quenching of the Pseudomonas Quinolone Signal (PQS): A Comparison between Naturally Occurring and Engineered PQS-Cleaving Dioxygenases.

The opportunistic pathogen Pseudomonas aeruginosa employs quorum sensing to govern the production of many virulence factors. Interference with quorum sensing signaling has therefore been put forward as an attractive approach to disarm this pathogen. Here, we analyzed the quorum quenching properties of natural and engineered (2-alkyl-)3-hydroxy-4(1H)-quinolone 2,4-dioxygenases (HQDs) that inactivate the P. aeruginosa signal molecule PQS (Pseudomonas quinolone signal; 2-heptyl-3-hydroxy-4(1H)-quinolone). When added exogenously to P. aeruginosa cultures, all HQDs tested significantly reduced the levels of PQS and other alkylquinolone-type secondary metabolites deriving from the biosynthetic pathway, such as the respiratory inhibitor 2-heptyl-4-hydroxyquinoline N-oxide. HQDs from Nocardia farcinica and Streptomyces bingchenggensis, which combine low KM values for PQS with thermal stability and resilience in the presence of P. aeruginosa exoproducts, respectively, attenuated production of the virulence factors pyocyanin and pyoverdine. A delay in mortality was observed when Galleria mellonella larvae were infected with P. aeruginosa suspensions treated with the S. bingchenggensis HQD or with inhibitors of alkylquinolone biosynthesis. Our data indicate that quenching of PQS signaling has potential as an anti-virulence strategy; however, an efficient anti-virulence therapy against P. aeruginosa likely requires a combination of agents addressing multiple targets.

Kinetics of Ion Migration in the Electric Field-Driven Manipulation of Magnetic Anisotropy of Pt/Co/Oxide Multilayers.

Magneto-ionics is a fast developing research field which opens the perspective of energy efficient magnetic devices, where the magnetization direction is controlled by an electric field which drives the migration of ionic species. In this work, the interfacial perpendicular magnetic anisotropy (PMA) of Pt/Co/oxide stacks covered by ZrO2 , acting as a ionic conductor, is tuned by a gate voltage at room temperature. A large variation of the PMA is obtained by modifying the oxidation of the cobalt layer through the migration of oxygen ions: the easy magnetization axis can be switched reversibly from in-plane, with under-oxidized Co, to in-plane, with over-oxidized Co, passing through an out-of-plane magnetization state. The switching time between the different magnetic states is limited by the ion drift velocity. This depends exponentially on the gate voltage, and is varied by over five orders of magnitude, from several minutes to a few ms. The variation of the PMA versus time during the application of the gate voltage can be modeled with a parabolic variation of the PMA and an exponential decrease of the Co oxidation rate. The possibility to explain the observed effect with a simple theoretical model opens the possibility to engineer materials with optimized properties.

Current-Driven Domain Wall Dynamics in Ferrimagnetic Nickel-Doped Mn4N Films: Very Large Domain Wall Velocities and Reversal of Motion Direction across the Magnetic Compensation Point.

Spin-transfer torque (STT) and spin-orbit torque (SOT) are spintronic phenomena allowing magnetization manipulation using electrical currents. Beyond their fundamental interest, they allow developing new classes of magnetic memories and logic devices, in particular based on domain wall (DW) motion. In this work, we report the study of STT-driven DW motion in ferrimagnetic manganese nickel nitride (Mn4-xNixN) films, in which magnetization and angular momentum compensation can be obtained by the fine adjustment of the Ni content. Large domain wall velocities, approaching 3000 m/s, are measured for Ni compositions close to the angular momentum compensation point. The reversal of the DW motion direction, observed when the compensation composition is crossed, is related to the change of direction of the angular momentum with respect to that of the spin polarization. This is confirmed by the results of ab initio band structure calculations.

Helium Ions Put Magnetic Skyrmions on the Track.

Magnetic skyrmions are deemed to be the forerunners of novel spintronic memory and logic devices. While their observation and their current-driven motion at room temperature have been demonstrated, certain issues regarding their nucleation, stability, pinning, and skyrmion Hall effect still need to be overcome to realize functional devices. Here, we demonstrate that focused He+-ion-irradiation can be used to create and guide skyrmions in racetracks. We show that the reduction of the perpendicular magnetic anisotropy and Dzyaloshinskii-Moriya interaction in the track defined by ion-irradiation leads to the formation of stable isolated skyrmions. Current-driven skyrmion motion experiments and simulations reveal that the skyrmions move along the irradiated track, resulting in the suppression of the skyrmion Hall effect, and that the maximum skyrmion velocity can be enhanced by tuning the magnetic properties. These results open up a new path to nucleate and guide magnetic skyrmions in racetrack devices.

In-Plane Magnetic Domains and Néel-like Domain Walls in Thin Flakes of the Room Temperature CrTe2 Van der Waals Ferromagnet.

The recent discovery of magnetic van der Waals (vdW) materials triggered a wealth of investigations in materials science and now offers genuinely new prospects for both fundamental and applied research. Although the catalog of vdW ferromagnets is rapidly expanding, most of them have a Curie temperature below 300 K, a notable disadvantage for potential applications. Combining element-selective X-ray magnetic imaging and magnetic force microscopy, we resolve at room temperature the magnetic domains and domain walls in micron-sized flakes of the CrTe2 vdW ferromagnet. Flux-closure magnetic patterns suggesting an in-plane six-fold symmetry are observed. Upon annealing the material above its Curie point (315 K), the magnetic domains disappear. By cooling back the sample, a different magnetic domain distribution is obtained, indicating material stability and lack of magnetic memory upon thermal cycling. The domain walls presumably have Néel texture, are preferentially oriented along directions separated by 120°, and have a width of several tens of nanometers. Besides microscopic mapping of magnetic domains and domain walls, the coercivity of the material is found to be of a few millitesla only, showing that the CrTe2 compound is magnetically soft. The coercivity is found to increase as the volume of the material decreases.

Immobilized Acylase PvdQ Reduces Pseudomonas aeruginosa Biofilm Formation on PDMS Silicone.

The bacterial biofilm plays a key role in nosocomial infections, especially those related to medical devices in sustained contact with patients. The active dispersion of bacterial cells out of biofilms acts as a reservoir for infectious diseases. The formation of such biofilms is a highly complex process, which is coordinated by many regulatory mechanisms of the pathogen including quorum sensing (QS). Many bacteria coordinate the expression of key virulence factors dependent on their population density through QS. The inhibition of this system is called quorum quenching (QQ). Thus, preventing the development of biofilms is considered a promising approach to prevent the development of hard to treat infections. Enzymatic QQ is the concept of interfering with the QS system of bacteria outside the cell. PvdQ is an acylase with an N-terminal nucleophile (Ntn-hydrolase) that is a part of the pyoverdine gene cluster (pvd). It is able to cleave irreversibly the amide bond of long chain N-acyl homoserine lactones (AHL) rendering them inactive. Long chain AHLs are the main signaling molecule in the QS system of the gram-negative pathogen Pseudomonas aeruginosa PA01, which is known for surface-associated biofilms on indwelling catheters and is also the cause of catheter-associated urinary tract infections. Furthermore, PA01 is a well characterized pathogen with respect to QS as well as QQ. In this study, we immobilized the acylase PvdQ on polydimethylsiloxane silicone (PDMS), creating a surface with quorum quenching properties. The goal is to control infections by minimizing the colonization of indwelling medical devices such as urinary catheters or intravascular catheters. The enzyme activity was confirmed by testing the degradation of the main auto-inducer that mediates QS in P. aeruginosa. In this article we report for the first time a successful immobilization of the quorum quenching acylase PvdQ on PDMS silicone. We could show that immobilized PvdQ retained its activity after the coating procedure and showed a 6-fold reduction of the auto-inducer 3-oxo-C12 in a biosensor setup. Further we report significant reduction of a P. aeruginosa PA01 biofilm on a coated PDMS surface compared to the same untreated material.

Large Current Driven Domain Wall Mobility and Gate Tuning of Coercivity in Ferrimagnetic Mn4N Thin Films.

Spintronics, which is the basis of a low-power, beyond-CMOS technology for computational and memory devices, remains up to now entirely based on critical materials such as Co, heavy metals and rare-earths. Here, we show that Mn4N, a rare-earth free ferrimagnet made of abundant elements, is an exciting candidate for the development of sustainable spintronics devices. Mn4N thin films grown epitaxially on SrTiO3 substrates possess remarkable properties, such as a perpendicular magnetization, a very high extraordinary Hall angle (2%) and smooth domain walls at the millimeter scale. Moreover, domain walls can be moved at record speeds by spin-polarized currents, in absence of spin-orbit torques. This can be explained by the large efficiency of the adiabatic spin transfer torque, due to the conjunction of a reduced magnetization and a large spin polarization. Finally, we show that the application of gate voltages through the SrTiO3 substrates allows modulating the Mn4N coercive field with a large efficiency.

Previously reported placebo-response-associated variants do not predict patient outcomes in inflammatory disease Phase III trial placebo arms.

In clinical trials, a placebo response refers to improvement in disease symptoms arising from the psychological effect of receiving a treatment rather than the actual treatment under investigation. Previous research has reported genomic variation associated with the likelihood of observing a placebo response, but these studies have been limited in scope and have not been validated. Here, we analyzed whole-genome sequencing data from 784 patients undergoing placebo treatment in Phase III Asthma or Rheumatoid Arthritis trials to assess the impact of previously reported variation on patient outcomes in the placebo arms and to identify novel variants associated with the placebo response. Contrary to expectations based on previous reports, we did not observe any statistically significant associations between genomic variants and placebo treatment outcome. Our findings suggest that the biological origin of the placebo response is complex and likely to be variable between disease areas.

Enabling genome-wide association testing with multiple diseases and no healthy controls.

MOTIVATION: While large-scale whole genome sequencing is feasible the high costs compel investigators to focus on disease subjects. As a result large sequencing datasets of samples with different diseases are often readily available, but not healthy controls to contrast them with. While it is possible to perform an association study using only diseases, the associations could be driven by a disease acting as a control and not the focal disease. METHODS: We developed a genotype-on-phenotype reverse regression with a Bayesian spike and slab prior to enable association testing in datasets with multiple diseases. This method, referred to as revreg, flagged associations (both common and rare) that were driven by diseases that were not of primary interest. RESULTS: Based on simulations, revreg had 80% power to detect an odds ratio of 1.74 for common variants (3500 samples total) and 3.73 for rare variants (14,000 samples total), with minimal type I error. For common variants, we tested this method on 3657 whole genome sequenced samples aimed at discovering variants associated with disease risk of Chronic Obstructive Pulmonary Disease using three other diseases as controls. We demonstrated detection of six highly significant associations likely due to Age-Related Macular Degeneration. In an exome dataset of 8836 samples aimed at characterizing rare variants associated with disease risk of Asthma, using five other diseases as controls, we detected and removed genic regions due to AMD (C3, CFH, CFHR5, CFI, and DNMT3A) and RA (KRTAP13-4).

Unraveling Dzyaloshinskii-Moriya Interaction and Chiral Nature of Graphene/Cobalt Interface.

A major challenge for future spintronics is to develop suitable spin transport channels with long spin lifetime and propagation length. Graphene can meet these requirements, even at room temperature. On the other side, taking advantage of the fast motion of chiral textures, that is, Néel-type domain walls and magnetic skyrmions, can satisfy the demands for high-density data storage, low power consumption, and high processing speed. We have engineered epitaxial structures where an epitaxial ferromagnetic Co layer is sandwiched between an epitaxial Pt(111) buffer grown in turn onto MgO(111) substrates and a graphene layer. We provide evidence of a graphene-induced enhancement of the perpendicular magnetic anisotropy up to 4 nm thick Co films and of the existence of chiral left-handed Néel-type domain walls stabilized by the effective Dzyaloshinskii-Moriya interaction (DMI) in the stack. The experiments show evidence of a sizable DMI at the gr/Co interface, which is described in terms of a conduction electron mediated Rashba-DMI mechanism and points opposite to the spin orbit coupling-induced DMI at the Co/Pt interface. In addition, the presence of graphene results in (i) a surfactant action for the Co growth, producing an intercalated, flat, highly perfect face-centered cubic film, pseudomorphic with Pt and (ii) an efficient protection from oxidation. The magnetic chiral texture is stable at room temperature and grown on insulating substrate. Our findings open new routes to control chiral spin structures using interfacial engineering in graphene-based systems for future spin-orbitronics devices fully integrated on oxide substrates.

Analysis of protein-altering variants in telomerase genes and their association with MUC5B common variant status in patients with idiopathic pulmonary fibrosis: a candidate gene sequencing study.

BACKGROUND: Idiopathic pulmonary fibrosis (IPF) risk has a strong genetic component. Studies have implicated variations at several loci, including TERT, surfactant genes, and a single nucleotide polymorphism at chr11p15 (rs35705950) in the intergenic region between TOLLIP and MUC5B. Patients with IPF who have risk alleles at rs35705950 have longer survival from the time of IPF diagnosis than do patients homozygous for the non-risk allele, whereas patients with shorter telomeres have shorter survival times. We aimed to assess whether rare protein-altering variants in genes regulating telomere length are enriched in patients with IPF homozygous for the non-risk alleles at rs35705950. METHODS: Between Nov 1, 2014, and Nov 1, 2016, we assessed blood samples from patients aged 40 years or older and of European ancestry with sporadic IPF from three international phase 3 clinical trials (INSPIRE, CAPACITY, ASCEND), one phase 2 study (RIFF), and US-based observational studies (Vanderbilt Clinical Interstitial Lung Disease Registry and the UCSF Interstitial Lung Disease Clinic registry cohorts) at the Broad Institute (Cambridge, MA, USA) and Human Longevity (San Diego, CA, USA). We also assessed blood samples from non-IPF controls in several clinical trials. We did whole-genome sequencing to assess telomere length and identify rare protein-altering variants, stratified by rs35705950 genotype. We also assessed rare functional variation in TERT exons and compared telomere length and disease progression across genotypes. FINDINGS: We assessed samples from 1510 patients with IPF and 1874 non-IPF controls. 30 (3%) of 1046 patients with an rs35705950 risk allele had a rare protein-altering variant in TERT compared with 34 (7%) of 464 non-risk allele carriers (odds ratio 0·40 [95% CI 0·24-0·66], p=0·00039). Subsequent analyses identified enrichment of rare protein-altering variants in PARN and RTEL1, and rare variation in TERC in patients with IPF compared with controls. We expanded our study population to provide a more accurate estimation of rare variant frequency in these four loci, and to calculate telomere length. The proportion of patients with at least one rare variant in TERT, PARN, TERC, or RTEL1 was higher in patients with IPF than in controls (149 [9%] of 1739 patients vs 205 [2%] of 8645 controls, p=2·44 × 10-8). Patients with IPF who had a variant in any of the four identified telomerase component genes had telomeres that were 3·69-16·10% shorter than patients without a variant in any of the four genes and had an earlier mean age of disease onset than patients without one or more variants (65·1 years [SD 7·8] vs 67·1 years [7·9], p=0·004). In the placebo arms of clinical trials, shorter telomeres were significantly associated with faster disease progression (1·7% predicted forced vital capacity per kb per year, p=0·002). Pirfenidone had treatment benefit regardless of telomere length (p=4·24 × 10-8 for telomere length lower than the median, p=0·0044 for telomere length greater than the median). INTERPRETATION: Rare protein-altering variants in TERT, PARN, TERC, and RTEL1 are enriched in patients with IPF compared with controls, and, in the case of TERT, particularly in individuals without a risk allele at the rs35705950 locus. This suggests that multiple genetic factors contribute to sporadic IPF, which might implicate distinct mechanisms of pathogenesis and disease progression. FUNDING: Genentech, National Institutes of Health, Francis Family Foundation, Pulmonary Fibrosis Foundation, Nina Ireland Program for Lung Health, US Department of Veterans Affairs.

Velocity Enhancement by Synchronization of Magnetic Domain Walls.

Magnetic domain walls are objects whose dynamics is inseparably connected to their structure. In this Letter, we investigate magnetic bilayers, which are engineered such that a coupled pair of domain walls, one in each layer, is stabilized by a cooperation of Dzyaloshinskii-Moriya interaction and flux-closing mechanism. The dipolar field mediating the interaction between the two domain walls links not only their position but also their structure. We show that this link has a direct impact on their magnetic-field-induced dynamics. We demonstrate that in such a system the coupling leads to an increased domain wall velocity with respect to single domain walls. Since the domain wall dynamics is observed in a precessional regime, the dynamics involves the synchronization between the two walls to preserve the flux closure during motion. Properties of these coupled oscillating walls can be tuned by an additional in-plane magnetic field enabling a rich variety of states, from perfect synchronization to complete detuning.

Corrigendum: Room-temperature chiral magnetic skyrmions in ultrathin magnetic nanostructures.

This corrects the article DOI: 10.1038/nnano.2015.315.

Deciphering Physiological Functions of AHL Quorum Quenching Acylases.

N-Acylhomoserine lactone (AHL)-acylase (also known as amidase or amidohydrolase) is a class of enzyme that belongs to the Ntn-hydrolase superfamily. As the name implies, AHL-acylases are capable of hydrolysing AHLs, the most studied signaling molecules for quorum sensing in Gram-negative bacteria. Enzymatic degradation of AHLs can be beneficial in attenuating bacterial virulence, which can be exploited as a novel approach to fight infection of human pathogens, phytopathogens or aquaculture-related contaminations. Numerous acylases from both prokaryotic and eukaryotic sources have been characterized and tested for the interference of quorum sensing-regulated functions. The existence of AHL-acylases in a multitude of organisms from various ecological niches, raises the question of what the physiological roles of AHL-acylases actually are. In this review, we attempt to bring together recent studies to extend our understanding of the biological functions of these enzymes in nature.