Bioluminescence technology offers highly sensitive and non-invasive imaging in living organisms without the need for external excitation. Naturally occurring luciferases, the enzymes responsible for catalyzing light emission, constrained the full potential of luminescence technology for the past several decades due to their poor protein folding, large size, ATP dependency, and low efficiency. Creation of the next generation of luciferases required breaking free of evolutionary constraints. This work describes the creation of novel bioluminescent enzymes that surpass qualities of native luciferase using AI-powered de novo protein design. These designer luciferase catalysts enable genetic labeling across molecular, cellular, and individual levels in a multiplexed manner, using the same underlying technology. This advancement showcases the design of efficient enzymes from scratch in which our de novo luciferases will enable researchers to study complex biological phenomena effectively.In the last three decades, the development of fluorescent protein families has brought a revolution in the way researchers study biological processes in living cells. However, the dependency on external excitation for FPs introduces inherent drawbacks, such as phototoxicity and autofluorescence background. These especially limit the applications for fluorescent proteins in vivo. Bioluminescence technologies, which rely on an enzyme-catalyzed chemiluminescent reaction of a chromophore substrate to emit photons without the need for external light sources, circumvent these limitations and offer several orders-of-magnitude-higher sensitivity than fluorescence for macro-scale imaging.Practically implementing luciferases as general molecular proges has not progressed as far as fluroescent proteins due to a number of factors. Firefly luciferase (FLuc) is used widely for in vivo imaging, but it is dim, large (61 kDa), and ATP dependent. Gaussia luciferase (GLuc) is brighter than FLuc, but has five disulfide bonds and therefore cannot be used intracellularly. It is also prone to misfolding. Engineered variants of Renilla luciferase (RLuc) and Oplophorus Luciferase (NLuc) are brighter and more stable, but they emit blue light and have poor substrate specificity and therefore are difficult to used in multiplexed applications.  LuxSit luciferase (Monod Bio Inc.) is the first de novo designed luciferase and has superior folding fidelity and stability to natural luciferases, but more de novo luciferase species are necessary to meet the needs of researchers.  

A transgenic zebrafish model enabling controlled pancreatic β-cell ablation to simulate chronic hyperglycemia and study diabetes-related pathology.

Professor Linlin Zhao and their team from the University of California, Riverside have developed mTAP, a new chemical probe engineered to selectively bind to abasic sites within mitochondrial DNA without affecting nuclear DNA. Unlike non-specific agents, mTAP is equipped with a mitochondria-targeting group, ensuring its precise localization. This invention is advantageous over current technology because its mechanism of action involves forming a stable chemical bond with damaged DNA sites, thereby protecting mtDNA from enzymatic cleavage and maintaining its replication and transcriptional activities.    Fig 1: The UCR mitochondria-targeting water-soluble probe mTAP exclusively reacts with mitochondrial abasic sites, and retains mitochondrial DNA levels under genotoxic stress which are responsible for certain mitochondrial diseases. 

A revolutionary drug modality for the selective modification and degradation of intracellular proteins in lysosomes.

Site-selective covalent modification of proteins is key to the development of new biomaterials, therapeutics, and other biological tools. As examples in the biomedical field, these techniques have been applied to the construction of antibody-drug conjugates, bispecific cell engagers, and targeted protein therapies, among other applications. While many bioconjugation strategies, such as azide-alkyne cycloaddition or thiol-maleimide coupling, have become widely adopted, the improvement of existing techniques is a highly active area of chemical biology research, as is the development of new synthetic applications of these methods. Key focuses of such efforts include increasing reaction efficiency and ease, balancing selectivity with tag size, and expanding the modification options beyond traditional cysteine and lysine residues. UC Berkeley researchers have developed compounds and methods using tyrosinase to couple small-molecule dithiols to tyrosine-tagged proteins, which effectively introduces a free thiol handle and provides a convenient method to bypass genetic incorporation of cysteine residues for bioconjugation. These newly thiolated proteins were then coupled to maleimide probes as well as other tyrosine-tagged proteins. The researchers were also able to conjugate targeting proteins to drugs, fluorescent probes, and therapeutic enzymes. This easy method to convert accessible tyrosine residues on proteins to thiol tags extends the use of tyrosinase-mediated oxidative coupling to a broader range of protein substrates. 

A novel method for selectively targeting and modulating brain border-associated myeloid cells for the treatment of neurological disorders.

An engineered polymerase enabling the synthesis of threose nucleic acid (TNA) for advanced therapeutic applications.

A groundbreaking method for the efficient isolation and preservation of high-purity small extracellular vesicles (sEVs - exosomes) from biofluids using a novel EXO-PEG-TR reagent.

Achieving durable engraftment and spatial localization of engineered microbes in complex environments, such as the gut microbiome, has been a persistent challenge. Current methods to select and isolate engineered microbes in the lab rely on antibiotic-based selection systems, which are unsuitable for in vivo applications due to safety concerns, environmental risks, and regulatory hurdles. Moreover, these methods lack the precision needed for selective recovery and targeting within diverse microbial communities.  UC Berkeley researchers have developed an innovative framework that integrates plasmid-based systems and CRISPR-associated transposase systems (CASTs) to enable precise delivery of genetic cargoes encoding surface display systems. These systems, when expressed, allow engineered microbes to display modular binding domains capable of interacting with a range of targets, including but not limited to host associated mucus and magnetic particles. This modularity expands the toolkit for selective enrichment, spatial targeting, and functionalization of engineered microbes in diverse contexts. For example, modified microbes can be magnetized for recovery through magnetic separation or equipped with binding domains to interact with other substrates or biomolecules, unlocking targeted applications in microbiome engineering, therapeutic delivery, and biomanufacturing. This approach not only enables the enrichment and spatial targeting of engineered microbes within complex communities, such as those in the gut, but also provides a versatile method for isolating bacterial strains or directing microbes to specific niches without relying on antibiotics. By combining plasmid modularity with the precision and stability of CASTs, the platform establishes a robust and adaptable solution for microbiome modulation. 

An innovative Palladium hydride catalyst that significantly enhances the electroreduction of carbon dioxide (CO2) to formate with exceptional tolerance for carbon monoxide (CO).

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. 

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

Prof. Min Xue from the University of California, Riverside and Prof. Wei Wei from the Institute for Systems Biology have developed materials and  methods to detect and measure FA uptake alone or simultaneously with protein detection in multiplex down to single-cell resolution. FA analogs with an azide functional group mimics natural FAs. Specially designed small polymers are used to efficiently assay the FA analogs and produce fluorescent or chemical signals upon binding. The technology is compatible with protein analysis and generally applicable to other metabolites and proteins. Fig 1: Schematic of the UCR-ISB method for detecting fatty acid uptake from single cells.  

New chemistries are emerging for the direct attachment of complex molecules to cell surfaces. Chemistries that modify cells must perform under a narrow set of conditions in order to maintain cell viability. They must proceed in buffered aqueous media at the optimal physiological pH—typically pH 7.4—and within a temperature range of 4 – 37 ºC. Furthermore, these reactions must have sufficiently rapid kinetics to achieve high conversion even when confronted with the limits of surface diffusion characteristics. Due to these requirements, few chemistries exist that can attach molecules and proteins to live cells.  There is a need for improved methods of attaching proteins to living cells.   UC researchers have developed a convenient enzymatic strategy for the modification of cell surfaces for targeted immunotherapy applications.  

Researchers at the University of California, Davis, have developed an environmentally friendly one-pot multienzyme (OPME) method for synthesizing sialidase reagents, probes, and inhibitors.

RNA-binding proteins (RBPs) play essential roles in gene expression and other cellular functions. Thus their identification and the understanding of their mechanisms of action and regulation is key to unraveling physiology and disease. To measure translation efficiency and different steps of ribosome recruitment, the state of the art is ribosome profiling (or Ribo‐seq) and polysome profiling which uses millions of cells, sucrose gradients, centrifugation and often requires the removal of ribosomal RNA as part of the sequencing library preparation as it contaminates more than 50% of most ribosome/polysome libraries. Also, we cannot distinguish full length isoforms here, as the ribosome‐fragments are short.

The number of color channels that can be concurrently probed in fluorescence microscopy is severely limited by the broad fluorescence spectral width. Spectral imaging offers potential solutions, yet typical approaches to disperse the local emission spectra notably impede the attainable throughput.    UC Berkeley researchers have discovered methods and systems for simultaneously imaging up to 6 subcellular targets, labeled by common fluorophores of substantial spectral overlap, in live cells at low (~1%) crosstalks and high temporal resolutions (down to ~10 ms), using a single, fixed fluorescence emission detection band. 

Prof. Talbot and her colleagues from the University of California, Riverside have developed a research tool to prolong the viability and pluripotency of stem cells in culture. The culture medium is supplemented with an additive that includes a source of acetate ions, a carboxylic acid, or a salt of the carboxylic acid, or a combination of these substances. Results have shown that this substrate medium allows for less stem cell death, faster colony growth, and causes cells to attach to and spread faster on the substrate. This provides tremendous advantages in stem cell colony morphology, growth, survival, maintenance of pluripotency, and dynamic behavior when compared to existing media.  Fig 1: Images of stem cells in culture before and after treatment  

Nonalcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease in the United States. It can be broadly sub-classified into nonalcoholic fatty liver (NAFL), which is thought to have minimal risk of progression to cirrhosis, and nonalcoholic steatohepatitis (NASH), which is thought to have an increased risk of progression to cirrhosis. The current diagnostic gold standard for differentiating whether a patient with NAFLD has NAFL versus NASH is liver biopsy. However, liver biopsy is an invasive procedure, which is limited by sampling variability, cost, and may be complicated by morbidity and even death, although rare. Accurate, non-invasive, biomarkers for the detection of liver disease and liver disease progression e.g., progression to NASH, are currently also not available.

Researchers at the University of California, Davis have developed monoclonal antibodies with multiple applications relevant to canine PD-1 and PD-L1.

Researchers at UCSF and Chan Zuckerberg Biohub have discovered a novel biomarker for an autoimmune disease that affects patients with testicular cancer.  The disease, known as “testicular cancer-associated paraneoplastic encephalitis,” can cause severe neurological symptoms.  The symptoms include loss of limb control, eye movement, and in some cases, speech.  The disease begins with testicular cancer, which in some cases causes the immune system to attack the brain.  Affected patients are often misdiagnosed and appropriate treatment is delayed. 

Control of gene expression is a general approach to treat diseases where there is too much or too little of a gene product. However, while there are many methods which are available to downregulate the expression of messenger RNA transcripts, very few strategies can upregulate the endogenous gene product. The vast majority of gene regulatory drugs which are commercially available or being developed are designed to knockdown gene expression (i.e. siRNAs, miRNAs, anti-sense, etc.). There exist some methods to enhance gene expression, such as the delivery of messenger RNAs; although, therapeutic delivery of such large and charged RNA molecules is technically challenging, inefficient, and may not be practical. There are also classical gene therapy approaches where a gene product is delivered as viral-encoded products (AAV or lentivirus-packaged). However, these methods suffer from not being able to accurately reproduce the correct alternatively spliced isoforms in the right ratios in cells.  

UCLA researchers in the Department of Chemistry and Biochemistry have developed a new chemical reaction that combines ozone, an iron salt, and a hydrogen atom donor to enable hydrodealkenylative cleavage of C(sp3)–C(sp2) bonds in a widely applicable manner.

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.

Puromycin is an aminonucleoside antibiotic produced by the bacterium Streptomyces alboniger. Its mode of action is to inhibit protein synthesis by disrupting peptide transfer on ribosomes, leading to premature chain termination during protein translation. Puromycin blocks protein synthesis in both eukaryotes and prokaryotes and is routinely used as a research tool in cell culture. The native Puromycin is also used assays such as mRNA display. As such, derivatives have been synthesized in which the amino acid of the 3' end of adenosine based antibiotics is altered to change the compound's antibiotic activity. Other compounds have been synthesized with differing amino acids and functionalities to examine the effect it has on bacterial viability. The majority do not show useful absorption or emission profiles. What is needed is a method to track the compounds in biological systems.