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

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.

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.

There are many applications in which there is the need for storage of matter prone to biological contamination for extended period, from days to years. These applications include food, agricultural products, biological matter, and biotechnological matter.  Isobaric (constant pressure) freezing is one method of food preservation, however, freezing causes the deterioration of the quality of the preserved matter. High pressure processing followed by sterilization by refrigerating it at 4 ºC is common, but microorganisms can grow at 4 ºC and the product is sterile for limited periods of time of days. Thus, there is still a need for good preservation technologies that inhibits or reduce growth of microbial contaminants while maintaining their fresh-like characteristics and nutritional value.  UC Berkeley inventors and others have developed a device and methods for long term preservation of matter that inhibits or eliminates biological contaminants with isochoric freezing. 

Certain difficult optimization problems, such as the traveling salesman problem, can be solved using so-called analog Ising machines, in which electronic components (such as certain arrangements of diodes or electronic switches) implement an analog of a well-studied physical system known as an Ising machine. The problem is recast so that its solution can be read off from the lowest-energy configuration of the analog Ising machine, a state which the system will naturally evolve towards. While promising, this methodology suffers major drawbacks. Firstly, the number of subunits, known as “spins”, in the analog Ising machines, as well as the number of connections between these subunits, can grow substantially with problem size. Secondly, existing implementations of this principle rely on chip constructions which are optimized for one or a few problems, and are not sufficiently reprogrammable to be repurposed efficiently for other applications. To address these problems, researchers at UC Berkeley have developed a device known as a Field-programmable Ising machine which can be adapted to implement an analog Ising machine using a variety of hardware designs, such as the diodes and switches mentioned above. These Ising machines can be effectively reprogrammed to efficiently solve a wide array of problems across various domains. The inventors have shown that this design can be applied to SAT (“Satisfiability”) problems, a class known to be similar to the traveling salesman problem, in that the number of spins needed and their level of connectivity do not grow too quickly with problem size.

Rhamnolipids (RLs) are a class of bacterially produced biosurfactants that possess antimicrobial as well as surface-active properties. While RLs have broad utility in industry as antimicrobial biosurfactants, their anionic nature limits the efficacy of these molecules in certain applications. Alternatively, rhamnolipid esters (RLEs) exhibit improved properties as nonionic surfactants. However, a major challenge in RLE application in the commercial arena is that, to date, they are only reliably accessed via chemical synthesis, a costly and unsustainable approach.To address this problem, UC Berkeley researchers have developed a novel, reliable microbial source for biosynthesized RLEs enabling their production in an efficient, sustainable, and renewable manner. Additionally, three novel rhamnolipid methyl ester (RLME) congeners have been produced and a new enzyme for RLE production identified. The produced RLEs are expected to be more effective than RLs in many ways, including antifungal activity and hydrocarbon solubilization.

Metamaterials are constructed from regular patterns of simpler constituents known as unit cells. These engineered metamaterials can exhibit exotic mechanical properties not found in naturally occurring materials, and accordingly they have the potential for use in a variety of applications from running shoe soles to automobile crumple zones to airplane wings. Practical design using metamaterials requires the specification of the desired mechanical properties based on understanding the precise unit cell structure and repeating pattern. Traditional design approaches, however, are often unable to take advantage of the full range of possible stress-strain relationships, as they are hampered by significant nonlinear behavior, process-dependent manufacturing errors, and the interplay between multiple competing design objectives. To solve these problems, researchers at UC Berkeley have developed a machine learning algorithm in which designers input a desired stress-strain curve that encodes the mechanical properties of a material. Within seconds, the algorithm outputs the digital design of a metamaterial that, once printed, fully encapsulates the desired properties from the inputted stress-strain curve. This algorithm produces results with a fidelity to the desired curve in excess of 90%, and can reproduce a variety of complex phenomena completely inaccessible to existing methods.

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.

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.

For decades, researchers have been developing “cool roof” materials to cool buildings and save on energy usage from air conditioning. Cool roof materials are engineered to maximize infrared thermal emission, allowing heat to be effectively radiated into outer space and the building to cool down. Conventional cool roof materials emit heat even when it is cold outside, which exacerbates space heating costs and can outweigh energy-saving benefits. A temperature adaptive radiative coating (TARC) material was developed in 2021 that adapts its thermal emittance to ambient temperatures using metal-insulator transitions in vanadium oxide. TARC is projected to outperform existing roof materials in most climate areas, but the complicated structure required high-cost fabrication techniques such as photolithography, pulsed laser deposition, and XeF2 etching, which are not scalable.To address this problem, UC Berkeley researchers have developed a new scalable temperature-adaptive radiative coating (STARC). STARC has the same thermal emittance switching capability as TARC, allowing the thermal emittance to be switched between high- and low- emittance states at a preset temperature. However, STARC can be produced using high-throughput, roll-to-roll methods and low-cost materials. The STARC material also has an improved lifetime. As an added benefit, while cool roof materials are often engineered with uniformly low solar-absorption, the color and solar absorption of STARC can be tuned for aesthetic purposes or to meet local climate-specific needs.

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.

BACKGROUND: Triacetic acid lactone (TAL) is an important building block for a diverse set of chemicals and plastic polymers. Native pathways using microbes can serve as an environmentally-friendly and renewable source of TAL production. However, microbial production of TAL is limited to a few platform microbes. Further, native pathways using platform microbes such as E. coli show toxicity to TAL, which reduces its production. Therefore, there is a need for thiolases that provide higher yield and can be used in additional microorganisms. TECHNOLOGY OVERVIEW: Researchers at the Joint BioEnergy Institute (JBEI) have discovered novel thiolases for production of Triacetic acid lactone (TAL) via platform microorganisms. The discovered thiolases achieved production of 2.77 g/L of TAL when expressed in E. coli, which is the highest titer production reported using E. coli. The discovered thiolases were identified from homologs of Cupriavidus necator, and their TAL production was verified by in vitro and in vivo testing. Unlike the energetically expensive native TAL-producing enzyme 2-pyrone synthase, the discovered thiolases utilize acetyl-CoA instead of malonyl-CoA as an extension unit. The Burkholderia thiolases identified by the researchers can be engineered to further boost production of TAL in existing platform microorganisms such as E. coli, as well as other microorganisms such as yeasts. DEVELOPMENT STAGE: Validated system

The CRISPR-Cas system is now understood to confer bacteria and archaea with acquired immunity against phage and viruses. CRISPR-Cas systems consist of Cas proteins, which are involved in acquisition, targeting and cleavage of foreign DNA or RNA, and a CRISPR array, which includes direct repeats flanking short spacer sequences that guide Cas proteins to their targets. The programmable nature of these systems has facilitated their use as a versatile technology that is revolutionizing the field of genome manipulation. There is a need in the art for additional CRISPR-Cas systems with improved cleavage and manipulation under a variety of conditions and ones that are particularly thermostable under those conditions. UCB researchers created a set of efficient CRISPR-Cas9 proteins from a thermostable Cas9 from the thermophilic bacterium Geobacillus stearothermophilus (GeoCas9) through directed evolution. The gene editing activity of the evolved mutant proteins was improved by up to four orders of magnitude compared to the wild-type GeoCas9. The researchers showed that the gene editors based on the evolved GeoCas9 can be effectively assembled into lipid nanoparticles (LNP) for the rapid delivery to different cell lines in vitro as well as different organs or tissues in vivo. The LNP-based delivery strategy could also be extended to other gene editors.  

The inventors have developed a novel 3D printing technique, named Non-Planar Granular 3D Printing (NGP), which selectively deposits a liquid binder into granular particles, enabling rapid fabrication of complex 3-dimensional objects. For this new method, an industrial robotic arm is equipped with a dispenser attached to a long metal needle, called a liquid deposition end-effector, and a container of granular particles, such as sand, beads, or powders. The needle moves freely as it injects the binding liquid into the granular material. Like other 3D printing methods, NGP can use a CAD 3D model and conventional slicing software to produce a robotic toolpath following a desired height and width. However, the advantage of the process lies in its ability to 3D print objects non-planarly, by moving the extruder’s dispensing tip freely within the granular medium. The selective application of the binding liquid causes the particles to bond together, forming parts of the 3D printed object. Meanwhile, the loose particles remaining in the container temporarily support the weight of the wet particles while they cure. This unique approach enables the creation of complex geometric forms without the need for supporting structures that are typical in traditional 3D printing methods, thereby eliminating material waste typically associated with such processes. After the completion of the process, and the binding material has cured, the hard objects can be easily extracted from the container, leaving behind the remaining loose particles, which can be repeatedly re-used.   

Injectable hydrogels are attracting increasing interest for the therapeutic delivery of cells to tissue. However, these hydrogel formulations can suffer from engraftment efficiencies of less than 5% when delivered to native tissue. These poor engraftment efficiency rates are often attributed to high shear stresses during delivery and inability to provide a stable three-dimensional niche at the delivery site. The inventors have developed a technique for encapsulating cells in the pore space between microscopic hydrogel particles by employing the yield stress fluid properties of packs of microgels. The technology protects the cells from mechanical stress during delivery and facilitates integration to the native tissue. During delivery, the packs of microgels undergo plug flow in which the pressure drop across the length of the pipe is compensated solely by frictional forces at the interface between the pipe wall and microgels. At the delivery site, the pack of microgels behave as an elastic solid across the range of physiological frequencies and provide a stable 3D culture paradigm to support engraftment.Furthermore, the inventors address the challenges associated with cryopreserving, transporting, and delivering this injectable formulation from benchtop-to-bedside with a concept for a perfusable delivery device. The device encapsulates cells in the pore space of the microgels and confines the formulation to a fixed volume where researchers can perfuse liquid freeze/thaw or maintenance media, differentiation factors, and anti-inflammatory agents at virtually any time prior to delivery to the tissue. The porous microgel network facilitates this process and makes the formulation amenable to transport and storage which would otherwise be unattainable in hydrogel formulations.

Xylella fastidiosa is a plant pathogenic bacterium that causes various diseases in California and elsewhere. UC Berkeley researchers have collected strains of this pathogen from symptomatic grapevines from different regions in California. These are pure cultures of a bacterial plant pathogen.

In this technology, the inventors introduce additives to purposely change the morphology of polycaprolactone (PCL) by increasing the bending and twisting of crystalline lamellae. These morphological changes immobilize chain-ends preferentially at the crystalline/amorphous interfaces and limit chain-end accessibility by the embedded processive enzyme. This chain end redistribution reduces the polymer-to-monomer conversion from >95% to less than 50%, causing formation of highly crystalline plastic pieces including microplastics. By synergizing both random chain scission and processive depolymerization, it is feasible to navigate morphological changes in polymer/additive blends and to achieve near complete depolymerization. The random scission enzymes in the amorphous domains create new chain ends that are subsequently bound and depolymerized by processive enzymes. Present studies further highlight the importance to consider host polymer morphological effects on the reactions catalyzed by embedded catalytic species.This is part of a patent family in compostable plastics.  

The inventors have developed ion-selective potentiometric sensors for monitoring soil analytes with naturally degradable substrate, conductor, electrode, and encapsulant materials that minimize pollution and ecotoxicity. This novel sensor-creation method uses printing technologies for the measurement of nitrate, ammonium, sodium, calcium, potassium, phosphate, nitrite, and others. Monitoring soil analytes is key to precision agriculture and optimizing the health and growth of plant life. 

The invention is flexible/stretchable soft battery for devices that seamlessly integrate for human-machine interface applications.  Such reconfigurable and soft batteries will play an important role as power sources can take up a large space in a system. To this end, the conformable/stretchable batteries of the embodiments provide an ideal power sources for these devices. Wearable devices attract lots of interest with a market share of over $116.2 billion/year, projected to be $265.4 billion by 2026

With the two-dimensional scaling of silicon field-effect transistors reaching fundamental limits, new functional improvements to transistors, as well as novel computing paradigms and vertical device integration at the architecture-level, are currently under intense study. Gate oxides play a critical role in this endeavor, as it’s a common performance booster for all devices, including silicon, new channel materials with potential for higher performance, and even materials suitable for three-dimensional integrated transistors.With the scaling of lateral dimensions in advanced transistors, an increased gate capacitance is desirable both to retain the control of the gate electrode over the channel and to reduce the operating voltage. To pursue these performance gains, UC Berkeley researchers invented a new heterostructure insulator material where: 1) the material possesses specific ferroic order such as ferroelectricity/anti-ferroelectricity or a mixture of both; 2) the overall dielectric property such as the permittivity is determined by the stacking order of different layers rather than exact volume fraction of the constituents; and 3) the material is composed of one or several repetition of ultra thin superlattice periods ranging from a few angstroms to 3 nm.

The inventors have developed a highly scalable multiplexed approach to increase the density of graphene nanoribbon- (GNR) based transistors. The technology forms a single device/chip (scale to 16,000 to >1,000,000 parallel transistors) on a single integrated circuit for single molecule biomolecular sensing, electrical switching, magnetic switching, and logic operations. This work relates to the synthesis and the manufacture of molecular electronic devices, more particularly sensors, switches, and complimentary metal-oxide semiconductor (CMOS) chip-based integrated circuits.Bottom-up synthesized graphene nanoribbons (GNRs) have emerged as one of the most promising materials for post-silicon integrated circuit architectures and have already demonstrated the ability to overcome many of the challenges encountered by devices based on carbon nanotubes or photolithographically patterned graphene. The new field of synthetic electronics borne out of GNRs electronic devices could enable the next generation of electronic circuits and sensors.