Plant virus diversity in bee and pollen samples from apple (Malus domestica) and sweet cherry (Prunus avium) agroecosystems.

Introduction: Honey bee (Apis mellifera) pollination is widely used in tree fruit production systems to improve fruit set and yield. Many plant viruses can be associated with pollen or transmitted through pollination, and can be detected through bee pollination activities. Honey bees visit multiple plants and flowers in one foraging trip, essentially sampling small amounts of pollen from a wide area. Here we report metagenomics-based area-wide monitoring of plant viruses in cherry (Prunus avium) and apple (Malus domestica) orchards in Creston Valley, British Columbia, Canada, through bee-mediated pollen sampling. Methods: Plant viruses were identified in total RNA extracted from bee and pollen samples, and compared with profiles from double stranded RNA extracted from leaf and flower tissues. CVA, PDV, PNRSV, and PVF coat protein nucleotide sequences were aligned and compared for phylogenetic analysis. Results: A wide array of plant viruses were identified in both systems, with cherry virus A (CVA), prune dwarf virus (PDV), prunus necrotic ringspot virus (PNRSV), and prunus virus F (PVF) most commonly detected. Citrus concave gum associated virus and apple stem grooving virus were only identified in samples collected during apple bloom, demonstrating changing viral profiles from the same site over time. Different profiles of viruses were identified in bee and pollen samples compared to leaf and flower samples reflective of pollen transmission affinity of individual viruses. Phylogenetic and pairwise analysis of the coat protein regions of the four most commonly detected viruses showed unique patterns of nucleotide sequence diversity, which could have implications in their evolution and management approaches. Coat protein sequences of CVA and PVF were broadly diverse with multiple distinct phylogroups identified, while PNRSV and PDV were more conserved. Conclusion: The pollen virome in fruit production systems is incredibly diverse, with CVA, PDV, PNRSV, and PVF widely prevalent in this region. Bee-mediated monitoring in agricultural systems is a powerful approach to study viral diversity and can be used to guide more targeted management approaches.

Passive doubly curved structures for determining clamping forces applied to X-ray optic assemblies.

Clamping of indirectly cryogenically cooled X-ray optics is required to ensure effective heat transfer between the optic and heat exchanger. However, clamping forces can result in distortion of the optical surface of monochromators and mirror systems, which causes angular distortions of the subsequent beam. As such, there is a need for greater understanding of how these optics are assembled and how this affects their performance throughout their life cycle. In this paper, the potential for non-contact, in-process monitoring of the clamping force both during and after assembly using an additively manufactured passive structure based on a doubly curved hyperbolic paraboloid and designed for application to the first crystal for the I20 monochromator at Diamond Light Source is investigated numerically and experimentally. The performance of the passive structure both pre- and post-cryogenic quenching is characterized experimentally. Laser displacement measurements reveal approximately 9 µm total displacement in the passive structure per 100 N of bolt preload, corresponding to an effective magnification of the preload adjustment of approximately 2.5×.

Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation.

Understanding of the molecular drivers of lineage diversification and tissue patterning during primary germ layer development requires in-depth knowledge of the dynamic molecular trajectories of cell lineages across a series of developmental stages of gastrulation. Through computational modeling, we constructed at single-cell resolution, a spatio-temporal transcriptome of cell populations in the germ-layers of gastrula-stage mouse embryos. This molecular atlas enables the inference of molecular network activity underpinning the specification and differentiation of the germ-layer tissue lineages. Heterogeneity analysis of cellular composition at defined positions in the epiblast revealed progressive diversification of cell types. The single-cell transcriptome revealed an enhanced BMP signaling activity in the right-side mesoderm of late-gastrulation embryo. Perturbation of asymmetric BMP signaling activity at late gastrulation led to randomization of left-right molecular asymmetry in the lateral mesoderm of early-somite-stage embryo. These findings indicate the asymmetric BMP activity during gastrulation may be critical for the symmetry breaking process.

Area Wide Monitoring of Plant and Honey Bee (Apis mellifera) Viruses in Blueberry (Vaccinium corymbosum) Agroecosystems Facilitated by Honey Bee Pollination.

Healthy agroecosystems are dependent on a complex web of factors and inter-species interactions. Flowers are hubs for pathogen transmission, including the horizontal or vertical transmission of plant-viruses and the horizontal transmission of bee-viruses. Pollination by the European honey bee (Apis mellifera) is critical for industrial fruit production, but bees can also vector viruses and other pathogens between individuals. Here, we utilized commercial honey bee pollination services in blueberry (Vaccinium corymbosum) farms for a metagenomics-based bee and plant virus monitoring system. Following RNA sequencing, viruses were identified by mapping reads to a reference sequence database through the bioinformatics portal Virtool. In total, 29 unique plant viral species were found at two blueberry farms in British Columbia (BC). Nine viruses were identified at one site in Ontario (ON), five of which were not identified in BC. Ilarviruses blueberry shock virus (BlShV) and prune dwarf virus (PDV) were the most frequently detected viruses in BC but absent in ON, while nepoviruses tomato ringspot virus and tobacco ringspot virus were common in ON but absent in BC. BlShV coat protein (CP) nucleotide sequences were nearly identical in all samples, while PDV CP sequences were more diverse, suggesting multiple strains of PDV circulating at this site. Ten bee-infecting viruses were identified, with black queen cell virus frequently detected in ON and BC. Area-wide bee-mediated pathogen monitoring can provide new insights into the diversity of viruses present in, and the health of, bee-pollination ecosystems. This approach can be limited by a short sampling season, biased towards pollen-transmitted viruses, and the plant material collected by bees can be very diverse. This can obscure the origin of some viruses, but bee-mediated virus monitoring can be an effective preliminary monitoring approach.

Observing separate spin and charge Fermi seas in a strongly correlated one-dimensional conductor.

An electron is usually considered to have only one form of kinetic energy, but could it have more, for its spin and charge, by exciting other electrons? In one dimension (1D), the physics of interacting electrons is captured well at low energies by the Tomonaga-Luttinger model, yet little has been observed experimentally beyond this linear regime. Here, we report on measurements of many-body modes in 1D gated wires using tunneling spectroscopy. We observe two parabolic dispersions, indicative of separate Fermi seas at high energies, associated with spin and charge excitations, together with the emergence of two additional 1D "replica" modes that strengthen with decreasing wire length. The interaction strength is varied by changing the amount of 1D intersubband screening by more than 45%. Our findings not only demonstrate the existence of spin-charge separation in the whole energy band outside the low-energy limit of the Tomonaga-Luttinger model but also set a constraint on the validity of the newer nonlinear Tomonaga-Luttinger theory.

Effect of clamping force on distortion of the optical surface of monochromators during assembly.

As Diamond Light Source embraces the move towards becoming a fourth-generation light source its optics will be required to perform under increasingly demanding conditions. Foremost amongst these conditions will be the increasing power densities the optics are subjected to and the reducing real estate they have to perform in. With these new challenges comes the need for greater understanding of how optics are assembled and how consistently the activity is carried out. In this paper, the effect of bolt pretension during assembly of monochromators on distortion of the optical surface is investigated through numerical simulation. The results reveal skewed convex distortion of the optical surface in the meridional direction when uneven clamping force is applied, highlighting the importance of taking the potential for distortion of the optical surface due to clamping force into consideration.

Tomato brown rugose fruit virus: An emerging and rapidly spreading plant RNA virus that threatens tomato production worldwide.

Tomato brown rugose fruit virus (ToBRFV) is an emerging and rapidly spreading RNA virus that infects tomato and pepper, with tomato as the primary host. The virus causes severe crop losses and threatens tomato production worldwide. ToBRFV was discovered in greenhouse tomato plants grown in Jordan in spring 2015 and its first outbreak was traced back to 2014 in Israel. To date, the virus has been reported in at least 35 countries across four continents in the world. ToBRFV is transmitted mainly via contaminated seeds and mechanical contact (such as through standard horticultural practices). Given the global nature of the seed production and distribution chain, and ToBRFV's seed transmissibility, the extent of its spread is probably more severe than has been disclosed. ToBRFV can break down genetic resistance to tobamoviruses conferred by R genes Tm-1, Tm-2, and Tm-22 in tomato and L1 and L2 alleles in pepper. Currently, no commercial ToBRFV-resistant tomato cultivars are available. Integrated pest management-based measures such as rotation, eradication of infected plants, disinfection of seeds, and chemical treatment of contaminated greenhouses have achieved very limited success. The generation and application of attenuated variants may be a fast and effective approach to protect greenhouse tomato against ToBRFV. Long-term sustainable control will rely on the development of novel genetic resistance and resistant cultivars, which represents the most effective and environment-friendly strategy for pathogen control. TAXONOMY: Tomato brown rugose fruit virus belongs to the genus Tobamovirus, in the family Virgaviridae. The genus also includes several economically important viruses such as Tobacco mosaic virus and Tomato mosaic virus. GENOME AND VIRION: The ToBRFV genome is a single-stranded, positive-sense RNA of approximately 6.4 kb, encoding four open reading frames. The viral genomic RNA is encapsidated into virions that are rod-shaped and about 300 nm long and 18 nm in diameter. Tobamovirus virions are considered extremely stable and can survive in plant debris or on seed surfaces for long periods of time. DISEASE SYMPTOMS: Leaves, particularly young leaves, of tomato plants infected by ToBRFV exhibit mild to severe mosaic symptoms with dark green bulges, narrowness, and deformation. The peduncles and calyces often become necrotic and fail to produce fruit. Yellow blotches, brown or black spots, and rugose wrinkles appear on tomato fruits. In pepper plants, ToBRFV infection results in puckering and yellow mottling on leaves with stunted growth of young seedlings and small yellow to brown rugose dots and necrotic blotches on fruits.

Molecular Identification of Prune Dwarf Virus (PDV) Infecting Sweet Cherry in Canada and Development of a PDV Full-Length Infectious cDNA Clone.

Prune dwarf virus (PDV) is a member of ilarviruses that infects stone fruit species such as cherry, plum and peach, and ornamentally grown trees worldwide. The virus lacks an RNA silencing suppressor. Infection by PDV either alone, or its mixed infection with other viruses causes deteriorated fruit marketability and reduced fruit yields. Here, we report the molecular identification of PDV from sweet cherry in the prominent fruit growing region of Ontario, Canada known as the Niagara fruit belt using next generation sequencing of small interfering RNAs (siRNAs). We assessed its incidence in an experimental farm and determined the full genome sequence of this PDV isolate. We further constructed an infectious cDNA clone. Inoculation of the natural host cherry with this clone induced a dwarfing phenotype. We also examined its infectivity on several common experimental hosts. We found that it was infectious on cucurbits (cucumber and squash) with clear symptoms and Nicotiana benthamiana without causing noticeable symptoms, and it was unable to infect Arabidopsis thaliana. As generating infectious clones for woody plants is very challenging with limited success, the PDV infectious clone developed from this study will be a useful tool to facilitate molecular studies on PDV and related Prunus-infecting viruses.

High-yield parallel fabrication of quantum-dot monolayer single-electron devices displaying Coulomb staircase, contacted by graphene.

It is challenging for conventional top-down lithography to fabricate reproducible devices very close to atomic dimensions, whereas identical molecules and very similar nanoparticles can be made bottom-up in large quantities, and can be self-assembled on surfaces. The challenge is to fabricate electrical contacts to many such small objects at the same time, so that nanocrystals and molecules can be incorporated into conventional integrated circuits. Here, we report a scalable method for contacting a self-assembled monolayer of nanoparticles with a single layer of graphene. This produces single-electron effects, in the form of a Coulomb staircase, with a yield of 87 ± 13% in device areas ranging from < 800 nm2 to 16 µm2, containing up to 650,000 nanoparticles. Our technique offers scalable assembly of ultra-high densities of functional particles or molecules that could be used in electronic integrated circuits, as memories, switches, sensors or thermoelectric generators.

Integrated Polygenic Tool Substantially Enhances Coronary Artery Disease Prediction.

BACKGROUND: There is considerable interest in whether genetic data can be used to improve standard cardiovascular disease risk calculators, as the latter are routinely used in clinical practice to manage preventative treatment. METHODS: Using the UK Biobank resource, we developed our own polygenic risk score for coronary artery disease (CAD). We used an additional 60 000 UK Biobank individuals to develop an integrated risk tool (IRT) that combined our polygenic risk score with established risk tools (either the American Heart Association/American College of Cardiology pooled cohort equations [PCE] or UK QRISK3), and we tested our IRT in an additional, independent set of 186 451 UK Biobank individuals. RESULTS: The novel CAD polygenic risk score shows superior predictive power for CAD events, compared with other published polygenic risk scores, and is largely uncorrelated with PCE and QRISK3. When combined with PCE into an IRT, it has superior predictive accuracy. Overall, 10.4% of incident CAD cases were misclassified as low risk by PCE and correctly classified as high risk by the IRT, compared with 4.4% misclassified by the IRT and correctly classified by PCE. The overall net reclassification improvement for the IRT was 5.9% (95% CI, 4.7-7.0). When individuals were stratified into age-by-sex subgroups, the improvement was larger for all subgroups (range, 8.3%-15.4%), with the best performance in 40- to 54-year-old men (15.4% [95% CI, 11.6-19.3]). Comparable results were found using a different risk tool (QRISK3) and also a broader definition of cardiovascular disease. Use of the IRT is estimated to avoid up to 12 000 deaths in the United States over a 5-year period. CONCLUSIONS: An IRT that includes polygenic risk outperforms current risk stratification tools and offers greater opportunity for early interventions. Given the plummeting costs of genetic tests, future iterations of CAD risk tools would be enhanced with the addition of a person's polygenic risk.

Diverse Routes toward Early Somites in the Mouse Embryo.

Somite formation is foundational to creating the vertebrate segmental body plan. Here, we describe three transcriptional trajectories toward somite formation in the early mouse embryo. Precursors of the anterior-most somites ingress through the primitive streak before E7 and migrate anteriorly by E7.5, while a second wave of more posterior somites develops in the vicinity of the streak. Finally, neuromesodermal progenitors (NMPs) are set aside for subsequent trunk somitogenesis. Single-cell profiling of T-/- chimeric embryos shows that the anterior somites develop in the absence of T and suggests a cell-autonomous function of T as a gatekeeper between paraxial mesoderm production and the building of the NMP pool. Moreover, we identify putative regulators of early T-independent somites and challenge the T-Sox2 cross-antagonism model in early NMPs. Our study highlights the concept of molecular flexibility during early cell-type specification, with broad relevance for pluripotent stem cell differentiation and disease modeling.

1GHz clocked distribution of electrically generated entangled photon pairs.

Quantum networks are essential for realising distributed quantum computation and quantum communication. Entangled photons are a key resource, with applications such as quantum key distribution, quantum relays, and quantum repeaters. All components integrated in a quantum network must be synchronised and therefore comply with a certain clock frequency. In quantum key distribution, the most mature technology, clock rates have reached and exceeded 1GHz. Here we show the first electrically pulsed sub-Poissonian entangled photon source compatible with existing fiber networks operating at this clock rate. The entangled LED is based on InAs/InP quantum dots emitting in the main telecom window, with a multi-photon probability of less than 10% per emission cycle and a maximum entanglement fidelity of 89%. We use this device to demonstrate GHz clocked distribution of entangled qubits over an installed fiber network between two points 4.6km apart.

High-Throughput Electrical Characterization of Nanomaterials from Room to Cryogenic Temperatures.

We present multiplexer methodology and hardware for nanoelectronic device characterization. This high-throughput and scalable approach to testing large arrays of nanodevices operates from room temperature to milli-Kelvin temperatures and is universally compatible with different materials and integration techniques. We demonstrate the applicability of our approach on two archetypal nanomaterials-graphene and semiconductor nanowires-integrated with a GaAs-based multiplexer using wet or dry transfer methods. A graphene film grown by chemical vapor deposition is transferred and patterned into an array of individual devices, achieving 94% yield. Device performance is evaluated using data fitting methods to obtain electrical transport metrics, showing mobilities comparable to nonmultiplexed devices fabricated on oxide substrates using wet transfer techniques. Separate arrays of indium-arsenide nanowires and micromechanically exfoliated monolayer graphene flakes are transferred using pick-and-place techniques. For the nanowire array mean values for mobility µFE = 880/3180 cm2 V-1 s-1 (lower/upper bound), subthreshold swing 430 mV dec-1, and on/off ratio 3.1 decades are extracted, similar to nonmultiplexed devices. In another array, eight mechanically exfoliated graphene flakes are transferred using techniques compatible with fabrication of two-dimensional superlattices, with 75% yield. Our results are a proof-of-concept demonstration of a versatile platform for scalable fabrication and cryogenic characterization of nanomaterial device arrays, which is compatible with a broad range of nanomaterials, transfer techniques, and device integration strategies from the forefront of quantum technology research.

Demonstration of electron focusing using electronic lenses in low-dimensional system.

We report an all-electric integrable electron focusing lens in n-type GaAs. It is shown that a pronounced focusing peak takes place when the focal point aligns with an on-chip detector. The intensity and full width half maximum (FWHM) of the focusing peak are associated with the collimation of injected electrons. To demonstrate the reported focusing lens can be a useful tool, we investigate the characteristic of an asymmetrically gate biased quantum point contact with the assistance of a focusing lens. A correlation between the occurrence of conductance anomaly in low conductance regime and increase in FWHM of focusing peak is observed. The correlation is likely due to the electron-electron interaction. The reported electron focusing lens is essential for a more advanced electron optics device.

Single-photon emission from single-electron transport in a SAW-driven lateral light-emitting diode.

The long-distance quantum transfer between electron-spin qubits in semiconductors is important for realising large-scale quantum computing circuits. Electron-spin to photon-polarisation conversion is a promising technology for achieving free-space or fibre-coupled quantum transfer. In this work, using only regular lithography techniques on a conventional 15 nm GaAs quantum well, we demonstrate acoustically-driven generation of single photons from single electrons, without the need for a self-assembled quantum dot. In this device, a single electron is carried in a potential minimum of a surface acoustic wave (SAW) and is transported to a region of holes to form an exciton. The exciton then decays and creates a single optical photon within 100 ps. This SAW-driven electroluminescence, without optimisation, yields photon antibunching with g(2)(0) = 0.39 ± 0.05 in the single-electron limit (g(2)(0) = 0.63 ± 0.03 in the raw histogram). Our work marks the first step towards electron-to-photon (spin-to-polarisation) qubit conversion for scaleable quantum computing architectures.

A single-cell molecular map of mouse gastrulation and early organogenesis.

Across the animal kingdom, gastrulation represents a key developmental event during which embryonic pluripotent cells diversify into lineage-specific precursors that will generate the adult organism. Here we report the transcriptional profiles of 116,312 single cells from mouse embryos collected at nine sequential time points ranging from 6.5 to 8.5 days post-fertilization. We construct a molecular map of cellular differentiation from pluripotency towards all major embryonic lineages, and explore the complex events involved in the convergence of visceral and primitive streak-derived endoderm. Furthermore, we use single-cell profiling to show that Tal1-/- chimeric embryos display defects in early mesoderm diversification, and we thus demonstrate how combining temporal and transcriptional information can illuminate gene function. Together, this comprehensive delineation of mammalian cell differentiation trajectories in vivo represents a baseline for understanding the effects of gene mutations during development, as well as a roadmap for the optimization of in vitro differentiation protocols for regenerative medicine.

Imaging the Zigzag Wigner Crystal in Confinement-Tunable Quantum Wires.

The existence of Wigner crystallization, one of the most significant hallmarks of strong electron correlations, has to date only been definitively observed in two-dimensional systems. In one-dimensional (1D) quantum wires Wigner crystals correspond to regularly spaced electrons; however, weakening the confinement and allowing the electrons to relax in a second dimension is predicted to lead to the formation of a new ground state constituting a zigzag chain with nontrivial spin phases and properties. Here we report the observation of such zigzag Wigner crystals by use of on-chip charge and spin detectors employing electron focusing to image the charge density distribution and probe their spin properties. This experiment demonstrates both the structural and spin phase diagrams of the 1D Wigner crystallization. The existence of zigzag spin chains and phases which can be electrically controlled in semiconductor systems may open avenues for experimental studies of Wigner crystals and their technological applications in spintronics and quantum information.

Detection and removal of barcode swapping in single-cell RNA-seq data.

Barcode swapping results in the mislabelling of sequencing reads between multiplexed samples on patterned flow-cell Illumina sequencing machines. This may compromise the validity of numerous genomic assays; however, the severity and consequences of barcode swapping remain poorly understood. We have used two statistical approaches to robustly quantify the fraction of swapped reads in two plate-based single-cell RNA-sequencing datasets. We found that approximately 2.5% of reads were mislabelled between samples on the HiSeq 4000, which is lower than previous reports. We observed no correlation between the swapped fraction of reads and the concentration of free barcode across plates. Furthermore, we have demonstrated that barcode swapping may generate complex but artefactual cell libraries in droplet-based single-cell RNA-sequencing studies. To eliminate these artefacts, we have developed an algorithm to exclude individual molecules that have swapped between samples in 10x Genomics experiments, allowing the continued use of cutting-edge sequencing machines for these assays.

Coherent Spin Amplification Using a Beam Splitter.

We report spin amplification using a capacitive beam splitter in n-type GaAs where the spin polarization is monitored via a transverse electron focusing measurement. It is shown that partially spin-polarized current injected by the emitter can be precisely controlled, and the spin polarization associated with it can be amplified by the beam splitter, such that a considerably high spin polarization of around 50% can be obtained. Additionally, the spin remains coherent as shown by the observation of quantum interference. Our results illustrate that spin-polarization amplification can be achieved in materials without strong spin-orbit interaction.

Using single-cell genomics to understand developmental processes and cell fate decisions.

High-throughput -omics techniques have revolutionised biology, allowing for thorough and unbiased characterisation of the molecular states of biological systems. However, cellular decision-making is inherently a unicellular process to which "bulk" -omics techniques are poorly suited, as they capture ensemble averages of cell states. Recently developed single-cell methods bridge this gap, allowing high-throughput molecular surveys of individual cells. In this review, we cover core concepts of analysis of single-cell gene expression data and highlight areas of developmental biology where single-cell techniques have made important contributions. These include understanding of cell-to-cell heterogeneity, the tracing of differentiation pathways, quantification of gene expression from specific alleles, and the future directions of cell lineage tracing and spatial gene expression analysis.