Abstract: The present disclosure provides systems, compositions, and methods for simultaneously editing both strands of a double-stranded DNA sequence at a target site to be edited. Further provided herein are pharmaceutical compositions, polynucleotides, vectors, cells, and kits for simultaneously editing both strands of a double-stranded DNA sequence.

Abstract: Provided herein are methods, systems, kits, and compositions useful for determining small molecule-protein interactions and protein-protein interactions. The photo-click tags provided herein can be conjugated to a small molecule or amino acid analog to provide compounds that can be integrated into a protein through photo-conjugation, allowing for identification of a small molecule-protein interaction or protein-protein interaction to elucidate the small molecules mechanism of action or the protein targeted by the small molecule. In some embodiments, the photo-click tags comprise a photo-conjugation moiety and a click chemistry handle, allowing for the attachment of various functional groups (e.g., affinity tags) to the small molecule or amino acid analog.

Abstract: Some aspects of this disclosure relate to strategies, systems, methods, compositions, and kits that are useful for production (e.g., evolution) of cytidine deaminase protein variants that are characterized by increased soluble expression and/or stability relative to the wild-type cytidine deaminase protein from which they are evolved. In some embodiments, evolved cytidine deaminase variants described by the disclosure are useful for incorporation into targeted nucleic acid editing proteins, for example in fusion proteins with a Cas9 domain or variant thereof.

Abstract: Methods and apparatus for modulating light using a tunable light modulation device. The tunable light modulation devices comprises an elastomer structure including at least one elastomer layer, a compliant electrode network of conducting fibers arranged on a first surface of the at least one elastomer layer, a patterned electric conductor arranged on a second surface of the at least one elastomer layer opposite the first surface. The patterned electric conductor includes a plurality of individually-addressable sections, and the compliant electrode network is configured to compress the at least one elastomer layer in the presence of an electric field between the compliant electrode network and one or more of the individually-addressable sections of the patterned electric conductor to produce a voltage-dependent roughening of the at least one elastomer layer.

Abstract: A method of fabricating a visible spectrum optical component includes: providing a substrate; forming a resist layer over a surface of the substrate; patterning the resist layer to form a patterned resist layer defining openings exposing portions of the surface of the substrate; performing deposition to form a dielectric film over the patterned resist layer and over the exposed portions of the surface of the substrate, wherein a top surface of the dielectric film is above a top surface of the patterned resist layer; removing a top portion of the dielectric film to expose the top surface of the patterned resist layer and top surfaces of dielectric units within the openings of the patterned resist layer; and removing the patterned resist layer to retain the dielectric units over the substrate.

Abstract: The present disclosure generally relates to systems and methods for multi-focal imaging, for example, for determining nucleic acids in cells or other samples. In some cases, multiple focal planes may simultaneously be determined, e.g., by using a plurality of detectors, such as a plurality of cameras, which image the same sample, but at least some of which are focused on different focal planes within the sample. Thus, the sample may be imaged in 3 dimensions, e.g., without sample refocusing. In certain cases, this may improve the resolution of imaging, in space and/or time. Various embodiments can be used to increase imaging throughput and/or resolution in image-based approaches, e.g., for single-cell molecular profiling such as multiplexed error robust fluorescence in situ hybridization (MERFISH), or for other applications.

Abstract: A microcalorimeter device capable of measuring cellular bioenergetics and systems that are limited in analytic volume. The microcalorimeter device provides sub-nWatt resolution and even tens of pico-Watt resolution, thus enabling resolution of the metabolic rate of a single cell.

Abstract: The present invention generally relates to a controlled fluidic device to develop spatially complex environments to enhance the rate of evolution in cell populations. The method further provides an enhanced understanding in the emergence, for example, drug resistance during cancer chemotherapy.

Abstract: Some aspects of the present disclosure provide methods for evolving recombinases to recognize target sequences that differ from the canonical recognition sequences. Some aspects of this disclosure provide evolved recombinases, e.g., recombinases that bind and recombine naturally-occurring target sequences, such as, e.g., target sequences within the human Rosa26 locus. Methods for using such recombinases for genetically engineering nucleic acid molecules in vitro and in vivo are also provided. Some aspects of this disclosure also provide libraries and screening methods for assessing the target site preferences of recombinases, as well as methods for selecting recombinases that bind and recombine a non-canonical target sequence with high specificity.

Abstract: Systems and methods are provided for characterizing shuttle capture events in a nanopore sensor. The method first collects time-dependent current blockage signatures for at least one bias voltage. The method then identifies each signature as corresponding to a permanent or transient event. The method then generates a protein dynamics landscape (PDL) for the transient event signatures. The PDL comprises a set of histograms of nanopore current data and characterizes current through the nanopore during shuttle capture events. The method can then comprise identifying an entrance level blockage value based on the permanent event signatures. Permanent event captures can be determined by time duration which is larger than a certain threshold time value. Applying a voltage between the fluidic chambers above a threshold voltage level can be used to control that the vast majority of events are permanent.

Abstract: The disclosure provides fusion proteins comprising a pleckstrin homology (PH) domain and a variant of Botulinum neurotoxin E (BoNT E) protease that cleaves certain non-canonical protein targets (e.g., PTEN). Fusion proteins described in the disclosure are useful for cleaving target proteins found in a cell, that is, in an intracellular environment. Aspects of the disclosure provide methods for inhibiting PTEN amount, activity, or function in a cell or subject, the methods comprising administering to a call or subject a fusion protein described herein.

Abstract: Provided herein is a reporter system for identifying a cytokine receptor modulator and uses thereof.

Abstract: A subwavelength resonator for acoustophoretic printing comprises a hollow resonator body for local enhancement of an acoustic field integrated with a nozzle body for delivery of an ink into the acoustic field. The nozzle body has a first end outside the hollow resonator body and a second end inside the hollow resonator body, and includes a fluid channel extending between a fluid inlet at the first end and a fluid outlet at the second end. The fluid channel passes through a side wall of the hollow resonator body and includes at least one bend. During acoustophoretic printing, an ink delivered through the fluid channel of the nozzle body and out of the fluid outlet is exposed to a high-intensity acoustic field.

Abstract: The present invention relates to methods of storing data using one or more nucleic acids.

Abstract: Provided herein are systems, compositions, kits, and methods for the suppression of pain (e.g., chronic pain). Genes encoding ion channels (e.g., SCN9A) responsible for the propagation pain signals in neurons (e.g., DRG neurons) may be edited using a genome editing agent (e.g., a nucleobase editor). In some embodiments, loss-of-function ion channel mutants are generated, leading to pain suppression. In some embodiments, the genome editing agent is administered locally to the site of pain or to the nerves responsible for propagation of the pain signal.

Abstract: The embodiments disclosed herein utilized RNA targeting effectors to provide a robust CRISPR-based diagnostic with attomolar sensitivity. Embodiments disclosed herein can detect both DNA and RNA with comparable levels of sensitivity and can differentiate targets from non-targets based on single base pair differences. Moreover, the embodiments disclosed herein can be prepared in freeze-dried format for convenient distribution and point-of-care (POC) applications. Such embodiments are useful in multiple scenarios in human health including, for example, viral detection, bacterial strain typing, sensitive genotyping, and detection of disease-associated cell free DNA.

Abstract: The present invention generally relates to microfluidics and labeled nucleic acids. For example, certain aspects are generally directed to systems and methods for labeling nucleic acids within microfluidic droplets or other compartments, for instance, arising from a cell. In one set of embodiments, particles may be prepared containing oligonucleotides that can be used to determine target nucleic acids, e.g., attached to the surface of the particles. The oligonucleotides may include “barcodes” or unique sequences that can be used to distinguish nucleic acids in a droplet from those in another droplet, for instance, even after the nucleic acids are pooled together or removed from the droplets. Certain embodiments of the invention are generally directed to systems and methods for attaching additional or arbitrary sequences to the nucleic acids within microfluidic droplets or other compartments, e.g.

Abstract: The present disclosure provides fusion proteins comprising a nanobody and a split glycosyl hydrolase enzyme. Also provided herein are split glycosyl hydrolase enzymes and fusion proteins comprising such enzymes. Further provided herein are polynucleotides, vectors, and cells. The present disclosure also provides methods of deglycosylating a protein and methods of studying the effects of glycosylation on protein function in cells. Also provided herein are methods of treating diseases.

Abstract: Articles and devices comprising fluorinated elastomers, as well as methods of preparing fluorinated elastomers, are generally described. In some cases, such fluorinated elastomers can be used for sensing neural activity, e.g., by encapsulating electronic circuits, or other applications. Furthermore, according to certain embodiments, polymers can, surprisingly, be directly deposited onto layers comprising low molecular weight fluorinated elastomers, e.g., without swelling in the presence of certain solvents. Some embodiments are generally directed to devices and methods for treating fluorinated elastomers and subsequently depositing material onto the treated fluorinated elastomers. This may allow the fabrication and patterning of multilayered articles comprising fluorinated elastomers.

Abstract: A sensing probe may be formed of a diamond material comprising one or more spin defects that are configured to emit fluorescent light and are located no more than 50 nm from a sensing surface of the sensing probe. The sensing probe may include an optical outcoupling structure formed by the diamond material and configured to optically guide the fluorescent light toward an output end of the optical outcoupling structure. An optical detector may detect the fluorescent light that is emitted from the spin defects and that exits through the output end of the optical outcoupling structure after being optically guided therethrough. A mounting system may hold the sensing probe and control a distance between the sensing surface of the sensing probe and a surface of a sample while permitting relative motion between the sensing surface and the sample surface.