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(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. 

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.

Recombinantly produced p27 for use in screening inhibitors of Cdk4/6;Cyc6/p27 kinase complex

Cyclin Dependent Kinases (Cdk) 4 and 6 promote cell proliferation through their kinase activity. The active cellular form of the Cdk 4 or 6 enzyme forms a complex with both cyclin D (CycD) and p27 in vivo. Current therapeutics that target Cdk4 or 6 were generated in a complex that lacked p27 because of difficulties in expressing a recombinant form of p27. This technology describes a recombinantly produced engineered form of p27 that forms stable complexes with Cdk4/6 and CycD in vitro.

Methods To Generate Novel Acyl-Trna Species

The inventors have discovered PylRS enzymes that accept -thio acids, N-formyl-L-amino acids, and diverse -carboxyl acid monomers (malonic acids) that are formally precursors to polyketide natural products. These monomers are all accommodated and accepted by the translation apparatus in vitro. High-resolution structural analysis of the complex between one such PylRS enzyme and a meta-substituted 2-benzylmalonate derivative reveals an active site that discriminates pro-chiral carboxylates and accommodates the large size and distinct electrostatics of an -carboxyl acid substituent.This discovery emphasizes the potential of PylRS for evolving new enzymes capable of encoding diverse non-L-amino acids in synergy with natural or evolved ribosomes. The absence of orthogonal aminoacyl-tRNA synthetase enzymes that accept non-L-amino acids is the primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers. 

Magnetometer Based On Spin Wave Interferometer

Brief description not available

Templated Synthesis Of Metal Nanorods

Brief description not available

Magnetically Responsive Photonic Nanochains

Brief description not available

(SD2020-421) Virtual Electrodes for Imaging of Cortex-Wide Brain Activity: Decoding of cortex-wide brain activity from local recordings of neural potentials

As an important tool for electrophysiological recordings, neural electrodes implanted on the brain surface have been instrumental in basic neuroscience research to study large-scale neural dynamics in various cognitive processes, such as sensorimotor processing as well as learning and memory. In clinical settings, neural recordings have been adopted as a standard tool to monitor the brain activity in epilepsy patients before surgery for detection and localization of epileptogenic zones initiating seizures and functional cortical mapping. Neural activity recorded from the brain surface exhibits rich information content about the collective neural activities reflecting the cognitive states and brain functions. For the interpretation of surface potentials in terms of their neural correlates, most research has focused on local neural activities.   From basic neuroscience research to clinical treatments and neural engineering, electrocorticography (ECoG) has been widely used to record surface potentials to evaluate brain function and develop neuroprosthetic devices. However, the requirement of invasive surgeries for implanting ECoG arrays significantly limits the coverage of different cortical regions, preventing simultaneous recordings from spatially distributed cortical networks. However, this rich information content of surface potentials encoded for the large-scale cortical activity remains unexploited and little is known on how local surface potentials are correlated with the spontaneous neural activities of distributed large-scale cortical networks. Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin-top:0in; mso-para-margin-right:0in; mso-para-margin-bottom:8.0pt; mso-para-margin-left:0in; line-height:107%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}

Nanopore Sequencing of RNA Using Reverse Transcription

This invention demonstrates that an engineered cellular reverse transcriptase is a potent motor protein that can processively thread single-stranded RNA (ssRNA) through the MspA biological nanopore in single nucleotide steps while it is synthesizing cDNA. Notably, this represents a first-ever achievement for threading of ssRNA through the engineered Mycobacterium smegmatis porin A (MspA) nanopore in discrete steps, and also for ssRNA sequencing with the MspA nanopore. The inventors constructed the “quadromer map” for ssRNA in the MspA nanopore, which is essentially a table that can convert measured nanopore ion current to RNA sequences, using ssRNAs of known sequences. In addition, the inventors discovered that the single-molecule kinetic rates of the reverse transcriptase are affected by the presence of stable RNA secondary structures. Monitoring this biophysical behavior can be used to determine RNA structures during nanopore sequencing.  Nanopore sequencing is a powerful third generation sequencing technology that offers advantages such as ultra-long read length and direct detection of chemically modified bases. One of the key components of developing a successful nanopore sequencer is identifying potent motor proteins (such as polymerases or helicases) that can thread single-stranded (ss) DNA or ssRNA through the nanopore in discrete steps with high processivity.   

Digital Microfluidic Plasmonic Polymerase Chain Reaction (PCR) Device

This technology automates the polymerase chain reaction (PCR) process using digital microfluidics for droplet manipulation. The invention also increases PCR speed and efficiency by combining electrowetting and plasmonic heating in a single device.PCR tests have a wide variety of applications, including the diagnosis of infectious organisms such as viruses and bacterias, as well as cloning, mutagenesis, sequencing, gene expression, and more. The test has become a gold standard for detecting SARS-CoV-2, the virus that causes COVID-19. In the PCR process, a gene or part of the DNA of the infecting organism is amplified exponentially to the extent that it can be detected using conventional methods like gel electrophoresis. This invention addresses the following challenges in current PCR methods: a long sample to answer time; and manual manipulation by humans, which increases the error rate in the tests.  

Deep Learning-Based Approach to Accelerate T cell Receptor Design

Researchers at the University of California, Davis have developed a deep learning simulation model to predict mutated T-cell receptor affinity and avidity for immunotherapy applications.

Reinforcement Learning with Real-time Docking of 3D Structures for SARS-COV-2

The inventors propose a novel framework generating new molecules that potentially inhibit the Mpro protein, the main protease of SARS-COV-2. The technology combines deep reinforcement learning (RL) with real-time molecular docking on the 3d structure of Mpro using AutoDock Vina, an open-source program for doing molecular docking. A second second docking software, Glide, was used to validate the generated molecules. The AutoDock and Glide docking softwares showed consensus on 41 molecules as potential potent Mpro inhibitors that were sufficiently easy to synthesize. The inventors show that this method samples the drug chemical space efficiently, covering a much broader space than molecules submitted to the COVID moonshot project, and the molecules have the correct shape and non-bonded interactions to fit into the binding pocket. Moreover, this approach only relies on the structure of the target protein, which means it can be easily adapted for future development of other inhibitors.

Programmable System that Mixes Large Numbers of Small Volume, High-Viscosity, Fluid Samples Simultaneously

Researchers at the University of California, Davis have developed a programmable machine that shakes and repeatedly inverts large numbers of small containers - such as vials and flasks – in order to mix high-viscosity fluids.

(SD2021-057) Electro-optical mechanically flexible microprobes for minimally invasive interfacing with intrinsic neural circuits

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.

(SD2020-497) Light-activated tetrazines enable live-cell spatiotemporal control of bioorthogonal reactions

Bioorthogonal ligations encompass coupling chemistries that have considerable utility in living systems. Among the numerous bioorthogonal chemistries described to date, cycloaddition reactions between tetrazines and strained dienophiles are widely used in proteome, lipid, and glycan labeling due to their extremely rapid kinetics. In addition, a variety of functional groups can be released after the cycloaddition reaction, and drug delivery triggered by in vivo tetrazine ligation is in human phase I clinical trials. While applications of tetrazine ligations are growing in academia and industry, it has so far not been possible to control this chemistry to achieve the high degrees of spatial and temporal precision necessary for modifying mammalian cells with single-cell resolution.

Hormonal Responsive White Adipose Tissue Micro-Physiological System

The inventors have developed a first-of-its-kind human stem cell-derived metabolically functioning white adipose tissue micro-physiological system (WAT-MPS). The system reconstructs actual physiological circulation and provides a supportive microenvironment that promotes differentiation and maintains long-term cell viability that is superior to traditional tissue culture conditions. Previous studies of stem cell-derived human adipocytes often result in insulin resistant cells due to suboptimal differentiation conditions. The inventors systematically screened key differentiation factors and identified a window of conditions that can create insulin sensitive human adipocytes from mesenchymal and induced pluripotent stem cells without decreasing adipogenesis. To facilitate the rapid and scalable assessment of these human adipocytes, the inventors also optimized an MPS platform that can be used to quantitate insulin responsiveness of adipocytes. This WAT-MPS platform will enable high throughput drug screening for insulin sensitizers, regulators of lipolyisis, and environmental insulin desensitizers, and power personalized medicine approaches to investigate genetic risks of insulin resistance and pharmaco-genetics.   

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