Whole-chromosome hitchhiking driven by a male-killing endosymbiont

Neo-sex chromosomes are found in many taxa, but the forces driving their emergence and spread are poorly understood. The female-specific neo-W chromosome of the African monarch (or queen) butterfly Danaus chrysippus presents an intriguing case study because it is restricted to a single 'contact zone' population, involves a putative colour patterning supergene, and co-occurs with infection by the male-killing endosymbiont Spiroplasma. We investigated the origin and evolution of this system using whole genome sequencing. We first identify the 'BC supergene', a broad region of suppressed recombination across nearly half a chromosome, which links two colour patterning loci. Association analysis suggests that the genes yellow and arrow in this region control the forewing colour pattern differences between D. chrysippus subspecies. We then show that the same chromosome has recently formed a neo-W that has spread through the contact zone within approximately 2,200 years. We also assembled the genome of the male-killing Spiroplasma, and find that it shows perfect genealogical congruence with the neo-W, suggesting that the neo-W has hitchhiked to high frequency as the male-killer has spread through the population. The complete absence of female crossing-over in the Lepidoptera causes whole-chromosome hitchhiking of a single neo-W haplotype, carrying a single allele of the BC supergene and dragging multiple non-synonymous mutations to high frequency. This has created a population of infected females that all carry the same recessive colour patterning allele, making the phenotypes of each successive generation highly dependent on uninfected male immigrants. Our findings show how hitchhiking can occur between the physically unlinked genomes of host and endosymbiont, with dramatic consequences.

Atomic-Scale Metal-Insulator Transition in SrRuO3 Ultrathin Films Triggered by Surface Termination Conversion

The metal-insulator transition (MIT) in transition-metal-oxide is fertile ground for exploring intriguing physics and potential device applications. Here, an atomic-scale MIT triggered by surface termination conversion in SrRuO₃ ultrathin films is reported. Uniform and effective termination engineering at the SrRuO₃ (001) surface can be realized via a self-limiting water-leaching process. As the surface termination converts from SrO to RuO₂ , a highly insulating and nonferromagnetic phase emerges within the topmost SrRuO₃ monolayer. Such a spatially confined MIT is corroborated by systematic characterizations on electrical transport, magnetism, and scanning tunneling spectroscopy. Density functional theory calculations and X-ray linear dichroism further suggest that the surface termination conversion breaks the local octahedral symmetry of the crystal field. The resultant modulation in 4d orbital occupancy stabilizes a nonferromagnetic insulating surface state. This work introduces a new paradigm to stimulate and tune exotic functionalities of oxide heterostructures with atomic precision.

Controlling Defects in Continuous 2D GaS Films for High-Performance Wavelength-Tunable UV-Discriminating Photodetectors

A chemical vapor deposition method is developed for thickness-controlled (one to four layers), uniform, and continuous films of both defective gallium(II) sulfide (GaS): GaS_0.87 and stoichiometric GaS. The unique degradation mechanism of GaS_0.87 with X-ray photoelectron spectroscopy and annular dark-field scanning transmission electron microscopy is studied, and it is found that the poor stability and weak optical signal from GaS are strongly related to photo-induced oxidation at defects. An enhanced stability of the stoichiometric GaS is demonstrated under laser and strong UV light, and by controlling defects in GaS, the photoresponse range can be changed from vis-to-UV to UV-discriminating. The stoichiometric GaS is suitable for large-scale, UV-sensitive, high-performance photodetector arrays for information encoding under large vis-light noise, with short response time (<66 ms), excellent UV photoresponsivity (4.7 A W^-1 for trilayer GaS), and 26-times increase of signal-to-noise ratio compared with small-bandgap 2D semiconductors. By comprehensive characterizations from atomic-scale structures to large-scale device performances in 2D semiconductors, the study provides insights into the role of defects, the importance of neglected material-quality control, and how to enhance device performance, and both layer-controlled defective GaS_0.87 and stoichiometric GaS prove to be promising platforms for study of novel phenomena and new applications.

Multiscale modelling and homogenisation of fibre-reinforced hydrogels for tissue engineering

Tissue engineering aims to grow artificial tissues in vitro to replace those in the body that have been damaged through age, trauma or disease. A recent approach to engineer artificial cartilage involves seeding cells within a scaffold consisting of an interconnected 3D-printed lattice of polymer fibres combined with a cast or printed hydrogel, and subjecting the construct (cell-seeded scaffold) to an applied load in a bioreactor. A key question is to understand how the applied load is distributed throughout the construct. To address this, we employ homogenisation theory to derive equations governing the effective macroscale material properties of a periodic, elastic-poroelastic composite. We treat the fibres as a linear elastic material and the hydrogel as a poroelastic material, and exploit the disparate length scales (small inter-fibre spacing compared with construct dimensions) to derive macroscale equations governing the response of the composite to an applied load. This homogenised description reflects the orthotropic nature of the composite. To validate the model, solutions from finite element simulations of the macroscale, homogenised equations are compared to experimental data describing the unconfined compression of the fibre-reinforced hydrogels. The model is used to derive the bulk mechanical properties of a cylindrical construct of the composite material for a range of fibre spacings and to determine the local mechanical environment experienced by cells embedded within the construct.

NatB-Mediated N-Terminal Acetylation Affects Growth and Biotic Stress Responses

N^∝-terminal acetylation (NTA) is one of the most abundant protein modifications in eukaryotes. In humans, NTA is catalyzed by seven N^α-acetyltransferases (NatA-F and NatH). Remarkably, the plant Nat machinery and its biological relevance remain poorly understood, although NTA has gained recognition as a key regulator of crucial processes such as protein turnover, protein-protein interaction, and protein targeting. In this study, we combined in vitro assays, reverse genetics, quantitative N-terminomics, transcriptomics, and physiological assays to characterize the Arabidopsis (Arabidopsis thaliana) NatB complex. We show that the plant NatB catalytic (NAA20) and auxiliary subunit (NAA25) form a stable heterodimeric complex that accepts canonical NatB-type substrates in vitro. In planta, NatB complex formation was essential for enzymatic activity. Depletion of NatB subunits to 30% of the wild-type level in three Arabidopsis T-DNA insertion mutants (naa20-1, naa20-2, and naa25-1) caused a 50% decrease in plant growth. A complementation approach revealed functional conservation between plant and human catalytic NatB subunits, whereas yeast NAA20 failed to complement naa20-1 Quantitative N-terminomics of approximately 1000 peptides identified 32 bona fide substrates of the plant NatB complex. In vivo, NatB was seen to preferentially acetylate N termini starting with the initiator Met followed by acidic amino acids and contributed 20% of the acetylation marks in the detected plant proteome. Global transcriptome and proteome analyses of NatB-depleted mutants suggested a function of NatB in multiple stress responses. Indeed, loss of NatB function, but not NatA, increased plant sensitivity toward osmotic and high-salt stress, indicating that NatB is required for tolerance of these abiotic stressors.

Towards comparable assessment of the soil nutrient status across scales-Review and development of nutrient metrics

Nutrient availability influences virtually every aspect of an ecosystem, and is a critical modifier of ecosystem responses to global change. Although this crucial role of nutrient availability in regulating ecosystem structure and functioning has been widely acknowledged, nutrients are still often neglected in observational and experimental synthesis studies due to difficulties in comparing the nutrient status across sites. In the current study, we explain different nutrient-related concepts and discuss the potential of soil-, plant- and remote sensing-based metrics to compare the nutrient status across space. Based on our review and additional analyses on a dataset of European, managed temperate and boreal forests (ICP [International Co-operative Programme on Assessment and Monitoring of Air Pollution Effects on Forests] Forests dataset), we conclude that the use of plant- and remote sensing-based metrics that rely on tissue stoichiometry is limited due to their strong dependence on species identity. The potential use of other plant-based metrics such as Ellenberg indicator values and plant-functional traits is also discussed. We conclude from our analyses and review that soil-based metrics have the highest potential for successful intersite comparison of the nutrient status. As an example, we used and adjusted a soil-based metric, previously developed for conifer forests across Sweden, against the same ICP Forests data. We suggest that this adjusted and further adaptable metric, which included the organic carbon concentration in the upper 20 cm of the soil (including the organic fermentation-humus [FH] layer), the C:N ratio and pH CaCl 2 of the FH layer, can be used as a complementary tool along with other indicators of nutrient availability, to compare the background nutrient status across temperate and boreal forests dominated by spruce, pine or beech. Future collection and provision of harmonized soil data from observational and experimental sites is crucial for further testing and adjusting the metric.

Redefining phenotypes to advance psychiatric genetics: Implications from hierarchical taxonomy of psychopathology

Genetic discovery in psychiatry and clinical psychology is hindered by suboptimal phenotypic definitions. We argue that the hierarchical, dimensional, and data-driven classification system proposed by the Hierarchical Taxonomy of Psychopathology (HiTOP) consortium provides a more effective approach to identifying genes that underlie mental disorders, and to studying psychiatric etiology, than current diagnostic categories. Specifically, genes are expected to operate at different levels of the HiTOP hierarchy, with some highly pleiotropic genes influencing higher order psychopathology (e.g., the general factor), whereas other genes conferring more specific risk for individual spectra (e.g., internalizing), subfactors (e.g., fear disorders), or narrow symptoms (e.g., mood instability). We propose that the HiTOP model aligns well with the current understanding of the higher order genetic structure of psychopathology that has emerged from a large body of family and twin studies. We also discuss the convergence between the HiTOP model and findings from recent molecular studies of psychopathology indicating broad genetic pleiotropy, such as cross-disorder SNP-based shared genetic covariance and polygenic risk scores, and we highlight molecular genetic studies that have successfully redefined phenotypes to enhance precision and statistical power. Finally, we suggest how to integrate a HiTOP approach into future molecular genetic research, including quantitative and hierarchical assessment tools for future data-collection and recommendations concerning phenotypic analyses. (PsycINFO Database Record (c) 2020 APA, all rights reserved).

Coupled steel slag and biochar amendment correlated with higher methanotrophic abundance and lower CH4 emission in subtropical paddies

Aerobic methanotrophs in paddies serve as methane (CH₄) filters and thereby reduce CH₄ emissions. Amending soil with waste products can mitigate CH₄ emissions in crops, but little is known about the impacts of amendments with steel slag and biochar on the populations and activities of aerobic methanotrophs in rice cropland. We used real-time quantitative PCR detecting system and high-throughput sequencing to determine the effects of slag and biochar amendments on CH₄ emission, abundance, and community structure of methanotrophs, and the relationships between soil properties and the abundance and community composition of methanotrophs during the rice growing season in both early and late paddies. Soil salinity and pH were significantly higher for an amendment with both slag and biochar than the control in both the early and late paddies, and pH was significantly higher for a slag amendment in the late paddy. Cumulative CH₄ emission was lower for the slag and slag + biochar amendments than the control in early paddy by-34.1%. Methanotrophic abundance was three- and sixfold higher for the slag + biochar amendment than the control in the early and late paddies (p < 0.05), respectively. The abundance of different groups of methanotrophs varied among the treatments. The relative abundance of Methylosarcina was higher for the slag amendment than the control, and the relative abundance of Methylomonas was lower for biochar, and slag + biochar amendments than the control. The relative abundance of Methylocystis was higher for the slag and slag + biochar amendments than the control in the early paddy, and the relative abundance of Methylocystis was higher for the slag, biochar, and slag + biochar amendments in the late paddy. Univariate and multivariate analyses indicated that the higher abundance of methanotrophic bacteria for the slag and slag + biochar amendments was correlated with soil pH, salinity, soil organic carbon, and C/N ratio, and the relative abundances of Methylocystis, Methylomonas, and Methylosarcina were associated with the effective mitigation of CH₄ emission in the paddies. A discriminant general analysis indicated that the total population of methanotrophs was larger for the slag + biochar amendment than the control, and that this effect was only weakly correlated with changes in the soil properties, demonstrating that this effect on the size and species composition of methanotrophic soil populations was mostly associated with a direct effect of the slag + biochar amendment.

Gene duplication and transposition of mobile elements drive evolution of the Rpv3 resistance locus in grapevine

A wild grape haplotype (Rpv3-1) confers resistance to Plasmopara viticola. We mapped the causal factor for resistance to an interval containing a TIR-NB-LRR (TNL) gene pair that originated 1.6-2.6 million years ago by a tandem segmental duplication. Transient coexpression of the TNL pair in Vitis vinifera leaves activated pathogen-induced necrosis and reduced sporulation compared with control leaves. Even though transcripts of the TNL pair from the wild haplotype appear to be partially subject to nonsense-mediated mRNA decay, mature mRNA levels in a homozygous resistant genotype were individually higher than the mRNA trace levels observed for the orthologous single-copy TNL in sensitive genotypes. Allelic expression imbalance in a resistant heterozygote confirmed that cis-acting regulatory variation promotes expression in the wild haplotype. The movement of transposable elements had a major impact on the generation of haplotype diversity, altering the DNA context around similar TNL coding sequences and the GC-content in their proximal 5'-intergenic regions. The wild and domesticated haplotypes also diverged in conserved single-copy intergenic DNA, but the highest divergence was observed in intraspecific and not in interspecific comparisons. In this case, introgression breeding did not transgress the genetic boundaries of the domesticated species, because haplotypes present in modern varieties sometimes predate speciation events between wild and cultivated species.

Targeting of temperate phages drives loss of type I CRISPR-Cas systems

On infection of their host, temperate viruses that infect bacteria (bacteriophages; hereafter referred to as phages) enter either a lytic or a lysogenic cycle. The former results in lysis of bacterial cells and phage release (resulting in horizontal transmission), whereas lysogeny is characterized by the integration of the phage into the host genome, and dormancy (resulting in vertical transmission)1. Previous co-culture experiments using bacteria and mutants of temperate phages that are locked in the lytic cycle have shown that CRISPR-Cas systems can efficiently eliminate the invading phages2,3. Here we show that, when challenged with wild-type temperate phages (which can become lysogenic), type I CRISPR-Cas immune systems cannot eliminate the phages from the bacterial population. Furthermore, our data suggest that, in this context, CRISPR-Cas immune systems are maladaptive to the host, owing to the severe immunopathological effects that are brought about by imperfect matching of spacers to the integrated phage sequences (prophages). These fitness costs drive the loss of CRISPR-Cas from bacterial populations, unless the phage carries anti-CRISPR (acr) genes that suppress the immune system of the host. Using bioinformatics, we show that this imperfect targeting is likely to occur frequently in nature. These findings help to explain the patchy distribution of CRISPR-Cas immune systems within and between bacterial species, and highlight the strong selective benefits of phage-encoded acr genes for both the phage and the host under these circumstances.

Intertropical convergence zone variability in the Neotropics during the Common Era

Large changes in hydroclimate in the Neotropics implied by proxy evidence, such as during the Little Ice Age, have been attributed to meridional shifts of the intertropical convergence zone (ITCZ), although alternative modes of ITCZ variability have also been suggested. Here, we use seasonally resolved stalagmite rainfall proxy data from the modern northern limit of the ITCZ in southern Belize, combined with records from across the Neotropics and subtropics, to fingerprint ITCZ variability during the Common Era. Our data are consistent with models that suggest ITCZ expansion and weakening during globally cold climate intervals and contraction and intensification during global warmth. As a result, regions currently in the margins of the ITCZ in both hemispheres are likely transitioning to more arid and highly variable conditions, aggravating current trends of increased social unrest and mass migration.

A Synergistic Anticancer FAK and HDAC Inhibitor Combination Discovered by a Novel Chemical-Genetic High-Content Phenotypic Screen

We mutated the focal adhesion kinase (FAK) catalytic domain to inhibit binding of the chaperone Cdc37 and ATP, mimicking the actions of a FAK kinase inhibitor. We reexpressed mutant and wild-type FAK in squamous cell carcinoma (SCC) cells from which endogenous FAK had been deleted, genetically fixing one axis of a FAK inhibitor combination high-content phenotypic screen to discover drugs that may synergize with FAK inhibitors. Histone deacetylase (HDAC) inhibitors represented the major class of compounds that potently induced multiparametric phenotypic changes when FAK was rendered kinase-defective or inhibited pharmacologically in SCC cells. Combined FAK and HDAC inhibitors arrest proliferation and induce apoptosis in a subset of cancer cell lines in vitro and efficiently inhibit their growth as tumors in vivo Mechanistically, HDAC inhibitors potentiate inhibitor-induced FAK inactivation and impair FAK-associated nuclear YAP in sensitive cancer cell lines. Here, we report the discovery of a new, clinically actionable, synergistic combination between FAK and HDAC inhibitors.

Exposure to air pollution during childhood and risk of developing schizophrenia: a national cohort study

BACKGROUND

Ambient air pollution affects neurological function, but its association with schizophrenia risk is unclear. We investigated exposure to nitrogen oxides (NO_X) as a whole and nitrogen dioxide (NO₂) specifically, as well as PM₁₀, and PM_2·5, during childhood and subsequent schizophrenia risk.

METHODS

People born in Denmark from 1980 to 1984 (N=230 844), who were residing in the country on their tenth birthday, and who had two Danish-born parents were followed-up from their tenth birthday until schizophrenia diagnosis or Dec 31, 2016. Mean daily exposure to each pollutant (NO₂, NO_X, PM₁₀, and PM_2·5) at all of an individual's residential addresses from birth to their tenth birthday was modelled. Incidence rate ratios, cumulative incidence, and population attributable risks were calculated using survival analysis techniques.

FINDINGS

We analysed data between Aug 1, 2018, and Nov 15, 2019. Of 230 844 individuals included, 2189 cohort members were diagnosed with schizophrenia during follow-up. Higher concentrations of residential NO₂ and NO_X exposure during childhood were associated with subsequent elevated schizophrenia risk. People exposed to daily mean concentrations of more than 26·5 μg/m³ NO₂ had a 1·62 (95% CI 1·41-1·87) times increased risk compared with people exposed to a mean daily concentration of less than 14·5 μg/m³. The absolute risks of developing schizophrenia by the age of 37 years when exposed to daily mean concentrations of more than 26·5 μg/m³ NO₂ between birth and 10 years were 1·45% (95% CI 1·30-1·62%) for men and 1·03% (0·90-1·17) for women, whereas when exposed to a mean daily concentration of less than 14·5 μg/m³, the risk was 0·80% (95% CI 0·69-0·92%) for men and 0·67% (0·57-0·79) for women. Associations between exposure to PM_2·5 or PM₁₀ and schizophrenia risk were less consistent.

INTERPRETATION

If the association between air pollution and schizophrenia is causal, reducing ambient air pollution including NO₂ and NO_X could have a potentially considerable effect on lowering schizophrenia incidence at the population level. Further investigations are necessary to establish a causal relationship.

FUNDING

Lundbeck Foundation, Stanley Medical Research Institute, European Research Council, NordForsk, Novo Nordisk Foundation, National Health and Medical Research Council, Danish National Research Foundation.

Engineering the interactions between a plant-produced HIV antibody and human Fc receptors

Plants can provide a cost-effective and scalable technology for production of therapeutic monoclonal antibodies, with the potential for precise engineering of glycosylation. Glycan structures in the antibody Fc region influence binding properties to Fc receptors, which opens opportunities for modulation of antibody effector functions. To test the impact of glycosylation in detail, on binding to human Fc receptors, different glycovariants of VRC01, a broadly neutralizing HIV monoclonal antibody, were generated in Nicotiana benthamiana and characterized. These include glycovariants lacking plant characteristic α1,3-fucose and β1,2-xylose residues and glycans extended with terminal β1,4-galactose. Surface plasmon resonance-based assays were established for kinetic/affinity evaluation of antibody-FcγR interactions, and revealed that antibodies with typical plant glycosylation have a limited capacity to engage FcγRI, FcγRIIa, FcγRIIb and FcγRIIIa; however, the binding characteristics can be restored and even improved with targeted glycoengineering. All plant-made glycovariants had a slightly reduced affinity to the neonatal Fc receptor (FcRn) compared with HEK cell-derived antibody. However, this was independent of plant glycosylation, but related to the oxidation status of two methionine residues in the Fc region. This points towards a need for process optimization to control oxidation levels and improve the quality of plant-produced antibodies.

The homeobox factor Irx3 maintains adipogenic identity

BACKGROUND

Inhibition of Irx3 and Irx5 has been shown to reduce body weight and white adipose tissue (WAT) mass through cell-autonomous and sympathetic-induced increases in adipocyte beiging and thermogenesis in mice and humans. However, the underlying mechanisms of the Irx control over beiging are still largely unknown, as illustrated by recent reports showing divergent effects of Irx3 on adipocyte metabolism and function. Here, we investigated the role of Irx3 in controlling beige preadipocyte function and differentiation.

METHODS

Stable knock out of Irx3 in ME3 mouse preadipocytes capable of beiging was performed using a CRISPR-Cas9 system, and the effect on cell differentiation was assessed by qPCR, RNA-seq, Oil-red-O lipid staining and Alcian Blue staining of proteoglycans. Changes in cell identities were validated using cell type enrichment analysis from RNA-seq data. Proliferation and cell cycle progression in undifferentiated cells were measured by WST-1 and flow cytometry, reactive oxygen species (ROS) generation was determined by fluorescence spectrometry and mitochondrial respiration was investigated by Seahorse assay.

RESULTS

Irx3 was found to be essential for the identity, function and adipogenic differentiation of beige adipocyte precursors. Irx3-KO impaired proliferation, ROS generation and mitochondrial respiration in the preadipocytes. We further observed profound changes in numerous genes during both early and late stages of adipogenic differentiation, including genes important for adipocyte differentiation, cell cycle progression, oxidative phosphorylation (OXPHOS) and morphogenesis. Irx3-KO cells failed to accumulate lipids following adipogenic stimuli, and cell enrichment analysis revealed a loss of preadipocyte identity and a gain of chondrocyte-like identity in Irx3-KO cells during early differentiation. Finally, unlike the control cells, the Irx3-KO cells readily responded to chondrogenic stimuli.

CONCLUSIONS

Irx3 is required for preadipocyte identity and differentiation capacity. Our findings suggest that, while inhibition of Irx3 may be beneficial during later developmental stages to modulate adipogenesis in the beige direction, constitutive and complete absence of Irx3 in the embryonic fibroblast stage leads to detrimental loss of adipogenic differentiation capacity.

Observation of Robust Néel Skyrmions in Metallic PtMnGa

Over the past decade the family of chiral noncollinear spin textures has continued to expand with the observation in metallic compounds of Bloch-like skyrmions in several B20 compounds, and antiskyrmions in a tetragonal inverse Heusler. Néel like skyrmions in bulk crystals with broken inversion symmetry have recently been seen in two distinct nonmetallic compounds, GaV₄ S₈ and VOSe₂ O₅ at low temperatures (below ≈13 K) only. Here, the first observation of bulk Néel skyrmions in a metallic compound PtMnGa and, moreover, at high temperatures up to ≈220 K is reported. Lorentz transmission electron microscopy reveals the chiral Néel character of the skyrmions. A strong variation is reported of the size of the skyrmions on the thickness of the lamella in which they are confined, varying by a factor of 7 as the thickness is varied from ≈90 nm to ≈4 µm. Moreover, the skyrmions are highly robust to in-plane magnetic fields and can be stabilized in a zero magnetic field using suitable field-cooling protocols over a very broad temperature range to as low as 5 K. These properties, together with the possibility of manipulating skyrmions in metallic PtMnGa via current induced spin-orbit torques, make them extremely exciting for future spintronic applications.

A helical inner scaffold provides a structural basis for centriole cohesion

The ninefold radial arrangement of microtubule triplets (MTTs) is the hallmark of the centriole, a conserved organelle crucial for the formation of centrosomes and cilia. Although strong cohesion between MTTs is critical to resist forces applied by ciliary beating and the mitotic spindle, how the centriole maintains its structural integrity is not known. Using cryo-electron tomography and subtomogram averaging of centrioles from four evolutionarily distant species, we found that MTTs are bound together by a helical inner scaffold covering ~70% of the centriole length that maintains MTTs cohesion under compressive forces. Ultrastructure Expansion Microscopy (U-ExM) indicated that POC5, POC1B, FAM161A, and Centrin-2 localize to the scaffold structure along the inner wall of the centriole MTTs. Moreover, we established that these four proteins interact with each other to form a complex that binds microtubules. Together, our results provide a structural and molecular basis for centriole cohesion and geometry.

Editing a γ-globin repressor binding site restores fetal hemoglobin synthesis and corrects the sickle cell disease phenotype

Sickle cell disease (SCD) is caused by a single amino acid change in the adult hemoglobin (Hb) β chain that causes Hb polymerization and red blood cell (RBC) sickling. The co-inheritance of mutations causing fetal γ-globin production in adult life hereditary persistence of fetal Hb (HPFH) reduces the clinical severity of SCD. HPFH mutations in the HBG γ-globin promoters disrupt binding sites for the repressors BCL11A and LRF. We used CRISPR-Cas9 to mimic HPFH mutations in the HBG promoters by generating insertions and deletions, leading to disruption of known and putative repressor binding sites. Editing of the LRF-binding site in patient-derived hematopoietic stem/progenitor cells (HSPCs) resulted in γ-globin derepression and correction of the sickling phenotype. Xenotransplantation of HSPCs treated with gRNAs targeting the LRF-binding site showed a high editing efficiency in repopulating HSPCs. This study identifies the LRF-binding site as a potent target for genome-editing treatment of SCD.

Automated structure discovery in atomic force microscopy

Atomic force microscopy (AFM) with molecule-functionalized tips has emerged as the primary experimental technique for probing the atomic structure of organic molecules on surfaces. Most experiments have been limited to nearly planar aromatic molecules due to difficulties with interpretation of highly distorted AFM images originating from nonplanar molecules. Here, we develop a deep learning infrastructure that matches a set of AFM images with a unique descriptor characterizing the molecular configuration, allowing us to predict the molecular structure directly. We apply this methodology to resolve several distinct adsorption configurations of 1S-camphor on Cu(111) based on low-temperature AFM measurements. This approach will open the door to applying high-resolution AFM to a large variety of systems, for which routine atomic and chemical structural resolution on the level of individual objects/molecules would be a major breakthrough.

Cerebellar ataxia, neuropathy, vestibular areflexia syndrome due to RFC1 repeat expansion

Ataxia, causing imbalance, dizziness and falls, is a leading cause of neurological disability. We have recently identified a biallelic intronic AAGGG repeat expansion in replication factor complex subunit 1 (RFC1) as the cause of cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS) and a major cause of late onset ataxia. Here we describe the full spectrum of the disease phenotype in our first 100 genetically confirmed carriers of biallelic repeat expansions in RFC1 and identify the sensory neuropathy as a common feature in all cases to date. All patients were Caucasian and half were sporadic. Patients typically reported progressive unsteadiness starting in the sixth decade. A dry spasmodic cough was also frequently associated and often preceded by decades the onset of walking difficulty. Sensory symptoms, oscillopsia, dysautonomia and dysarthria were also variably associated. The disease seems to follow a pattern of spatial progression from the early involvement of sensory neurons, to the later appearance of vestibular and cerebellar dysfunction. Half of the patients needed walking aids after 10 years of disease duration and a quarter were wheelchair dependent after 15 years. Overall, two-thirds of cases had full CANVAS. Sensory neuropathy was the only manifestation in 15 patients. Sixteen patients additionally showed cerebellar involvement, and six showed vestibular involvement. The disease is very likely to be underdiagnosed. Repeat expansion in RFC1 should be considered in all cases of sensory ataxic neuropathy, particularly, but not only, if cerebellar dysfunction, vestibular involvement and cough coexist.

Injectable Cardiac Cell Microdroplets for Tissue Regeneration

One of the strategies for heart regeneration includes cell delivery to the defected heart. However, most of the injected cells do not form quick cell-cell or cell-matrix interactions, therefore, their ability to engraft at the desired site and improve heart function is poor. Here, the use of a microfluidic system is reported for generating personalized hydrogel-based cellular microdroplets for cardiac cell delivery. To evaluate the system's limitations, a mathematical model of oxygen diffusion and consumption within the droplet is developed. Following, the microfluidic system's parameters are optimized and cardiac cells from neonatal rats or induced pluripotent stem cells are encapsulated. The morphology and cardiac specific markers are assessed and cell function within the droplets is analyzed. Finally, the cellular droplets are injected to mouse gastrocnemius muscle to validate cell retention, survival, and maturation within the host tissue. These results demonstrate the potential of this approach to generate personalized cellular microtissues, which can be injected to distinct regions in the body for treating damaged tissues.

Extracellular matrix anisotropy is determined by TFAP2C-dependent regulation of cell collisions

The isotropic or anisotropic organization of biological extracellular matrices has important consequences for tissue function. We study emergent anisotropy using fibroblasts that generate varying degrees of matrix alignment from uniform starting conditions. This reveals that the early migratory paths of fibroblasts are correlated with subsequent matrix organization. Combined experimentation and adaptation of Vicsek modelling demonstrates that the reorientation of cells relative to each other following collision plays a role in generating matrix anisotropy. We term this behaviour 'cell collision guidance'. The transcription factor TFAP2C regulates cell collision guidance in part by controlling the expression of RND3. RND3 localizes to cell-cell collision zones where it downregulates actomyosin activity. Cell collision guidance fails without this mechanism in place, leading to isotropic matrix generation. The cross-referencing of alignment and TFAP2C gene expression signatures against existing datasets enables the identification and validation of several classes of pharmacological agents that disrupt matrix anisotropy.

Frataxin deficiency in Friedreich's ataxia is associated with reduced levels of HAX-1, a regulator of cardiomyocyte death and survival

Frataxin deficiency, responsible for Friedreich's ataxia (FRDA), is crucial for cell survival since it critically affects viability of neurons, pancreatic beta cells and cardiomyocytes. In FRDA, the heart is frequently affected with typical manifestation of hypertrophic cardiomyopathy, which can progress to heart failure and cause premature death. A microarray analysis performed on FRDA patient's lymphoblastoid cells stably reconstituted with frataxin, indicated HS-1-associated protein X-1 (HAX-1) as the most significantly upregulated transcript (FC = +2, P < 0.0006). quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR) and western blot analysis performed on (I) HEK293 stably transfected with empty vector compared to wild-type frataxin and (II) lymphoblasts from FRDA patients show that low frataxin mRNA and protein expression correspond to reduced levels of HAX-1. Frataxin overexpression and silencing were also performed in the AC16 human cardiomyocyte cell line. HAX-1 protein levels are indeed regulated through frataxin modulation. Moreover, correlation between frataxin and HAX-1 was further evaluated in peripheral blood mononuclear cells (PBMCs) from FRDA patients and from non-related healthy controls. A regression model for frataxin which included HAX-1, group membership and group* HAX-1 interaction revealed that frataxin and HAX-1 are associated both at mRNA and protein levels. Additionally, a linked expression of FXN, HAX-1 and antioxidant defence proteins MnSOD and Nrf2 was observed both in PBMCs and AC16 cardiomyocytes. Our results suggest that HAX-1 could be considered as a potential biomarker of cardiac disease in FRDA and the evaluation of its expression might provide insights into its pathogenesis as well as improving risk stratification strategies.

Gene duplication and transposition of mobile elements drive evolution of the Rpv3 resistance locus in grapevine

A wild grape haplotype (Rpv3-1) confers resistance to Plasmopara viticola. We mapped the causal factor for resistance to an interval containing a TIR-NB-LRR (TNL) gene pair that originated 1.6-2.6 million years ago by a tandem segmental duplication. Transient coexpression of the TNL pair in Vitis vinifera leaves activated pathogen-induced necrosis and reduced sporulation compared with control leaves. Even though transcripts of the TNL pair from the wild haplotype appear to be partially subject to nonsense-mediated mRNA decay, mature mRNA levels in a homozygous resistant genotype were individually higher than the mRNA trace levels observed for the orthologous single-copy TNL in sensitive genotypes. Allelic expression imbalance in a resistant heterozygote confirmed that cis-acting regulatory variation promotes expression in the wild haplotype. The movement of transposable elements had a major impact on the generation of haplotype diversity, altering the DNA context around similar TNL coding sequences and the GC-content in their proximal 5'-intergenic regions. The wild and domesticated haplotypes also diverged in conserved single-copy intergenic DNA, but the highest divergence was observed in intraspecific and not in interspecific comparisons. In this case, introgression breeding did not transgress the genetic boundaries of the domesticated species, because haplotypes present in modern varieties sometimes predate speciation events between wild and cultivated species.

Local Berry curvature signatures in dichroic angle-resolved photoelectron spectroscopy from two-dimensional materials

Topologically nontrivial two-dimensional materials hold great promise for next-generation optoelectronic applications. However, measuring the Hall or spin-Hall response is often a challenge and practically limited to the ground state. An experimental technique for tracing the topological character in a differential fashion would provide useful insights. In this work, we show that circular dichroism angle-resolved photoelectron spectroscopy provides a powerful tool that can resolve the topological and quantum-geometrical character in momentum space. In particular, we investigate how to map out the signatures of the momentum-resolved Berry curvature in two-dimensional materials by exploiting its intimate connection to the orbital polarization. A spin-resolved detection of the photoelectrons allows one to extend the approach to spin-Chern insulators. The present proposal can be extended to address topological properties in materials out of equilibrium in a time-resolved fashion.