Quantum sensing is rapidly reshaping our ability to discern chemical processes with high sensitivity and spatial resolution. Many quantum sensors are based on nitrogen-vacancy (NV) centers in diamond, with nanodiamonds (NDs) providing a promising approach to chemical quantum sensing compared to single crystals for benefits in cost, deployability, and facile integration with the analyte. However, high-precision chemical quantum sensing suffers from large statistical errors from particle heterogeneity, fluorescence fluctuations related to particle orientation, and other unresolved challenges.      To overcome these obstacles, UC Berkeley researchers have developed a novel microfluidic chemical quantum sensing device capable of high-precision, background-free quantum sensing at high-throughput. The microfluidic device solves problems with heterogeneity while simultaneously ensuring close interaction with the analyte. The device further yields exceptional measurement stability, which has been demonstrated over >103s measurement and across ~105 droplets.  Greatly surpassing the stability seen in conventional quantum sensing experiments, these properties are also resistant to experimental variations and temperature shifts. Finally, the required ND sensor volumes are minuscule, costing only about $0.63 for an hour of analysis. 

Worldwide, over 2.5 million people live with spinal cord injury, with over 100,000 new cases occurring annually. Spinal cord injury often causes motor dysfunction below the level of the injury. For example, thoracic and lumbar spinal cord injury can cause paraplegia and cervical spinal cord injury can cause quadriplegia. Such injury is permanent and often severe and there is no effective treatment. Various neurologic diseases also involve damaged or dysfunctional spinal cord neurons. Neural stem cell grafts have potential for treating such conditions. However, it has not been possible to obtain sufficient numbers of appropriately patterned neural stem cells, having a spinal cord positional identity, for implanted cells to survive and functionally engraft.

Brief description not available

Aberrant splicing contributes to the etiology of many inherited diseases. Pathogenic variants impact pre-mRNA splicing through a variety of mechanisms. Most notably, variants remodel the cis-regulatory landscape of pre-mRNAs by ablation or creation of splice sites, and auxiliary splicing regulatory sequences such as exonic or intronic splicing enhancers (ESE and ISE, respectively) and splicing silencers (ESS and ISS, respectively). Splicing-sensitive variants cripple the integrity of the gene, resulting in the production of a faulty message that is either unstable or encodes an internally deleted protein. Antisense oligonucleotides (ASOs) are a promising therapeutic modality for rescuing pathogenic aberrant splicing patterns as their direct base pairing abilities make them highly customizable and specific to targets. Although challenges such as toxicity, delivery and stability represent barriers to the clinical translation of ASOs, solutions to these challenges exist, as exemplified by the recent FDA approval of multiple ASO drugs.Generally, ASO's that target splicing mutations are limited to mutations in and around splicing enhancers and exonic mutations are commonly not targeted because of the idea that the mutation causes a significant change in protein function. 

Various plasmids from Michael Rape's lab, including but not limited to:pQE-UbcH5c/pET-Ube2D3-6xHispET28-E2NpET28-UEV1ApET28a-UBE2S-6xHISpET28a-E2R1-6xHIS 

Various ubiquitin plasmids from Michael Rape lab, including but not limited to: pCS2-no his-ubiquitin wtpCS2-no his-ubiquitin all RpET30a-ubiquitin (no tag)pET30a-ubiquitin K0 (no tag) 

Various plasmid constructs and cell lines for E3 Ligase project from Julia Schaletzky lab, including but not limited to:  pET28-ubiquitin wtpET28-ubiquitin deltaGGpLentiX1hygropLentiX1 blastpLentiX1 puropLentiX1 neopCS2-6xHIS-Htt-73QpCS2-6xHIS-Htt-23QpInducer Htt-23Q-GFPpInducer Htt-73Q-GFP

Stem cells have the potential to develop into different types of cells. They are key to an organism’s development. Producing stem cell lines are important for research. Currently, avian embryonic stems cells are cultured on a layer of feeder cells. Feeder cells ensure that the stem cells survive and do not differentiate into other types of cells. However, using feeder cells can be costly and inconvenient.

Researchers at the University of California, Davis have developed a unique peptide that induces cell differentiation by inhibiting cellular protein CHD4, a promising approach to target dedifferentiated cancer cells and for cell therapy.

Volumetric additive manufacturing and vat-polymerization 3D printing methods rapidly solidify freeform objects via photopolymerization, but problematically raises the local temperature in addition to degree-of-conversion (DOC). The generated heat can critically affect the printing process as it can auto-accelerate the polymerization reaction, trigger convection flows, and cause optical aberrations. Therefore, temperature measurement alongside conversion state monitoring is crucial for devising mitigation strategies and implementing process control. Traditional infrared imaging suffers from multiple drawbacks such as limited transmission of measurement signal, material-dependent absorptions, and high background signals emitted by other objects. Consequently, a viable temperature and DOC monitoring method for volumetric 3D printing doesn’t exist.To address this opportunity, UC Berkeley researchers have developed a tomographic imaging technique that detects the spatiotemporal evolution of temperature and DOC during volumetric printing. The invention lays foundations for the development of volumetric measurement systems that uniquely resolve both temperature and DOC in volumetric printing.This novel Berkeley measurement system is envisaged as an integral tool for existing manufacturing technologies, such as computed axial lithography (CAL, Tech ID #28754), and as a new research tool for commercial biomanufacturing, general fluid dynamics, and more.

Brief description not available

Researchers at UC Irvine have developed an organoid culture system capable of generating three-dimensional molecular gradients. This recapitulates in vivo tissue development more accurately than current two-dimensional organoid culture systems and will allow scientists to study human-specific disease mechanisms in native tissue.

UC Berkeley researchers have developed variant Listeria bacteria that have one or more  nucleic acids that encode polypeptides required for isoprenoid synthesis through the non-mevalonate pathway, wherein the Listeria bacterium grows aerobically in the presence or absence of a functional mevalonate pathway. The Listeria strain can be used to induce enhanced activation and expansion of human gamma delta T-cells and have been shown to do so in vitro.  

Cellulose, the major component of plant biomass, is considered the most abundant biopolymer. Certain microorganisms are able to convert the monomer of cellulose, glucose, into various products useful in the production of biofuels and other methods. Cellulose is highly stable, has a high storage potential, low cost, and plentiful supply. Based on these and other properties, cellulose and enzymes capable of degrading and hydrolyzing it are useful in the sequestration, storage, and production of bioenergy.  Crystalline cellulose is composed of linear polymers of β1-4 linked glucose, held in a tightly crosslinked crystalline lattice by a high degree of intermolecular hydrogen bonding. This structure confers stability but also hinders efficient deconstruction of cellulose. Strategies for commercial depolymerization of cellulose typically combine pretreatment to disrupt the crystalline structure, followed by enzymatic hydrolysis. Disruption of the crystalline structure and chemical hydrolysis typically requires high temperatures and low pH. Enzymatic hydrolysis generally occurs under milder conditions. The degree of pretreatment required and the expense of subsequent cleanup steps are affected by properties of the enzymes used. Bacteria capable of degrading cellulose include those belonging to the genera Aquifex, Rhodothermus, Thermobifida, Anaerocellum, and Caldicellulosiruptor. A recombinant thermostable endoglucanase of Aquifex aeolicus produced in E. coli showed maximal activity at 80° C. and pH 7.0 with a half-life of 2 h at 100° C.  UC Berkeley investigators have engineered a polypeptide having cellulase activity for hydrolysis and degradation of cellulose-containing biomass.

For the growing list of "undruggable" targets that lack well defined binding pockets  a consensus is emerging that successful inhibìtors will necessarily be larger and more complex than typical small molecule drugs. The targets of existing small molecule drugs make up only a small fraction of the protein encoding genome, and it is estimated that the total "druggable" genome (accessible to inhibition by classic small molecules) represents a small fraction of the total number of potential targets. The number of therapeutic targets that have been unexploited due to poor druggability, such as transcription factors and non-coding RNAs, therefore represent a vast opportunity to make therapeutic advances in virtually every disease category. Macrocycles - in particular, cyclic peptides - have shown remarkable versatility as ligands against challenging therapeutic targets such as protein-protein interactions (PPls). Cyclization is an established method for improving potency in peptides, and cyclization can dramatically improve proteolytic stability. Importantly, the synthesis of cyclic peptides is much more modular and straightforward than the synthesis of organic molecules of similar size and complexity. Large combinatorial lìbraries of cyclic peptides, derived from methods such as DNA-encoded synthesis, phage display and mRNA-d¡splay, have yielded potent inhibitors against a variety of undruggable or challenging targets.

Researchers at the University of California, Davis have developed a self-assembling, fibrous photosensitizer that targets mitochondria in tumor cells for destruction via photodynamic therapy with enhanced localization and potency.

Tech ID 32985/Case number 2018-408 describes the generation of E. coli expressed, peptide receptive MHC-I monomers and multimers using the TAPBPR chaperone. In this case, the technology was improved based upon the surprising discovery that the TAPBPR chaperone acts catalytically on MHC-I-placeholder peptide complexes to create peptide receptive MHC-I species. 

Typically, peptide receptive MHC-I multimer reagents are prepared in bacterial (E. coli) culture. While this is efficient, it does not result in glycosylation of the MHC-I peptide fragments as is done in mammalian cells. As a result, if such reagents are produced in mammalian cells, proper glycosylation would result and the reagents would have a potentially more accurate representation of the natural T-cell target.  

Plastics are essential for the modern world but are also non-sustainable products of the petrochemical industry that negatively impact our health, environment, and food chain. Natural biogenic plastics, such as polyhydroxyalkanoates (PHA), are readily biodegradable, can be produced more sustainably, and offer an attractive alternative. The global demand for bioplastics is increasing with the 2019 market value of $8.3B expected to reach a compound annual growth rate of 16.1% from 2020-2027 (https://www.grandviewresearch.com/industry-analysis/bioplastics-industry). However, current PHA production is constrained by the underlying physiology of the microorganisms which produce them, meaning bioplastic production is currently limited to inefficient, batch fermentation processes that are difficult to scale.To address this problem, UC Berkeley researchers have developed a new system for PHA production wherein the PHA are generated continuously throughout microorganism growth lifecycles. The invention allows these sustainable bioplastics to be produced via precision continuous fermentation technology, a scalable and efficient approach.

DP-L4056 is a prophage-cured strain of Listeria monocytogenes based on wild-type strain 10403S. A prophage is a bacteriophage genome that is integrated into a bacterial genome. It remains latent until activation by an external factor, and activation leads to production of new bacteriophage particles that lyse the bacterial cell and spread. Curing the prophages in Listeria monocytogenes strain 10403S, which is ubiquitous in the microbiology community as a wild-type reference strain, allows for more predictable engineering and performance of Listeria monocytogenes.

The mammary gland is responsible for producing milk in mammals. Producing a milk supply involves significantly accelerated cell growth and differentiation. It is thought that alveologenesis, the process by which milk-producing alveoli are made, occurs when alveolar progenitor cells differentiate into milk-producing alveolar cells. Thus, promoting alveolar differentiation is important in increasing milk production. Various industries, such as the dairy industry, may be interested in increasing milk production generally or increasing milk production without the use of hormones.

Biological fluids are complex, with compositions that vary constantly and evade molecular definition. Nevertheless, within these fluids proteins fluctuate, fold, function, and evolve as programmed. Synthetic heteropolymers capable of emulating such interactions would replicate how proteins behave in biological fluids, individually and collectively, leading the way toward synthetic biological fluids. However, while there exist known monomeric sequence requirements, the chemical and sequence characteristics of proteins at the segmental level, rather than the monomeric level, may be the key factor governing how proteins transiently interact with neighboring molecules (and how biological fluids collectively behave). To address this opportunity, UC Berkeley researchers have developed a new process of heteropolymer design for protein stabilization and synthetic mimics of biological fluids. The process leverages chemical characteristics and sequential arrangements along protein chains at the segmental level to design heteropolymer ensembles as mixtures of disordered, partially folded, and folded proteins. In studies, for each heteropolymer ensemble, the level of segmental similarity to that of natural proteins determines its ability to replicate many functions of biological fluids, including: assisting protein folding during translation; preserving the viability of fetal bovine serum without refrigeration; enhancing the thermal stability of proteins; and, behaving like synthetic cytosol under biologically relevant conditions. Molecular studies further translated protein sequence information at the segmental level into intermolecular interactions with a defined range, degree of diversity and temporal and spatial availability.

MHC Class I multimers are key reagents that are used in the identification of antigen specific T cells + an antigenic peptide. The most useful form of such a reagent involves a Class I MHC molecule that is provided ready to be loaded with an antigenic peptide of interest. However, such molecules are inherently unstable. Potential solutions to the instability have major drawbacks. Some MHC Class I molecules are provided with a conditional ligand that can be cleaved by exposure to UV light. These constructs are prone to aggregation and precipitation, must be stored and worked with in the dark, and they can have relatively poor peptide exchange efficiency. Other peptide receptive MHC class I molecules are engineered to have disulfide links holding the peptide to the MHC-I binding groove. In addition to altering natural peptide-MHC-I binding, such molecules are diffficult to express in bacterial vectors.

The implementation of ortho-quinone methide (o-QM) intermediates in complex molecule assembly represents a remarkably efficient strategy designed by Nature and utilized by synthetic chemists. o-QMs have been taken advantage of in biomimetic syntheses for decades, yet relatively few examples of o-QM-generating enzymes in natural product biosynthetic pathways have been reported. The biosynthetic enzymes that have been discovered thus far exhibit tremendous potential for biocatalytic applications, enabling the selective production of desirable compounds that are otherwise intractable or inherently difficult to achieve by traditional synthetic methods. Characterization of this biosynthetic machinery has the potential to shine a light on new enzymes capable of similar chemistry on diverse substrates, thus expanding our knowledge of Nature's catalytic repertoire.

Single-cell analyses are revolutionizing biomedicine and biology, with genomics (DNA) and transcriptomics (RNA) tools leading the way. At the protein-level, single-cell analyses are limited to mass spectrometry and immunoassays. Neither assay provides comprehensive coverage of proteome for single cells, missing key protein forms (called isoforms).  UC Berkeley researchers have developed a hybrid droplet-electrophoresis device, termed “DropBlot”, to detect proteins from patient-derived tissue biospecimens relevant to clinical medicine and pathology. The DropBlot takes advantage of water-in-oil (W/O) droplets to encapsulate single cells derived from chemically fixed tissues, thus providing a picoliter-volume reaction chamber in which said cells are lysed and subjected to harsh lysis conditions (100ºC, 2 hours), as needed for fixed cells. We report an all-in-one microdevice to facilitate cell-laden droplet loading with >98% microwell occupancy. Droplets remain intact under the electric field and protein isoforms are shown to electromigrate out of the droplet and into a microfluidic separation channel where protein sizing takes place via the action of electrophoresis in a photoactive polyacrylamide (PA) gel. DropBlot has been successfully applied to live and fixed cancer cell lines and resolved proteins with high sensitivity.