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Generalizable and Non-genetic Approach to Create Metabolically-active-but-non-replicating Bacteria

Researchers at the University of California, Davis have developed a method to stop bacterial growth while maintaining desirable metabolic functions for therapeutic and biotechnological applications.

Reducing Risk Of Aerosol-Transmitted Infection From Dental Ultrasonic Instrumentation

Pathogenic transmission of dental aerosol created by ultrasonic scaling is considered a major concern during dental procedures. Researchers at UC Irvine have developed a novel tool/method to address this concern by removing the created aerosol at the source.

High-Throughput Selection Platform to Obtain NMN+-Utilizing Enzymes Through Directed Evolution

Noncanonical redox cofactor-based biotransformation is an attractive low-cost alternative to traditional cell-free reductive biotransformation. However, engineering enzymes to utilize noncanonical redox cofactors has been challenging. Addressing this problem, researchers at UC Irvine have developed a high-throughput directed evolution platform that enables development of such enzymes with ~147-fold improved catalytic efficiency, which translates to an industry-viable total turnover number of ~45,000 in cell-free biotransformation without requiring high cofactor concentrations.

Discovery of Gene Overexpression Combinations to Improve Therapeutic T Cell Constructs with Pooled CRISPR Knockin Screens

Scientists at UCSF have developed a method for highly parallel testing of gene knockins/overexpression in combination with a cancer-specific T cell receptor (TCR) or chimeric antigen receptor (CAR). The method enables researchers to evaluate what constructs can improve anti-tumor efficacy of conventional T-cell therapies. 

A Broadly Neutralizing Molecule Against Clostridium Difficile Toxin B

Researchers at UCI have developed a family of recombinant protein therapeutics against Clostridium difficile designed to provide broad-spectrum protection and neutralization against all isoforms of its main toxin, TcdB. These antitoxin molecules feature fragments of TcdB’s human receptors (CSPG4 and FZD) which compete for TcdB binding, significantly improving upon existing antibody therapeutics for Clostridium difficile infections.

(2022-099) Repeat expansion disease therapy with antisense RNA vectors

Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, Duchenne muscular dystrophy, and spinal muscular atrophy. Small nuclear RNA (snRNA) components of the U snRNP family have been proposed as a therapeutic modality for the treatment of mis-splicing. U1 snRNAs offer great promise, with prior studies demonstrating in vivo efficacy, suggesting additional preclinical development is merited. Improvements in enabling technologies, including screening methodologies, gene delivery vectors, and relevant considerations from gene editing approaches justify further advancement of U1 snRNA as a therapeutic and research tool.

Highly Selective MMP-12 Antibodies

Researchers from the University of California, Riverside have developed potent monoclonal antibody inhibitors with high MMP-12 selectivity.  These antibodies have applications in pharmaceuticals and biomedical sciences. Specifically, these antibodies may be developed as  therapies for inflammatory and neurological diseases. Fig 1: Inhibitory function of the MMP-12 antibodies LG4, LH6, and LH11 towards cdMMP-12. 

(SD2022-270) Algorithm for de novo drug discovery

Generation of drug-like molecules with high binding affinity to target proteins remains a difficult and resource-intensive task in drug discovery. Existing approaches primarily employ reinforcement learning, Markov sampling, or deep generative models guided by Gaussian processes, which can be prohibitively slow when generating molecules with high binding affinity calculated by computationally-expensive physicsbased methods. In drug discovery, a common paradigm today involves performing an initial high-throughput experimental screening of available compounds to identify hit compounds, which is both resource-intensive and can only identify which existing compounds are promising, relying on the further work of medicinal chemists to optimize these hit compounds into lead compounds. As an alternative, many computational methods have been proposed for de novo drug design, including genetic algorithms and other deep learning-based approaches. Methods outside of deep learning are generally not flexible enough to be entirely useful in drug discovery, while current state-of-the-art deep learning methods are either prohibitively slow or cannot generate molecules with an adequate level of desirability.

Method to Identify Vomocytosis Events via Time-Lapse Fluorescence Microscopy

Researchers at the University of California, Davis have developed a method to identify vomocytosis events in time-lapse microscopy videos.

(SD2021-057) Electro-optical mechanically flexible neural probes

Microelectrodes are the gold standard for measuring the activity of individual neurons at high temporal resolution in any nervous system region and central to defining the role of neural circuits in controlling behavior. Microelectrode technologies such as the Utah or Michigan arrays, have allowed tracking of distributed neural activity with millisecond precision. However, their large footprint and rigidity lead to tissue damage and inflammation that hamper long-term recordings. State of the art Neuropixel and carbon fiber probes have improved on these previous devices by increasing electrode density and reducing probe dimensions and rigidity. Although these probes have advanced the field of recordings, next-generation devices should enable targeted stimulation in addition to colocalized electrical recordings. Optogenetic techniques enable high-speed modulation of cellular activity through targeted expression and activation of light-sensitive opsins. However, given the strong light scattering and high absorption properties of neural tissue optogenetic interfacing with deep neural circuits typically requires the implantation of large-diameter rigid fibers, which can make this approach more invasive than its electrical counterpart.Approaches to integrating optical and electrical modalities have ranged from adding fiber optics to existing Utah arrays to the Optetrode or other integrated electro-optical coaxial structures. These technologies have shown great promise for simultaneous electrical recordings and optical stimulation in vivo. However, the need to reduce the device footprint to minimize immune responses for long-term recordings is still present.

(SD2021-089) Unbiased approach for identification of regulators of materials and molecular uptake into cells

A major bottleneck in nanocarrier and macromolecule development for therapeutic delivery is our limited understanding of the processes involved in their uptake into target cells. This includes their active interactions with membrane transporters that co-ordinate cellular uptake and processing. Current strategies to elucidate the mechanism of uptake, such as painstaking manipulation of individual effectors with pharmacological inhibitors or specific genetic knockdowns, are limited in scope and biased towards previously studied pathways or the intuition of the investigators. Furthermore, each of these approaches present significant off-target effects, clouding the outcomes. Methods for intracellular transport of nucleic acids are much sought after in the context of both in vitro delivery reagents and in vivo therapeutics. Recently, we found that micellar assemblies of hundreds of amphiphiles consisting of single-stranded DNA which has been covalently linked to a hydrophobic polymer, referred to as DNA-polymer amphiphile nanoparticles or DPANPs, can readily access the cytosol of cells where they modulate mRNA expression of target genomes without transfection or other helper reagents, making them potential therapeutic nucleic acid carriers. However, despite their effective uptake properties and efficacy in the cytosol, it was unknown how these polyanionic structures can enter cells. Indeed, generally, bottlenecks in understanding and achieving delivery and uptake remain a forefront issue in translatability of macromolecular and nanomaterials-based therapeutics generally, including with respect to nucleic acid therapies. The nature of pooled screening requires amplifying a single ~200nt region per cell, leading to screens that require amplification from tens-to hundreds of micrograms of genomic DNA. Inhibitory effects of high DNA concentration per PCR have led to a variety of solutions, ranging from simply pooling hundreds of PCR reactions to utilizing restriction enzyme sites present in the lentiviral backbone constant regions flanking the sgRNA to perform DNA gel electrophoresis and size selection to remove undesired gDNA. However, these approaches can be both expensive and have significant handling challenges when scaled to large screens.

CRISPR-Cas Inhibiting Polypeptides

Brief description not available

Apodization Specific Peak Fitting In Charge Detection Mass Spectrometry

Short-time Fourier transforms with short segment lengths are typically used to analyze single ion charge detection mass spectrometry (CDMS) data either to overcome effects of frequency shifts that may occur during the trapping period or to more precisely determine the time at which an ion changes mass, charge or enters an unstable orbit. The short segment lengths can lead to scalloping loss unless a large number of zero-fills are used, making computational time a significant factor in real time analysis of data.    To address the foregoing deficiencies in prior approaches, UC Berkeley researchers have developed an apodization specific fitting that can lead to a 9-fold reduction in computation time compared to zero-filling to a similar extent of accuracy. This makes possible real-time data analysis using a standard desktop computer and capable of separating ions with similar frequencies.  

CRISPR-Cas Effector Polypeptides and Methods of Use Thereof

CRISPR-Cas systems comprise a CRISPR-associated (Cas) effector polypeptide and a guide nucleic acid. Such CRISPR-Cas systems can bind to and modify a targeted nucleic acid. The programmable nature of these CRISPR-Cas effector systems has facilitated their use as a versatile technology for use in, e.g., gene editing.   UC Berkeley researchers have discovered new CRISPR-Cas effector Cas12L/Cas Lambda/Casλ polypeptides and methods of modifying a target nucleic acid using a Cas12L/Cas Lambda polypeptide.

COMPOSITIONS AND METHODS FOR REDUCING RNA LEVELS

Human diseases that follow a dominant negative inheritance pattern present a great challenge for treatment using gene therapy methods. In such cases, a copy of an allele is inherited from each parent: one is a pathogenic allele causing a disease phenotype (e.g., by exerting a toxic, gain-of-function effect) and the other is a wild-type (non-pathogenic) allele. Allele-specific targeting is especially important when the wild-type allele is crucial to normal function, e.g., the wild-type allele encodes a protein whose function is critical. There is therefore a need for compositions and methods of allele-specific gene editing.   UC Berkeley researchers have created methods and systems for reducing the level of an RNA transcript from a target nucleic acid in an allele-specific manner. Such systems and methods can be used to treat a disease that results from or is caused by a toxic gain-of-function protein.   

(SD2022-010) Method for transmembrane protein semisynthesis and reconstitution in lipid membranes

Cellular lipid membranes are embedded with transmembrane proteins crucial to cell function. Elucidating membrane proteins’ diverse structures and biophysical mechanisms is increasingly necessary due to their growing prevalence as a therapeutic target and sheer ubiquity in cells. Most biophysical characterization strategies of transmembrane proteins rely on the tedious overexpression and isolation of recombinant proteins and their reconstitution in model phospholipid bilayers.Unfortunately, membrane protein reconstitution depends on the use of denaturing and unnatural detergents that can interfere with protein structure and function. We have developed a detergent‐free method to reconstitute transmembrane proteins in model phospholipid vesicles and GUVs. Additionally, transmembrane proteins are difficult to express in cells due to the extreme insolubility of their transmembrane domain. By incorporating a synthetic transmembrane peptide into liposomes and simply expressing soluble portions of transmembrane proteins in cells, we can use this semisynthetic ligation strategy to more easily construct functional transmembrane proteins and reconstitute them into liposomes for biophysical and biochemical studies.Inteins can be found contiguously or non contiguously within some proteins. Non‐contiguous inteins are called “split inteins”. Inteins can be thought of as a type of protein intron which splices itself out of proteins. When non‐contiguous inteins find and bind to each other, they are then able to excise themselves resulting in the ligation of their respective exteins. Split intein pairs (C‐intein and N‐intein) can be attached to proteins of interest in synthetic and cellular systems to ligate protein sequences together.

(SD2021-085) Method for sequestering RNA binding proteins to affect their activity

The main way to reduce the activity of RBPs in cells is through gene expression knockdown (i.e. siRNAs or antisense oligonucleotides). More recently, circular RNAs have been used as a competitive inhibitor of miRNA activity by capturing the Argonaute proteins – which already occurs naturally in cells. There are also no known small molecule inhibitors of RBPs.

SCITO-SEQ: SINGLE CELL COMBINATORIAL INDEXED CYTOMETRY SEQUENCING

Researchers at UCSF have developed SCITO-seq, a new workflow for single cell sequencing-based proteomics. 

Nuclear Delivery and Transcriptional Repression with a Cell-penetrant MeCP2

Methyl-CpG-binding-protein 2 (MeCP2) is a nuclear protein expressed in all cell types, especially neurons. Mutations in the MECP2 gene cause Rett syndrome (RTT), an incurable neurological disorder that disproportionately affects young girls. Strategies to restore MeCP2 expression phenotypically reverse RTT-like symptoms in male and female MeCP2-deficient mice, suggesting that direct nuclear delivery of functional MeCP2 could restore MeCP2 activity.The inventors have discovered that ZF-tMeCP2, a conjugate of MeCP2(aa13-71, 313-484) and the cell-permeant mini-protein ZF5.3, binds DNA in a methylation-dependent manner and reaches the nucleus of model cell lines intact at concentrations above 700 nM. When delivered to live cells, ZF-tMeCP2 engages the NCoR/SMRT co-repressor complex and selectively represses transcription from methylated promoters. Efficient nuclear delivery of ZF-tMeCP2 relies on a unique endosomal escape portal provided by HOPS-dependent endosomal fusion.In a comparative evaluation, the inventors observed the Tat conjugate of MeCP2 (Tat-tMeCP2) (1) degrades within the nucleus, (2) is not selective for methylated promoters, and (3) traffics in a HOPS-independent manner. These results support the feasibility of a HOPS-dependent portal for delivering functional macromolecules to the cell interior using the cell-penetrant mini-protein ZF5.3. Such a strategy could broaden the impact of multiple families of protein-derived therapeutics.

Type III CRISPR-Cas System for Robust RNA Knockdown and Imaging in Eukaryotes

Type III CRISPR-Cas systems recognize and degrade RNA molecules using an RNA-guided mechanism that occurs widely in microbes for adaptive immunity against viruses. The inventors have demonstrated that this multi-protein system can be leveraged for programmable RNA knockdown of both nuclear and cytoplasmic transcripts in mammalian cells. Using single-vector delivery of the S. thermophilus Csm complex, RNA knockdown was achieved with high efficiency (90-99%) and minimal off-targets, outperforming existing technologies of shRNA- and Cas13-mediated knockdown. Furthermore, unlike Cas13, Csm is devoid of trans-cleavage activity and thus does not induce non-specific transcriptome-wide degradation and cytotoxicity. Catalytically inactivated Csm can also be used for programmable RNA-binding, which the inventors exploit for live-cell RNA imaging. This work demonstrates the feasibility and efficacy of multi-subunit CRISPR-Cas effector complexes as RNA-targeting tools in eukaryotes.

RNA Writing: Programmable Splicing for Transcriptome Engineering

RNA splicing is a fundamental biological process, in which a pre-mRNA transcript is modified by the endogenous spliceosomal complex into a mature mRNA transcript. This standard process involves a single pre-mRNA molecule “in cis.”  Whereas methods for editing DNA using editing enzymes have been described and are currently in use for various gene editing applications, there is a need in the art for methods of editing RNA.   UC Berkeley researchers have created a hybrid RNA molecule comprising a targeting region and a donor RNA, and compositions comprising the hybrid RNA molecule which is useful in methods of modifying a target RNA by employing a splicing reaction that joins two distinct RNA molecules “in trans.”  

Compositions and Methods for Modification of Cells

New chemistries are emerging for the direct attachment of complex molecules to cell surfaces. Chemistries that modify cells must perform under a narrow set of conditions in order to maintain cell viability. They must proceed in buffered aqueous media at the optimal physiological pH—typically pH 7.4—and within a temperature range of 4 – 37 ºC. Furthermore, these reactions must have sufficiently rapid kinetics to achieve high conversion even when confronted with the limits of surface diffusion characteristics. Due to these requirements, few chemistries exist that can attach molecules and proteins to live cells.  There is a need for improved methods of attaching proteins to living cells.   UC researchers have developed a convenient enzymatic strategy for the modification of cell surfaces for targeted immunotherapy applications.  

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