Bento is an open-source software toolkit that uses single-molecule information to enable spatial analysis at the subcellular scale. Bento ingests molecular coordinates and segmentation boundaries to perform three analyses: defining subcellular domains, annotating localization patterns, and quantifying gene-gene colocalization. The toolkit is compatible with datasets produced by commercial and academic platforms. Bento is integrated with the open-source single-cell analysis software ecosystem.

Researchers at the University of California, Davis have developed advancements in understanding exodermal differentiation in plant roots highlighting the role of two transcription factors in plant adaptation and survival.

A novel bioluminescent platform for in vivo tracking and visualization of RNA dynamics without the need for excitation light.

Researchers at the University of California, Davis have developed a novel cell segmentation technology for accurate analysis of non-spherical cells and that offers a comprehensive, high-throughput approach for analyzing the transcriptomic and metabolomic data to study complex biological processes at the single-cell level.

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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.

      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.

      Goniophotometers measure the luminance distribution of light emitted or reflected from a point in space or a material sample. Increasingly there is a need for such measurements in real-time, and in real-world situations, for example, for daylight monitoring or harvesting in commercial and residential buildings, design and optimization of greenhouses, and testing laser and display components for AR/VR and autonomous vehicles, to name a few. However, current goniophotometers are ill-suited for real-time measurements; mechanical scanning goniophotometers have a large form factor and slow acquisition times. Parallel goniophotometers take faster measurements but suffer from complexity, expense, and limited angular view ranges (dioptric angular mapping systems) or strict form factor and sample positioning requirements (catadioptric angular mapping systems). Overall, current goniophotometers are therefore limited to in-lab environments.      To overcome these challenges, UC Berkeley researchers have invented an optical sensor  for parallel goniophotometry that is compact, cost-effective, and capable of real-time daylight monitoring. The novel optical design addresses key size and flexibility constraints of current state-of-the-art catadioptric angular mapping systems, while maximizing the view angle measurement at 90°. This camera-like, angular mapping device could be deployed at many points within a building to measure reflected light from fenestrations, in agricultural greenhouses or solar farms for real-time monitoring, and in any industry benefitting from real-time daylight data.

A novel method for producing dissolvable alginate microfibers critical for advanced tissue engineering and microfluidic network fabrication.

         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.

Researchers at the University of California, Davis have discovered an Arthrobacter bacterial strain that promotes suberization of the endodermis in sorghum roots. Suberin, a poly-fatty acid polymer, acts as a physical barrier in sorghum roots, helping to prevent infection by the parasitic plant Striga hermonthica, a significant threat to sorghum production. These microbial-based solutions offer a cost-effective and easily deployable strategy to manage Striga infection in the predominantly smallholder farmer-driven sorghum cultivation of sub-Saharan Africa.

      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. 

Cell culture plates are an essential tool for cell biology research. They are used to grow cells in a controlled environment, which allows for study of the effects of different conditions on cell growth and development. The plates are typically made of plastic or glass and may have one or more wells, each of which can hold a small amount of cell culture media. The media provides the cells with the nutrients the cells need to grow and divide. Cell culture plates may be used in incubators to grow cells in a controlled environment as well as in glove boxes. The incubator provides the cells with the necessary conditions for growth, including a constant temperature, humidity, and atmosphere.Conventional cell culture plates are susceptible to evaporation, which causes increased osmolarity of cell culture media. This in turn causes unnatural growth of cells and well-to-well variability due to uneven evaporation. In addition, evaporation causes increased concentration of the salts involved in electrical signaling of electrically active cell types, changing the ionic gradients across the cell membrane, and affecting all characteristics of the initiation, transmission (and computation) in electrically active cells such as cardiac or neuronal cells. It is also difficult to maintain desired dissolved gas concentration with standard cell culture plates. This generally requires use of a compressed gas system, which uses gas regulators, sensors that are expensive and have limited lifetimes, and feedback control as well as a glove box for culture and/or handling.An incubator is used to maintain the desired temperature of the cell culture plates. The incubator impedes access to the cultures for feeding, for microscopy, etc. Furthermore, observation equipment for use inside an incubator needs to be designed to resist incubator conditions (e.g., body temperature heat and humidity). Incubators also take up significant space and packing of incubators in a laboratory is space-inefficient relative to the form factor of the cell culture plates. As the number of cell culture plates in a single incubator increases, the ability of the incubator to perform its function decreases, since there is a minimum number of times an incubator may be accessed per week per cell culture vessel. However, every time the incubator is accessed, it is unable to perform its functions for a prolonged period of time, e.g., over 30 minutes. Another technical problem is that cell culture devices that use an air gap for gas exchange have an increased risk of microbial contamination via that air gap. This makes it difficult to perform manual cell culture experiments over the course of months without contamination. In addition, cross-contamination is more likely if multiple different experiments are being performed in the same laboratory. Thus, there is a need for cell culture vessels and systems that overcome these problems.

Researchers at the University of California, Davis have developed a technology providing the creation of stable analogs of glycosphingosines and gangliosides containing O-acetylated sialic acid for extensive biological and medical applications.

The invention presents a microfluidic platform equipped with specialized trapping arrays and droplet generation capabilities, enabling precise control over the formation of microvortices within cell-laden droplets. This novel system facilitates the study of cell-cell interactions at a single-cell level, offering configurable microenvironments for analyzing cell dynamics and pair relationships.

An innovative sulfoxide-containing MS-cleavable cross-linker, DBrASO, specifically designed for cysteine residues and aimed at enhancing protein-protein interactions studies and protein complexes architecture analysis.

An innovative mass spectrometry platform that utilizes sulfoxide-containing MS-cleavable heterobifunctional photoactivated cross-linkers to enhance protein structural elucidation.

A breakthrough technology using insulin-secreting cells and stem cells to enhance wound healing and reduce scar formation.

A novel method and device for high-throughput sorting of cells in suspension, particularly focusing on the separation of key cellular blood components of the immune system. The patent application presents a novel approach to high-throughput cell sorting, particularly suitable for applications in medicine and biotechnology where precise separation of cell populations is crucial.

A design for compact and energy-efficient microvalves for use in lab-on-a-chip microfluidic devices

Researchers at the University of California, Davis have developed improved variants of a Heparosan synthase supporting efficient synthesis of heparosan, heparin, and heparan sulfate analogs.

Researchers at the University of California, Davis have developed an innovative method for efficient, high-yield production and easy purification of Human Milk Oligosaccharides (HMOs) using a Multistep One-Pot Multienzyme (MSOPME) process.

Researchers at the University of California, Davis have developed a method for preparing a glycan product containing a nonulosonic acid moiety by means of legionaminic acid transferase fusion proteins

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