Glioblastoma is a malignant primary brain tumor that is highly invasive and infiltrative. Surgical resection and radiation therapy are not able to remove all tumor cells. Consequently, residual tumor is found in the majority of patients after surgery, causing early recurrence and decreased survival. Magnetic Resonance Imaging (MRI) is routinely used in the diagnosis, treatment planning and monitoring of glioblastoma. The contrast-enhancing region identified with MRI is generally used to guide surgery and to provide a reference for radiotherapy planning. While edema and non-enhancing regions surrounding the tumor arepotential sites of tumor infiltration, usually they are not included in surgical resection as routine MRI cannot differentiate tumorous tissues in those regions. UC Berkeley researchers have developed a novel MRI technique that can identify, non-invasively and in-vivo, areas of altered iron metabolism associated with tumor activities in the edema tissue surrounding glioblastoma. The technique uniquely delineates a hyperintense area within the edema. The method can be used to guide surgery and radiotherapy and to monitor treatment response.

The targeted intracellular delivery of protein cargos is critical for therapeutic applications such as enzyme inhibition, transcriptional modulation, and genome editing. For most tissues, the delivery of these molecules must occur in-vivo. This has historically been achieved using viral vectors or lipid nanoparticles. While significant progress has been made in engineering the tropisms of these particles towards different tissues, delivery specificity and packaging limits remain challenging. UC Berkeley researchers have developed engineered immune cells that produce and intercellularly transfer a protein and/or RNA cargo in response to contact with a predetermined antigen. Proof of concept experiments demonstrated that production of EDVs can be induced in a T cell line through either the presence of a small molecule or recognition by the T cells of a specific antigen on co-cultured cells. The researchers showed that delivery can be achieved using multiple strategies and that the system is compatible with multiple cargo proteins of interest, including Cre recombinase and S.pyogenes Cas9. 

IS110 family transposons encode a protein component (also referred to as the transposase) and a non coding RNA component (also referred to as the bridgeRNA or bRNA). In its naturally occurring context, a bRNA-bound transposase directs the integration of its cognate transposon (also referred to as the donor) into target DNA sites. The nucleic acid sequence and structure of the bRNA partially determines the sequence identify of the terminal ends of the mobilized donor, and the sequence identify of the target DNA molecule (also referred to as the target or target DNA). UC Berkeley researchers have developed a programmable gene editing technology based on IS110 family transposons that can be used for targeted insertions, deletions, excisions, inversions, replacements, and capture of DNA in vitro and in vivo. Additionally, this technology can be multiplexed to achieve complex assembles of multiple fragments of DNA.

Efficient delivery and expression of exogenous proteins in cell populations (e.g., cells in the body) for gene therapy / gene editing applications, is an important goal in biomedicine. This can be hampered by inefficient transport of enzymes from outside the body to cells within the body. When delivering nucleic acids or proteins of interest (e.g., DNA editing enzymes), most delivery methods can only reach and enter a small subset of cells within a tissue. There is a need for compositions and methods for improved delivery of proteins of interest, and such is provided herein. UC Berkeley researchers have discovered that delivery of a molecular cargo to a target cell can be more efficiently achieved by using a cell as the delivery vehicle. This can be accomplished by delivering a nucleic acid encoding an enveloped delivery vehicle (EDV) (one that comprises a molecular cargo), to a producer cell where the producer cell produces the EDV and thereby delivers the molecular cargo to neighboring cells (referred to herein as receiver cells). Thus, there is no human intervention between delivery of a subject nucleic acid (encoding the EDV) and subsequent delivery of EDVs to target cells (receiver cells).  

      Poorly designed healthcare environments can increase patient stress and delay recovery, particularly in pediatric settings (see, e.g., Devlin & Andrade 2017; Park et al. 2018; Jafarifiroozabadi et al. 2023). Traditional methods for gathering architectural design feedback, such as interviews, surveys, and focus groups, rely heavily on subjective user input, and often fail to capture the voices of children by relying on parent proxies. Physical mock-ups, a common alternative to traditional methods, provide a full-scale model of a room or space, often constructed from materials like cardboard or foam. While these mock-ups allow for some degree of spatial exploration, they are time-intensive, and limited in their ability to replicate real-world conditions; high-fidelity mock-ups which incorporate more realistic materials and finishes add expense and limit flexibility for testing multiple design iterations.       To overcome these challenges UC Berkeley researchers have developed an innovative participatory design methodology that leverages advanced virtual reality (VR), eye-tracking, and physiological/emotional biofeedback technologies to evaluate the design of pediatric healthcare environments. This comprehensive system is further enhanced by custom-developed workflows for creating dynamic, interactive room simulations that are randomized to ensure rigorous, unbiased data collection. The methodology is uniquely capable of gathering objective, quantifiable data on how pediatric patients and their families respond physiologically and emotionally to specific environmental design features.

Lipid Nanoparticles (LNPs) are a leading platform for nucleic acid delivery, widely used in therapeutics and vaccine development. However, the process of optimizing new LNP formulations has been significantly hindered by labor-intensive and costly screening methods, which require individual injections into animal models. Given the vast array of potential lipid compositions and formulation variables, these constraints severely impede the efficiency of research and development.To overcome these challenges, UC Berkeley researchers have developed a novel approach for identifying and characterizing functional nucleic acid delivery vehicles. This innovative method leverages circular RNA barcoding technology, enabling a more efficient screening process. Instead of relying on conventional cell sorting techniques, which restrict screening to specific organs and host species, this breakthrough allows direct detection of barcoded nucleic acids within circular RNAs in treated cells. By analyzing the barcodes detected, researchers can accurately determine which lipid compositions and formulations successfully delivered RNA molecules.  This technology represents a significant advancement in LNP research, offering a scalable, cost-effective solution that enhances the precision and scope of nucleic acid delivery screening.

Influenza A virus (IAV) poses an ever-evolving threat due to its high mutation rate and ability to reassort, leading to new viral variants that evade existing vaccines and treatments. Historically responsible for devastating global pandemics, including the infamous Spanish Flu, and currently fueling concerns with the spread of highly pathogenic Avian Influenza (HPAI H5N1), IAV remains a pressing global health challenge.UC Berkeley researchers have developed an Antisense Oligonucleotides (ASO) therapy that is an next-gen approach to combating influenza by modulating IAV activity at its genetic level. Unlike traditional antivirals or seasonal vaccines that struggle to keep up with mutating strains, this ASOs therapy targets the ultra-conserved U12 region within the IAV RNA genome, offering broad-spectrum efficacy against even the most elusive influenza strains.  

      Biologics are antibodies produced by genetically engineered cells and are widely used in therapeutic applications. Examples include pembrolizumab (Keytruda) and atezolizumab (Tecentriq), both employed in cancer immunotherapy as checkpoint inhibitors to restore T- cell immune responses against tumor cells. These biologics are produced by engineered cells in bioreactors in a process that is highly sensitive to the bioreactor environment, making it essential to integrate process analytical technologies (PAT) for closed-loop, real-time adjustments. Recent trends have focused on leveraging integrated circuit (IC) solutions for system miniaturization and enhanced functionality, for example enabling a single IC that monitors O2, pH, oxidation-reduction potential (ORP), temperature, and glucose levels. However, no current technology can directly and continuously quantify the concentration and quality of the produced biologics in real-time within the bioreactor. Such critical measurements still rely on off-line methods such as immunoassays and mass spectrometry, which are time-consuming and not suitable for real- time process control.       UC Berkeley researchers have developed a microsystem for real-time, in-vivo monitoring of antibody therapeutics using structure-switching aptamers by employing an integrator-based readout front-end. This approach effectively addresses the challenge of a 100× reduction in signal levels compared to the measurement of small-molecule drugs in prior works. The microsystem is also uniquely suited to the emerging paradigm of “living pharmacies.” In living pharmacies, drug-producing cells will be hosted on implantable devices, and real-time monitoring of drug production/diffusion rates based on an individual’s pharmokinetics will be crucial.

      Current clinical practice for detecting low-concentration molecular biomarkers requires sending samples to centralized labs, leading to high costs and delays. Successful point-of-care (POC) diagnostic technology exist, such as the paper-based lateral-flow assay (LFA) used for pregnancy tests and SARS-CoV-2 rapid antigen tests, or miniaturized instruments such as the Abbot i-Stat Alinity. However, the former provides binary results or limited quantitative accuracy, and the latter is too expensive for in-home deployment. A promising approach for POC diagnostics, offering tailored circuit optimization, multiplexed detection, and significant cost and size reductions, is millimeter-sized CMOS integrated circuits coupled with microfluidics. Recent demonstrations include protein, DNA/RNA, and cell detection. The current complexity of system packaging (e.g., wire/flip-chip bonding) makes integrating microfluidics with more sophisticated functions challenging, and often-required syringe pumps and tubing are operationally unfriendly, limiting current approaches.       UC Berkeley researchers have developed a fully integrated, multi-mode POC device that requires single-step assembly and operates autonomously. Drawing inspiration from RFID technology and implantables, they have introduced inductively-coupled wireless powering and communication functionality into a CMOS bio-analyzer. With the chip being fully wireless, the die can be easily integrated into a substrate carrier, achieving a completely flat surface that allows for seamless bonding with the microfluidic module. In the final product, the device will be sealed in a pouch inside a vacuum desiccator. The user tears the pouch, adds a drop of sample, and the system automatically begins operation. The operation window can last up to 40 minutes, making the process insensitive to time delays. The present CMOS bio-analyzer integrates pH-sensing and amperometric readout circuits for both proton-based and redox-based immunoassays.

      Integrating microelectronics with microfluidics, especially those implemented in silicon-based CMOS technology, has driven the next generation of in vitro diagnostics. CMOS/microfluidics platforms offer (1) close interfaces between electronics and biological samples, and (2) tight integration of readout circuits with multi-channel microfluidics, both of which are crucial factors in achieving enhanced sensitivity and detection throughput. Conventionally bulky benchtop instruments are now being transformed into millimeter-sized form factors at low cost, making the deployment for Point-of-Care (PoC) applications feasible. However, conventional CMOS/microfluidics integration suffers from significant misalignment between the microfluidics and the sensing transducers on the chip, especially when the transducer sizes are reduced or the microfluidic channel width shrinks, due to limitations of current fabrication methods.       UC Berkeley researchers have developed a novel methodology for fabricating microfluidics platforms closely embedded within a silicon chip implemented in CMOS technology. The process utilizes a one-step approach to create fluidic channels directly within the CMOS technology and avoids the previously cited misalignment. Three types of structures are presented in a TSMC 180-nm CMOS chip: (1) passive microfluidics in the form of a micro-mixer and a 1:64 splitter, (2) fluidic channels with embedded ion-sensitive field-effect transistors (ISFETs) and Hall sensors, and (3) integrated on-chip impedance-sensing readout circuits including voltage drivers and a fully differential transimpedance amplifier (TIA). Sensors and transistors are functional pre- and post-etching with minimal changes in performance. Tight integration of fluidics and electronics is achieved, paving the way for future small-size, high-throughput lab-on-chip (LOC) devices.

Programmable base editors are a class of genome editing effector proteins that can make precise, targeted changes to DNA base pairs in a narrow window of genomic sequence without reliance on double-stranded breaks in chromosomal DNA. Base editor proteins include a deaminase fused to a CRISPR-Cas effector protein (e.g., nCas9). Base editor proteins are challenging to produce in high yields via recombinant expression in E. coli. This has limited its clinical use to mRNA/gRNA delivery; this is in stark contrast to Cas9 nuclease, which has been used in multiple clinical trials in its protein-based RNP format. There is a need for base editor proteins that are highly active and can be produced with high yield. Such is provided by the compositions and methods described herein. UC Berkeley researchers have overcome the limitations associated with producing a CRISPR-Cas base editor by creating a CRISPR-Cas fusion protein with the deaminase fusion protein.  

In magnetic resonance imaging (MRI) scanners, the detection of nuclear magnetic resonance (NMR) signals is achieved using radiofrequency, or RF, coils. RF coils are often equivalently called “resonance coils” due to their circuitry being engineered for resonance at a single frequency being received, for low-noise voltage gain and performance. However, such coils are therefore limited to a small bandwidth around the center frequency, restricting MRI systems from imaging more than one type of nucleus at a time (typically just hydrogen-1, or H1), at one magnetic field strength.To overcome the inherent restriction without sacrificing performance, UC Berkeley researchers have developed an MRI coil that can perform low-noise voltage gain at arbitrary relevant frequencies. These frequencies can be programmably chosen and can include magnetic resonance signals from any of various nuclei (e.g., 1H, 13C, 23Na, 31P, etc.), at any magnetic field strength (e.g., 50 mT, 1.5T, 3T, etc.). The multi-frequency resonance can be performed in a single system. The invention has further advantages in terms of resilience due to its decoupled response relative to other coils and system elements.

Although viral delivery of CRISPR genome editors is the most widely used method for in vivo cell editing, viral vectors can be immunogenic, carry the risk of vector genome integration and can induce off-target DNA damage due to continuous genome editor expression. Lipid-nanoparticle (LNP):mRNA complexes are non-virally derived vehicles for in vivo delivery that have provided for genome editing in the liver. However, developing LNP:mRNA complexes that can edit non-liver tissues remains a challenge.  UCB researchers have created new LNP compositions and methods for delivery that have increased efficiency for delivering a molecular payload such as CRISPR-Cas effector proteins, guide RNAs, and/ nucleic acids encoding same. 

Optimizing the editing efficiency of CRISPR-mediated enzymes is still needed.  This is especially true in therapeutic use cases, when it would be ideal to attain high rates of editing via a low, transient dose of the enzyme in the ribonucleoprotein (RNP) format used for multiple ex vivo clinical trials. Because many CRISPR enzymes are of bacterial origin, fusion to NLS motifs can greatly enhance editing efficiency. However, CRISPR protein yields can decrease – sometimes dramatically – if the construct bears toomany NLSs. UC Berkeley researchers have developed CRISPR proteins with enhanced editing efficiencies by introducing multiple nuclear localization signal (NLS) fused at rationally selected sites within the backbone of CRISPR-Cas9. These Cas9 variants showed they can improve editing efficiency in T cells compared to constructs with terminally-fused NLS sequences and can be produced with high purity and yield.  

Inflatable pouches are attractive as actuators and structural links in soft robots due to their low deflated profile and high deformation ratio. Particularly compelling for minimally invasive surgery, deflated robots/actuators may be deployed in small form factors and maneuver delicately in tight spaces once inflated. However, current fabrication methods do not readily scale for production of actuators with less than 1 mm feature sizes; they often require precision handling of separator films; and/or there are limited multilayer integration capabilities. Fully miniaturized, high degree-of-freedom surgical pouch robots and actuators have not yet been realized.To overcome these challenges, UC Berkeley researchers have developed a rapid, monolithic, and scalable manufacturing method for fabricating thin-film-based pneumatic pouch soft robots. Small features (less than 0.3 mm) can be patterned at high speeds and using commercially available manufacturing tools while maintaining film planarity. Resulting robots can have complex, multilayer structures including single- and bi-directional joint actuators, structural links, integrated in-plane air channels, through-holes for interlayer connectivity, and air inlets to a supply manifold—from a single integrated processing step. Researchers have demonstrated a miniature four finger hand which can dexterously manipulate a cube (8 degrees of freedom), as well as an 10 degree-of-freedom planar arm with a gripper which can maneuver around obstacles. Entire pouch robot structures can have un-inflated thickness of less than 300 um and be inherently soft, allowing the robots to be used in tight spaces with fragile tissues for surgical applications.

High flux (e.g., greater than 1012 n/s/cm2) neutrons with energies between 8 and 30 MeV are needed for a number of applications including radioisotope production. However, none of the existing neutron sources available can fulfill these requirements. Neutron flux intensities from typical neutron sources using Deuterium-Tritium (DT) fusion are typically more than 2 orders of magnitude lower in intensity than what is needed for making production practical. Deuterium-Deuterium (DD) fusion sources provide a spectrum which is too low in energy to perform the nuclear reactions needed for isotope production. High-energy proton accelerator-driven spallation sources produce isotopes with significant co-production of unwanted radioisotopes, due to a neutron spectrum which is far higher in energy than required. While accelerator-driven neutron sources using deuteron breakup have been shown to be a viable pathway for producing a range of isotopes including actinium-225 1, a limited number of machines capable of producing ~30 MeV deuteron beams exist commercially. To address this problem, researchers at UC Berkeley have developed systems and methods for producing radionuclides using accelerator-driven fast neutron sources, and more specifically for producing actinium-225, an inherently-safe, fast neutron source based on low energy proton accelerators used throughout the world to support positron emission tomography.

      While robots have proven effective in enhancing the precision and time efficiency of MRI-guided interventions across various medical applications, safety remains a formidable challenge for robots operating within MRI environments. As the robots assume full control of medical procedures, the reliability of their operation becomes paramount. Precise control over robot forces is particularly crucial to ensure safe interaction within the MRI environment. Furthermore, the confined space in the MRI bore complicates the safe operation of human-robot interaction, presenting challenges to maneuverability. However, there exists a notable scarcity of force-controlled robot actuators specifically tailored for MRI applications.       To overcome these challenges, UC Berkeley researchers have developed a novel MRI-compatible rotary series elastic actuator module utilizing velocity-sourced ultrasonic motors for force-controlled robots operating within MRI scanners. Unlike previous MRI-compatible SEA designs, the module incorporates a transmission force sensing series elastic actuator structure, while remaining compact in size. The actuator is cylindrical in shape with a length shorter than its diameter and integrates seamlessly with a disk-shaped motor. A precision torque controller enhances the robustness of the invention’s torque control even in the presence of varying external impedance; the torque control performance has been experimentally validated in both 3 Tesla MRI and non-MRI environments, achieving a settling time of 0.1 seconds and a steady-state error within 2% of its maximum output torque. It exhibits consistent performance across low and high external impedance scenarios, compared to conventional controllers for velocity-sourced SEAs that struggle with steady-state performance under low external impedance conditions.

UCB researchers have developed a novel class of bright, fluorescent rhodamine dyes with a novel structural modification resulting in a deep red shift relative to the parent carborhodamine dye, with the new dye absorbing and emitting near-infrared light in the same region as the commercially successful silicon rhodamine dyes. Biological imaging with near-infrared light is advantageous for numerous biological and surgical applications.  Furthermore, bis-trifluoromethyl carborhodamines offer improved properties desirable for biological imaging applications due to their unique physical and electronic properties. 

UC Berkeley researchers have developed systems and methods of using a split guide RNA (gRNA) to extend the lower size range of RNA detectable by Cas13a. When Cas13a is in complex with a split gRNA and capture RNA (capRNA), it can directly detect single-stranded RNA ranging from 8-24 nucleotides. The Cas13a split gRNA system is sensitive, enabling detection of femtomolar levels of RNA, and specific to sequence mismatches and gaps. We show that the split Cas13a RNP can detect miRNAs from extracted cell RNA. To detect a new RNA target, only the sequence of the capRNA needs to be modified; the same Cas13a RNP can be used for all targets. The capRNA can be tuned to maximize sensitivity of specificity, depending on the desired application. The split gRNA system expands the current use of Cas13a in molecular diagnostics and opens the door for its use in miRNA discovery.

Electrodermal activity (EDA) has traditionally been used for monitoring mental activity by measuring skin conductance (SkinG) at locations with high sweat gland density. However, EDA has not been considered useful for physical activity due to baseline shifts caused by sweat accumulation at the skin/electrode interface.

         While nuclear magnetic resonance (NMR) is one of the most universal synthetic chemistry tools for its ability to measure highly specific kinetic and structural information nondestructively/noninvasively, it is costly and low-throughput primarily due to the small sample-size volumes and expensive equipment needed for stringent magnetic field homogeneity. Conversely, zero-to-ultralow field (ZULF) NMR is an emerging alternative offering similar chemical information but relaxing field homogeneity requirements during detection. ZULF NMR has been further propelled by recent advancements in key componentry, optically pumped magnetometers (OPMs), but suffers in scope due to its low sensitivity and its susceptibility to noise. It has not been possible to detect most organic molecules without resorting to hyperpolarization or 13C enrichment using ZULF NMR.         To overcome these challenges, UC Berkeley researchers have developed a multi-channel ZULF spectrometer that greatly improves on both the sensitivity and throughput abilities of state-of-the art ZULF NMR devices. The novel spectrometer was used in the first reported detection of organic molecules in natural isotopic abundance by ZULF NMR, with sensitivity comparable to current commercial benchtop NMR spectrometers. A proof-of-concept multichannel version of the ZULF spectrometer was capable of measuring three distinct chemical samples simultaneously. The combined sensitivity and throughput distinguish the present ZULF NMR spectrometer as a novel chemical analysis tool at unprecedented scales, potentially enabling emerging fields such as robotic chemistry, as well as meeting the demands of existing fields such as chemical manufacturing, agriculture, and pharmaceutical industries.

         Recent advancements in nuclear magnetic resonance (NMR) spectroscopy have underscored the need for novel instrumentation, but current commercial instrumentation performs well primarily for pre-existing, mainstream applications. Modalities involving, in particular, integrated electron-nuclear spin control, dynamic nuclear polarization (DNP), and non-traditional NMR pulse sequences would benefit greatly from more flexible and capable hardware and software. Advances in these areas would allow many innovative NMR methodologies to reach the market in the coming years.          To address this opportunity, UC Berkeley researchers have developed a novel high-speed, high-memory NMR spectrometer and hyperpolarizer. The device is compact, rack-mountable and cost-effective compared to existing spectrometers. Furthermore, the spectrometer features robust, high-speed NMR transmit and receive functions, synthesizing and receiving signals at the Larmor frequency and up to 2.7GHz. The spectrometer features on-board, phase-sensitive detection and windowed acquisition that can be carried out over extended periods and across millions of pulses. These and additional features are tailored for integrated electron-nuclear spin control and DNP. The invented spectrometer/hyperpolarizer opens up new avenues for NMR pulse control and DNP, including closed-loop feedback control, electron decoupling, 3D spin tracking, and potential applications in quantum sensing.

Class 2 CRISPR-Cas are streamlined versions in which a single Cas protein bound to RNA is responsible for binding to and cleavage of a targeted sequence. Theprogrammable nature of these minimal systems has facilitated their use as a versatile technology for genome editing.  CRISPR-Cas enzymes with reduced requirements for a protospacer-adjacent motif (PAM) sequence adjacent to the target site could improve the breadth of target sites available for genome editing.  UC Berkeley researchers have developed a novel PAM-loose 12a variants, nucleic acids encoding the variant Cas12a proteins and systems using these variants that make the Cas12a-based CRISPR technology much easier to design a DNA target for carrying out genome editing in human cells. 

mRNA-based cancer therapies include vaccination via mRNA delivery of tumor neoantigens, delivery of mRNA encoding for immune checkpoint and other protein therapeutics, and induced expression of anticancer surface proteins such as CAR expression in T cells. Success requires transfection of a critical number of immune cells together with appropriate immune-stimulation to effectively drive anti-tumor responses. UC Berkeley researchers have developed an adjuvant-assisted mRNA LNP delivery method that uses mRNA LNP and adjuvant to enhance delivery of nucleic acids to immune cells in vivo and stimulate immune cells. They demonstrated the use of this system to reduce mRNA reporter protein expression in the liver and enhance protein expression in the spleen in mice and also demonstrated this system can be used to genetically engineer T cells by delivering a Cre-recombinase mRNA construct- transfection and editing of approximately 4% of T cells is achieved in vivo. The immune response is superior in our system compared to current, commercial lipid nanoparticle delivery technologies.

TnpB protein has generated interest as a potential compact genome-editing tool, due to the short amino acid sequence (408 AAs for ISDra2 TnpB), which overlaps with the wRNA sequence in their genomes of origin. There is a need for compositions and methods that provide more efficient TnpB systems. UC Berkeley researchers have created variant TnpB proteins and variant wRNAs that increase cleavage activity and/or DNA binding activity (e.g., revealed as endonuclease activity such as on-target endonuclease activity). These variant TnpB proteins include an amino acid sequence having one or more amino acid substitutions relative to a corresponding wild type TnpB protein. Also provided are variant TnpB wRNAs that can form a complex with a TnpB protein and a second nucleotide sequence that can hybridize to a target sequence of a target nucleic acid, thereby guiding the complex to the target sequence.