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(2020-266) Protein Domains For Modulation Of Rna Stability And/Or Translation

Existing art in modulation of gene expression by nucleic acid targeting mechanisms primarily comprises methods for REDUCING gene expression, e.g. via DNA targeting (CRISPR gene knockout, reduction of transcription via CRISPR-i), or RNA targeting (shRNAs/siRNAs, ASOs, microRNA mimics). ENHANCEMENT of gene expression on the RNA level has been achieved using microRNA inhibitors; however the effects are typically small and are not target-specific (many other microRNA target-RNAs are also upregulated).The molecular functions of the majority of RNA-binding proteins (RBPs) remain unclear, highlighting a major bottleneck to a full understanding of gene expression regulation. 

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.

High-throughput Microfluidic Research Platform for Performing Versatile Single-Cell Molecular Timed-Release Assays within Droplets

Researchers at UCI have designed a high-throughput, cost-effective microfluidic platform as a research tool for performing genomic, proteomic, single-cell, pharmacological, and agricultural studies across multiple cell types.

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.   

Method For Rapid In Situ Detection Of Ammonia

This invention, a simple and robust method for ammonia detection, offers high-speed in situ quantification of ammonia concentrations with high sensitivity. The ammonia detection system does not require complex instrumentation, analysis, or labeling, which would allow for widespread adoption in chemistry-based fields and surrounding disciplines.

3D-Bioprinted All-Inclusive Bioanalytical Platforms for Cell Studies

Common drug screen models, such as animals and 2D cell cultures, do not properly recapitulate human organ structure and environment. Using 3D bioprinting technology, researchers at UCI have developed all-inclusive customized organ-on-a-chip-like platforms. These platforms produce cell models that properly mimic the microenvironment of cells for drug screening and cell-therapeutic response studies.

Particle-Sorting Device for Isolation, and Enrichment of Particles at Ultra-Low Concentrations

The ability to detect and sort particles by type is important to many fields, such as medical diagnostics, environmental monitoring, and food safety.UCI researchers have developed a platform to sort and isolate particles from a turbid medium with minimal pre-processing. The platform is very desirable for applications in which enrichment of particles or biological substances at low concentrations is necessary.

Profiling Translation Rate With Ribo-Eclip

The eukaryotic ribosome is composed of 79 ribosomal protein – large (RPL) and ribosomal protein – small (RPS) subunit proteins that interweave with 4 highly structured RNAs (5S, 5.8S, 18S, and 28S rRNAs) to form the final translation-capable ribonucleoprotein. Thus, quantification of ribosome-associated RNA is highly similar to profiling of RNAs associated with other RNA binding proteins. We recently described the development of enhanced crosslinking and immunoprecipitation (eCLIP), a method to profile RNAs bound by an RNA binding protein of interest that showed thousand-fold improved recovery of protein-bound RNA [Van Nostrand et al 2016]. Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang MY, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, et al: Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 2016, 13:508-514. https://pubmed.ncbi.nlm.nih.gov/27018577/

Personalized Oncology Drug Efficacy Monitoring Chip

Researchers at UCI have developed a novel microfluidic-based platform that enables personalized drug screening of patient-derived cancer cells. This versatile device features real-time, continuous screening of patient samples without the need for expensive labeling reagents, large sample sizes, or bulky readout equipment.

Breast Milk Biomarkers for Child Chronic Health Disorders

Autism Spectrum Disorder (ASD) is a developmental disorder associated with difficulties in social interaction and communication as well as repetitive behavior. ASD is thought to be the result of genetic and environmental factors that affect approximately 1 in 59 children in the US, and 25 million people worldwide. The current method of diagnosis for ASD involves evaluations and tests performed by a team of specialists.  The latest forms of diagnosis can detect ASD as early as 18 months. However, more standard methods take until 4 years of age before the diagnosis of ASD is confirmed. There remains an unmet need to develop a reliable and accurate diagnostic methods for early detection for a child at risk with chronic and/or developmental disorders, such as ASD, so that an early intervention measures will be applied before the first symptoms appear.

Compression of Genetic Information in Multiple Reading Frames

Techniques such as genome editing, gene therapy, and CRISPR-based gene expression require robust methods of delivering genetic information. The effectiveness of delivery depends on the amount of DNA or RNA that can be delivered.  In some cases there is a strict upper-limit on the amount of DNA or RNA that can be delivered.  For example, AAV vectors for mammalian gene delivery are limited to genetic cargos of < 5 kb.  In general, and irrespective of the delivery vector, larger DNA constructs are delivered less efficiently and so it is advantageous to use smaller constructs where possible. It is therefore advantageous to compress constructs. Methods of compression that do not require removal of genetic elements (“lossless compression”) are very desirable since size requirements can be met without compromising functionality.     In order to reduce the number of bases (DNA or RNA) required to encode larger constructs, UC Berkeley researchers have developed a method for compressing genetic information.   The method can be applied to two elements which be encoded in the same or different reading and can also be applied to a single genetic elements. 

A Microfluidic Single-Cell Pairing Array for Studying Cell-Cell Interaction in Isolated Compartments

Cell interactions are fundamental to biological processes. Microfluidics provides a reliable platform to study these intricate phenomena. The researchers have developed a microfluidic trapping array which efficiently pairs single cells in isolated compartments in an easy to operate manner to study cell-cell interaction, especially at single-cell level.

Drug Repurposing To Explore Novel Treatment For Cushing Disease

UCLA researchers in the Department of Medicine and the Department of Molecular and Medicinal Pharmacology have identified several small molecule reagents to treat Cushing disease.

Novel Fret Method

Dr. Jiayu Liao and colleagues at the University of California, Riverside have developed a FRET assay using nitrobenzoxadiazole (NBD) and coumarin (CUM) amino acid analogs as a FRET pair.  These fluorophores are genetically encoded into peptides and proteins surrounding a protease cleavage site or ligand binding site and used for FRET-based high throughput screening for enzymes or small molecule inhibitors involved in pathways such as SUMOylation. Researchers have demonstrated FRET for peptides encoded with NBD and CUM separated by 4 and 6 amino acids and excited at 340 nm (Figure 1). Figure 1.  Fluorescent intensity of peptide I (6 amino acids between CUM and NBD) and II (4 amino acids between CUM and NBD) excited at 340 nm.  

Very-Small-Nuclear Circulating Tumor Cell (vsnCTC) as a Diagnostic Biomarker of Visceral Metastasis in Advanced Prostate Cancer

UCLA researchers in the Department of Molecular and Medical Pharmacology have identified a novel biomarker that can be used to diagnose prostate cancer patients for the presence of visceral metastasis with 54% sensitivity and 100% specificity.

DNA Methylation: A New Method for the Quantitative Predictor Of Age In Dogs

The ability to properly estimate the age of dogs would be quite useful in a variety of ways. For example, proper age estimation is important because age often plays a significant role when making medical decisions for pets. Currently, the accepted method to estimate age in dogs is based on the quality of teeth as well as ocular features. Estimating age based on tooth-wear (the commonly used metric in shelters) is very inaccurate after the teeth have fully erupted, generally by 6-7 months of age in dogs. Unfortunately, these methods have an accuracy of ~50% at best for domesticated pets and is error-prone for dogs between 2-8 years, encompassing a large portion of a dog’s adult life. Thus, shelters commonly underestimate the ages of these dogs to increase the likelihood of dogs being adopted, as people generally have a preference for younger pets. 

Capture And Stimulated Release Of Circulating Tumor Cells On Polymer Grafted Silicon Nanostructures

UCLA researchers in the department of Molecular and Medical Pharmacology have developed a novel capture system of circulating tumor cells for the early detection of metastatic cancer.

Single Circulating Tumor Cell Isolation Using Laser Microdissection And A Polymer Enrichment Assay

UCLA researchers in the department of Molecular and Medical Pharmacology have developed a novel matrix polymer capture system of circulating tumor cells that preserves biomolecular integrity through laser microdissection for the early detection of metastatic cancer.

Novel Steroid Hormone Assay

Researchers at the University of California have identified in insects that the membrane transporter, Ecdysone Importer (EcI), is involved in the cellular uptake of the primary steroid hormone ecdysone. Specifically after transport through Ecl, ecdysone’s active form (20-hydroxyecdysone or 20E and related ecdysteroids) enters its target cells and binds to the ecdysone receptor (EcR), which forms a heterodimer with another nuclear receptor and activates transcription of multiple genes involved in molting and metamorphosis. This new discovery of Ecl’s role counters the prevailing consensus that steroid hormones diffuse through cell membranes.  This will enable the screening of new compounds that interact with Ecl.  Such new compounds may be used for insect pest control. Fig. 1 membrane transporters (blue) guide steroid hormones (blue dots) into cells. This new discovery counters the conventionally held scientific consensus that steroid hormones passively diffuse through cell membranes.   Fig. 2 EcI mutants (bottom) were not able to enter into metamorphosis when compared to the control (top).

Phenotypic Profiling Of Hepatocellular Carcinoma Circulating Tumor Cells For Treatment Selection

Researchers in the UCLA Departments of Surgery and Molecular and Medical Pharmacology have developed a novel blood-based assay that can capture and characterize circulating tumor cells indicative of both early- and late-staged hepatocellular carcinoma (HCC).

Predicting the Placebo Response and Placebo Responders in Medicated and Unmedicated Patients Using Baseline Psychometric and Clinical Assessment Score

UCLA researchers have developed a method and model to predict the placebo effect and placebo responsiveness using the 30-item baseline positive and negative syndrome scales (PANSS) scores, within both the medicated and unmedicated Schizophrenia patients.

Lipid-Modified Oligonucleotides For Sample Barcoding in Droplet Microfluidics-Based Single-Cell RNA Sequencing

A new strategy for barcoding single living cells using lipid-modified oligonucleotides that can vastly enhance sample multiplexing in droplet microfluidics-based RNA sequencing

Optimizing B Cell Epitope-Based Autoantibody Detection In Cancer Patients

UCLA researchers from the Department of Urology have invented a new approach to optimize detection of autoantibody response using Luminex microbead-based multiplex assay. This approach bypasses the difficult process of purifying whole proteins by using select combinations of short B-cell epitopes.

A Micro-Bubble Plate For Patterning Biological and Non-Biological Materials

A method for creating a 3D micro-bubble plate for patterning biological and non-biological materials. Because each sample is at a known location, large numbers of samples may be studied and allow for significant statistical data sets, which will aid in diagnosing unknown agents or diseases inexpensively.

A Micro-Patterned Plate Composed Of An Array Of Releaseable Elements Surrounded With Solid Or Gel Walls

This technology is a micro-patterned plate made of an array of releasable elements surrounded by a gel or solid wall, and a process for manufacturing the micro-patterned plate. This is an efficient way of studying samples for statistically significant data sets of cells or biological materials for important scientific research and medicines.

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