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.

Deoxyribonucleic acid- (DNA-) based identification in forensics is typically accomplished via genotyping allele length at a defined set of short tandem repeat (STR) loci via polymerase chain reaction (PCR). These PCR assays are robust, reliable, and inexpensive. Given the multiallelic nature of each of these loci, a small panel of STR markers can provide suitable discriminatory power for personal identification. Massively parallel sequencing (MPS) technologies and genotype array technologies invite new approaches for DNA-based identification. Application of these technologies has provided catalogs of global human genetic variation at single-nucleotide polymorphic (SNP) sites and short insertion-deletion (INDEL) sites. For example, from the 1000 Genomes Project, there is now a catalog of nearly all human SNP and INDEL variation down to 1% worldwide frequency. Genotype files, generated via MPS or genotype array, can be compared between individuals to find regions that are co-inherited or identical-by-descent (IBD). These comparisons are the basis of the relative finder functions in many direct-to-consumer genetic testing products. A special case of relative-finding is self-identification. This is a trivial comparison of genotype files as self-comparisons will be identical across all sites, minus the error rate of the assay. For many forensic samples, however, the available DNA may not be suitable for PCR-based STR amplification, genotype array analysis, or MPS to the depth required for comprehensive, accurate genotype calling. In the case of PCR, one of the most common failure modes occurs when DNA is too fragmented for amplification. For these samples, it may be possible to directly observe the degree of DNA fragmentation from the decreased amplification efficiency of larger STR amplicons from a multiplex STR amplification. In the case of severely fragmented samples, where all DNA fragments are shorter than the shortest STR amplicon length, PCR simply fails with no product.

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

Aberrant splicing contributes to the etiology of many inherited diseases. Pathogenic variants impact pre-mRNA splicing through a variety of mechanisms. Most notably, variants remodel the cis-regulatory landscape of pre-mRNAs by ablation or creation of splice sites, and auxiliary splicing regulatory sequences such as exonic or intronic splicing enhancers (ESE and ISE, respectively) and splicing silencers (ESS and ISS, respectively). Splicing-sensitive variants cripple the integrity of the gene, resulting in the production of a faulty message that is either unstable or encodes an internally deleted protein. Antisense oligonucleotides (ASOs) are a promising therapeutic modality for rescuing pathogenic aberrant splicing patterns as their direct base pairing abilities make them highly customizable and specific to targets. Although challenges such as toxicity, delivery and stability represent barriers to the clinical translation of ASOs, solutions to these challenges exist, as exemplified by the recent FDA approval of multiple ASO drugs.Generally, ASO's that target splicing mutations are limited to mutations in and around splicing enhancers and exonic mutations are commonly not targeted because of the idea that the mutation causes a significant change in protein function. 

Researchers at the University of California, Davis have developed a method of using artificial intelligence for assessing the effectiveness or efficacy of drugs that is cheaper, faster, and more accurate than commonly used assay analyses.

Many genomes encode Restriction-Modification systems (RMs) that act to protect the host cell from invading DNA by cutting at specific sites (frequently short 4-6 base reverse complement palindromes). RMs also protect host DNA from unfavorably being cut by modifying sites within the host DNA that could be targets by the host’s own surveillance enzymes. It is also not unusual to find that these enzymes are adjacent to each other in the host genome. Traditional approaches to understanding these sites involve finding a methylase that is typically adjacent to a restriction enzyme, and then extracting DNA, expressing protein and then testing DNA sequence for evidence of cutting. In certain laboratory research (e.g., programs that involve transforming DNA/RNA) it may be desirable to more comprehensively understand the sequences being surveilled by the host. Moreover, it may be desirable in certain laboratory research to know/predict which surveillance enzymes are present in a genome in order to affect cell transformation efficiency through evasion of those sequences.

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Optical chromatography (OC) is an optofluidic technique enabling label-free fractionation of microscopic particles, e.g., bioparticles from heterogenous mixtures. This technique relies on a laser beam along a microfluidic channel to create opposing optical scattering and fluidic drag forces. Variable strength and balance of these forces may be harnessed for selective sorting of bioparticles based on their size, composition, and morphology. OC has been successfully applied to fractionation of blood components such as human erythrocytes, monocytes, granulocytes, and lymphocytes. OC offers unique capabilities as a modern separation technique, especially when combined with multi-stage sequential fractionation and microfluidic network-based purification approaches, and it particularly excels in distinguishing bioparticles with subtle differences. However, there are several key limitations with OC being widely adopted. In order to create strong optical scattering forces along the microfluidic channels, expensive and sophisticated laser sources must be precisely aligned along the fluidic channel with a well-controlled beam waist profile, requiring a complicated optical alignment procedure that employs multiple multi-axis positioners. While microfluidic approaches using OC hold promise for broader use, multiplexed and high throughput systems remain overly complicated and cost-prohibitive.

High-throughput next-generation sequencing (NGS) systems have allowed for large scale collection of transcriptomic data with single cell resolution. Within this data lies variability allowing researchers to characterize and/or infer certain morphological aspects of interest, such as single cell type, cell state, cell growth trajectories, and inter-cellular gene regulatory networks. All of these qualities are important parts of understanding how cells interact with one another, both for building better cellular models in vitro and for understanding biological processes in vivo. While the size of single cell data has increased massively, NGS techniques for key pieces of analysis have not kept pace, using slow, manual pipelines of domain experts for initial clustering. Attempts to improve NGS classification performance have fallen short as the numbers of cell types (often asymmetric) and cell subtypes have increased while the number of samples per label has become small. The technical variability between NGS experiments can make robust classification between multiple tissue samples difficult. Moreover, the high-dimensional nature of NGS transcriptomic data makes this type of analysis statistically and computationally intractable.

       Our ability to experimentally measure the biomacromolecular structure of proteins and their complexes down to the atomic scale has progressed at a staggering pace in recent years. However, the dynamical conformational changes that affect, to name a few examples, DNA transcription, energy-transfer in photosynthesis and enzyme activity, and the transition from healthy to diseased states, remain difficult to capture. A non-perturbative, label-free approach that is sensitive to individual conformational states is single-protein Raman spectroscopy. However, the time resolution of single-protein Raman spectroscopy is typically limited to milliseconds (10-3 sec), limited by inherent signal strength. Protein conformational dynamics occur over a timescale ranging from tens of seconds down to microseconds (10-6 sec) or even nanoseconds (10-9 sec).       To address these challenges UC Berkeley researchers have developed a novel, high-temporal dynamic range Raman spectrometer capable of measuring sub-microsecond, and even nanosecond, fluctuations in single- and few-molecule spectra. The available dynamic range can be used to study and control of biomolecular dynamics as related to protein-protein interactions, drug discovery, validating computational biophysics capabilities, and many other additional applications. 

Long read sequencing (e.g. nanopore sequencing) involves a tradeoff between the length of the DNA fragment sequenced, which allows for greater ease of data assembly relative to massively parallel sequencing technologies (e.g. Illumina (R) sequencing) and accuracy of individual base calls.This technology takes advantage of the long read capabilities of nanopore sequencing to improve the accuracy of reads of highly variable nucleic acid species, including cDNAs, and which can be highly variable due to alternative RNA splicing. 

Nanopore sequencing requires a processive motor or other element to control the rate of RNA movement in single nucleotide steps through the nanopore sensor. The control element is typically situated several nucleotides from the sensor, therefore it necessarily releases before the end of the native RNA strand reaches the sensor. Thus, the bases along that terminal interval cannot be sequenced using conventional nanopore strategies. Furthermore the nucleotide sequence near that end in many eukaryotic RNAs is not typical. An important example is polyadenylated (poly A) RNA which often bears a 7 methylguanosine cap at the 5 prime end. The linkage between this modied cap and its neighbor is inverted, i.e. the two nucleotides are connected via the 5 prime carbons of their ribose sugars through triphosphate linker, rather than by a typical 5 prime to 3 prime linkage via a phosphodiester bond. 

The gene expression profile of a cell can indicate the current status of the cell, such as its cell type, proliferation status, and degree of maturation or differentiation. The health of a cell in tissues is always in transition, such as diseased state (e.g., tumor cells), healthy state, and states in between. To fully understand and leverage the nature and pathways of cell states towards better diagnosis, treatment, and medical outcomes, it may be beneficial to forecast cell health as a function of certain gene-related configuration. Traditionally it has been difficult to predict ad hoc whole transcriptome alterations caused by gene-related perturbations.

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Although Next Generation Sequencing has vastly improved sequencing throughput while reducing sequencing costs, preparation of nucleic acid libraries for sequencing has become a bottleneck. In addition, it is difficult using short read next generation sequencing to assemble highly variable sequences that exceed 500 base pairs such as cDNAs derived from antibody heavy chain, antibody light chain, and T cell variable regions RNA.  

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Researchers at UC Berkeley have developed a machine learning model that can aide in the design of more efficient viral vector libraries.Directed evolution of biomolecules to generate large numbers of randomized variants is an important innovation in biochemistry. This methodology can be applied to myriad biomolecules of interest, including viruses. In the case of viral variants, this method may be used to select viral variants or viral vectors with specific properties such as tissue type specificity, increased replication capacity, or enhanced evasion of the immune system. However, testing large numbers of viral variants for specific properties is inherently time consuming and limits potential innovation.The inventors have devised a new method to optimize the functionality of viral libraries with many random variants. Specifically, this methodology comprises a machine learning model that systematically designs more effectively starting libraries by optimizing for a chosen factor. This method works by using a training set of viruses that can be evaluated experimentally for the chosen optimization factor (e.g., packaging efficiency, infectivity of a cell line, etc.). These experiments will then provide a fitness value for each viral variant, and the fitness value matched with viral variant sequences will in turn be used in a supervised machine learning model to select sequences for a larger library that is optimized for the chosen factor.

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.  

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This invention leverages the nuclease activity of CRISPR proteins for the direct, sensitive detection of specific nucleic acid sequences. This all-in-one detection modality includes an internal Nuclease Chain Reaction (NCR), which possesses an amplifying, feed-forward loop to generate an exponential signal upon detection of a target nucleic acid.Cas13 or Cas12 enzymes can be programmed with a guide RNA that recognizes a desired target sequence, activating a non-specific RNase or DNase activity. This can be used to release a detectable label. On its own, this approach is inherently limited in sensitivity and current methods require an amplification of genetic material before CRISPR-base detection. 

UCLA researchers in the Department of Molecular and Medical Pharmacology have developed a classifier for the identification and treatment of small cell neuroendocrine cancers and small-round-blue cell tumors not previously identified.

To develop a novel imaging-based single cell RNA-sequencing (scRNA-Seq) platform that allows capturing of spatiotemporal information and cellular behavior of the sequenced cells within tissue.