The AnnotSV webserver in 2023: updated visualization and ranking.

Much of the human genetics variant repertoire is composed of single nucleotide variants (SNV) and small insertion/deletions (indel) but structural variants (SV) remain a major part of our modified DNA. SV detection has often been a complex question to answer either because of the necessity to use different technologies (array CGH, SNP array, Karyotype, Optical Genome Mapping…) to detect each category of SV or to get an appropriate resolution (Whole Genome Sequencing). Thanks to the deluge of pangenomic analysis, Human geneticists are accumulating SV and their interpretation remains time consuming and challenging. The AnnotSV webserver (https://www.lbgi.fr/AnnotSV/) aims at being an efficient tool to (i) annotate and interpret SV potential pathogenicity in the context of human diseases, (ii) recognize potential false positive variants from all the SV identified and (iii) visualize the patient variants repertoire. The most recent developments in the AnnotSV webserver are: (i) updated annotations sources and ranking, (ii) three novel output formats to allow diverse utilization (analysis, pipelines), as well as (iii) two novel user interfaces including an interactive circos view.

Biocompatibility and feasibility of VisiPlate, a novel ultrathin, multichannel glaucoma drainage device.

BACKGROUND: Glaucoma is the leading cause of blindness worldwide. Glaucoma drainage devices and minimally invasive glaucoma surgeries (MIGS) often present with tradeoffs in safety and durability of efficacy. Using a rabbit model, we examined the biocompatibility and feasibility of VisiPlate, a novel, ultrathin, tubeless subconjunctival shunt comprised of a network of microchannels. METHODS: Six naive female New Zealand White rabbits received implants (three only in the right eye with contralateral eye untreated and three in both eyes) composed of a 400-nm-thick aluminum oxide core coated with 2 µm of parylene-C, manufactured with microelectromechanical systems (MEMS) techniques. Tonometry, slit lamp exam, clinical exam, fluorescein patency testing, and histopathology were performed. RESULTS: VisiPlate demonstrated IOP-lowering of 20-40% compared to baseline at each time point over the course of 3 months in the nine implanted eyes. All eyes developed blebs over the implant, and fluorescein testing demonstrated fluid patency at 22 days post-implantation. Slit lamp and clinical observations showed that VisiPlate was well tolerated, with low levels of conjunctival congestion, conjunctival swelling, aqueous flare, hyphema, and iris involvement from surgery that resolved over time. At sacrifice time points of 93 days and 180 days, the only notable observations were mild levels of conjunctival congestion in implanted eyes. Histopathology showed minimal tissue response and no obvious inflammation, fibrosis, or necrosis around the implant. CONCLUSIONS: The results of this in vivo study demonstrate the biocompatibility and IOP-lowering effect of a multichannel, ultrathin subconjunctival shunt in a rabbit model. The data suggest that VisiPlate may safely enhance aqueous outflow and significantly reduce intraocular pressure.

Hollow Atomic Force Microscopy Cantilevers with Nanoscale Wall Thicknesses.

In atomic force microscopy, the cantilever probe is a critical component whose properties determine the resolution and speed at which images with nanoscale resolution can be obtained. Traditional cantilevers, which have moderate resonant frequencies and high quality factors, have relatively long response times and low bandwidths. In addition, cantilevers can be easily damaged by excessive deformation, and tips can be damaged by wear, requiring them to be replaced frequently. To address these issues, new cantilever probes that have hollow cross-sections and walls of nanoscale thicknesses made of alumina deposited by atomic layer deposition are introduced. It is demonstrated that the probes exhibit spring constants up to ≈100 times lower and bandwidths up to ≈50 times higher in air than their typical solid counterparts, allowing them to react to topography changes more quickly. Moreover, it is shown that the enhanced robustness of the hollow cantilevers enables them to withstand large bending displacements more readily and to be more resistant to tip wear.

A BBS1 SVA F retrotransposon insertion is a frequent cause of Bardet-Biedl syndrome.

Bardet-Biedl syndrome (BBS) is a ciliopathy characterized by retinitis pigmentosa, obesity, polydactyly, cognitive impairment and renal failure. Pathogenic variants in 24 genes account for the molecular basis of >80% of cases. Toward saturated discovery of the mutational basis of the disorder, we carefully explored our cohorts and identified a hominid-specific SINE-R/VNTR/Alu type F (SVA-F) insertion in exon 13 of BBS1 in eight families. In six families, the repeat insertion was found in trans with c.1169 T > G, p.Met390Arg and in two families the insertion was found in addition to other recessive BBS loci. Whole genome sequencing, de novo assembly and SNP array analysis were performed to characterize the genomic event. This insertion is extremely rare in the general population (found in 8 alleles of 8 BBS cases but not in >10 800 control individuals from gnomAD-SV) and due to a founder effect. Its 2435 bp sequence contains hallmarks of LINE1 mediated retrotransposition. Functional studies with patient-derived cell lines confirmed that the BBS1 SVA-F is deleterious as evidenced by a significant depletion of both mRNA and protein levels. Such findings highlight the importance of dedicated bioinformatics pipelines to identify all types of variation.

Photophoretic Levitation of Macroscopic Nanocardboard Plates.

Scaling down miniature rotorcraft and flapping-wing flyers to sub-centimeter dimensions is challenging due to complex electronics requirements, manufacturing limitations, and the increase in viscous damping at low Reynolds numbers. Photophoresis, or light-driven fluid flow, was previously used to levitate solid particles without any moving parts, but only with sizes of 1-20 µm. Here, architected metamaterial plates with 50 nm thickness are leveraged to realize photophoretic levitation at the millimeter to centimeter scales. Instead of creating lift through conventional rotors or wings, the nanocardboard plates levitate due to light-induced thermal transpiration through microchannels within the plates, enabled by their extremely low mass and thermal conductivity. At atmospheric pressure, the plates hover above a solid substrate at heights of ≈0.5 mm by creating an air cushion beneath the plate. Moreover, at reduced pressures (10-200 Pa), the increased speed of thermal transpiration through the plate's channels creates an air jet that enables mid-air levitation and allows the plates to carry small payloads heavier than the plates themselves. The macroscopic metamaterial structures demonstrate the potential of this new mechanism of flight to realize nanotechnology-enabled flying vehicles without any moving parts in the Earth's upper atmosphere and at the surface of other planets.

A comprehensive resource for retrieving, visualizing, and integrating functional genomics data.

The enormous amount of freely accessible functional genomics data is an invaluable resource for interrogating the biological function of multiple DNA-interacting players and chromatin modifications by large-scale comparative analyses. However, in practice, interrogating large collections of public data requires major efforts for (i) reprocessing available raw reads, (ii) incorporating quality assessments to exclude artefactual and low-quality data, and (iii) processing data by using high-performance computation. Here, we present qcGenomics, a user-friendly online resource for ultrafast retrieval, visualization, and comparative analysis of tens of thousands of genomics datasets to gain new functional insight from global or focused multidimensional data integration.

Micron-gap spacers with ultrahigh thermal resistance and mechanical robustness for direct energy conversion.

In thermionic energy converters, the absolute efficiency can be increased up to 40% if space-charge losses are eliminated by using a sub-10-µm gap between the electrodes. One practical way to achieve such small gaps over large device areas is to use a stiff and thermally insulating spacer between the two electrodes. We report on the design, fabrication and characterization of thin-film alumina-based spacers that provided robust 3-8 µm gaps between planar substrates and had effective thermal conductivities less than those of aerogels. The spacers were fabricated on silicon molds and, after release, could be manually transferred onto any substrate. In large-scale compression testing, they sustained compressive stresses of 0.4-4 MPa without fracture. Experimentally, the thermal conductance was 10-30 mWcm-2K-1 and, surprisingly, independent of film thickness (100-800 nm) and spacer height. To explain this independence, we developed a model that includes the pressure-dependent conductance of locally distributed asperities and sparse contact points throughout the spacer structure, indicating that only 0.1-0.5% of the spacer-electrode interface was conducting heat. Our spacers show remarkable functionality over multiple length scales, providing insulating micrometer gaps over centimeter areas using nanoscale films. These innovations can be applied to other technologies requiring high thermal resistance in small spaces, such as thermophotovoltaic converters, insulation for spacecraft and cryogenic devices.

Nanocardboard as a nanoscale analog of hollow sandwich plates.

Corrugated paper cardboard provides an everyday example of a lightweight, yet rigid, sandwich structure. Here we present nanocardboard, a monolithic plate mechanical metamaterial composed of nanometer-thickness (25-400 nm) face sheets that are connected by micrometer-height tubular webbing. We fabricate nanocardboard plates of up to 1 centimeter-square size, which exhibit an enhanced bending stiffness at ultralow mass of ~1 g m-2. The nanoscale thickness allows the plates to completely recover their shape after sharp bending even when the radius of curvature is comparable to the plate height. Optimally chosen geometry enhances the bending stiffness and spring constant by more than four orders of magnitude in comparison to solid plates with the same mass, far exceeding the enhancement factors previously demonstrated at both the macroscale and nanoscale. Nanocardboard may find applications as a structural component for wings of microflyers or interstellar lightsails, scanning probe cantilevers, and other microscopic and macroscopic systems.

Modeling gene-regulatory networks to describe cell fate transitions and predict master regulators.

Complex organisms originate from and are maintained by the information encoded in the genome. A major challenge of systems biology is to develop algorithms that describe the dynamic regulation of genome functions from large omics datasets. Here, we describe TETRAMER, which reconstructs gene-regulatory networks from temporal transcriptome data during cell fate transitions to predict "master" regulators by simulating cascades of temporal transcription-regulatory events.

Multilayer block copolymer meshes by orthogonal self-assembly.

Continued scaling-down of lithographic-pattern feature sizes has brought templated self-assembly of block copolymers (BCPs) into the forefront of nanofabrication research. Technologies now exist that facilitate significant control over otherwise unorganized assembly of BCP microdomains to form both long-range and locally complex monolayer patterns. In contrast, the extension of this control into multilayers or 3D structures of BCP microdomains remains limited, despite the possible technological applications in next-generation devices. Here, we develop and analyse an orthogonal self-assembly method in which multiple layers of distinct-molecular-weight BCPs naturally produce nanomesh structures of cylindrical microdomains without requiring layer-by-layer alignment or high-resolution lithographic templating. The mechanisms for orthogonal self-assembly are investigated with both experiment and simulation, and we determine that the control over height and chemical preference of templates are critical process parameters. The method is employed to produce nanomeshes with the shapes of circles and Y-intersections, and is extended to produce three layers of orthogonally oriented cylinders.

Dimensional Tailoring of Hydrothermally Grown Zinc Oxide Nanowire Arrays.

Hydrothermally synthesized ZnO nanowire arrays are critical components in a range of nanostructured semiconductor devices. The device performance is governed by relevant nanowire morphological parameters that cannot be fully controlled during bulk hydrothermal synthesis due to its transient nature. Here, we maintain homeostatic zinc concentration, pH, and temperature by employing continuous flow synthesis and demonstrate independent tailoring of nanowire array dimensions including areal density, length, and diameter on device-relevant length scales. By applying diffusion/reaction-limited analysis, we separate the effect of local diffusive transport from the c-plane surface reaction rate and identify direct incorporation as the c-plane growth mechanism. Our analysis defines guidelines for precise and independent control of the nanowire length and diameter by operating in rate-limiting regimes. We validate its utility by using surface adsorbents that limit reaction rate to obtain spatially uniform vertical growth rates across a patterned substrate.

Control of zinc oxide nanowire array properties with electron-beam lithography templating for photovoltaic applications.

Hydrothermally synthesized zinc oxide nanowire arrays have been used as nanostructured acceptors in emerging photovoltaic (PV) devices. The nanoscale dimensions of such arrays allow for enhanced charge extraction from PV active layers, but the device performance critically depends on the nanowire array pitch and alignment. In this study, we templated hydrothermally-grown ZnO nanowire arrays via high-resolution electron-beam-lithography defined masks, achieving the dual requirements of high-resolution patterning at a pitch of several hundred nanometers, while maintaining hole sizes small enough to control nanowire array morphology. We investigated several process conditions, including the effect of annealing sputtered and spincoated ZnO seed layers on nanowire growth, to optimize array property metrics-branching from individual template holes and off-normal alignment. We found that decreasing template hole size decreased branching prevalence but also reduced alignment. Annealing seed layers typically improved alignment, and sputtered seed layers yielded nanowire arrays superior to spincoated seed layers. We show that these effects arose from variation in the size of the template holes relative to the ZnO grain size in the seed layer. The quantitative control of branching and alignment of the nanowire array that is achieved in this study will open new paths toward engineering more efficient electrodes to increase photocurrent in nanostructured PVs. This control is also applicable to inorganic nanowire growth in general, nanomechanical generators, nanowire transistors, and surface-energy engineering.

Sacrificial-post templating method for block copolymer self-assembly.

A sacrificial-post templating method is presented for directing block copolymer self-assembly to form nanostructures consisting of monolayers and bilayers of microdomains. In this approach, the topographical post template is removed after self-assembly and therefore is not incorporated into the final microdomain pattern. Arrays of nanoscale holes of different shapes and symmetries, including mesh structures and perforated lamellae with a bimodal pore size distribution, are produced. The ratio of the pore sizes in the bimodal distributions can be varied via the template pitch, and agrees with predictions of self consistent field theory.

Neon Ion Beam Lithography (NIBL).

Existing techniques for electron- and ion-beam lithography, routinely employed for nanoscale device fabrication and mask/mold prototyping, do not simultaneously achieve efficient (low fluence) exposure and high resolution. We report lithography using neon ions with fluence <1 ion/nm(2), ∼1000× more efficient than using 30 keV electrons, and resolution down to 7 nm half-pitch. This combination of resolution and exposure efficiency is expected to impact a wide array of fields that are dependent on beam-based lithography.