Lawrence Berkeley National Laboratory

A noncontiguous code for RNA-guided DNA recognition at the origin of CRISPR-Cas

CRISPR-Cas provides RNA-mediated adaptive immunity, but how its first RNA-guided effector arose is unclear. In this study, we report the discovery of Viral Interference Programmable Repeat (VIPR) systems consisting of a Vipr protein ancestral to the earliest CRISPR-Cas effectors...

Suspended thin-film lithium niobate modulator for broadband mid-infrared light modulation and frequency comb generation

Abstract The mid-infrared (MIR) spectral regime is central to applications including remote sensing, precision spectroscopy, higher harmonic generation, and free-space optical communication. However, coherent and broadband MIR modulation remains challenging owing to high optical...

The chromosomal genome sequence of the boulder star coral, Orbicella franksi (Gregory, 1895) (Scleractinia: Merulinidae)

We present a genome assembly from a specimen of Orbicella franksi (boulder star coral; Cnidaria; Anthozoa; Scleractinia; Merulinidae). The genome sequence has a total length of 496.97 megabases. Most of the assembly (95.24%) is scaffolded into 15 chromosomal pseudomolecules. The...

Engineered Orthogonal Translation Systems from Metagenomic Libraries Expand the Genetic Code

Abstract Genetic code expansion with noncanonical amino acids (ncAAs) opens new opportunities for the design and engineering of proteins by broadening their chemical repertoire. Unfortunately, ncAA incorporation into proteins is limited both by a small collection of orthogonal am...

Electrical noise produced by micron-sized particles above a surface Paul trap

Electric field noise produced by the surface of ion trap electrodes reduces the fidelity of quantum computing operations. Despite decades of investigation, its microscopic origins remain unclear. Here, we measure electric field noise at trapping locations along the symmetry axis...

Enhanced infrared-to-visible upconversion imaging via metasurface–lanthanide nanoparticle hybrid screens

Abstract Accessing the rich information carried by infrared light typically relies on bulky, complex optoelectronic systems. Lanthanide-based upconverting nanoparticles (UCNPs) offer a compelling alternative by converting infrared light into visible photons through nonlinear anti...

Continuous-time random walk description of anomalous spin transport in dilute dipolar networks

Nuclear spin diffusion is often summarized by a single diffusion coefficient, but this coarse-grained description can fail in dilute solids where positional disorder and long-range dipolar couplings generate a broad distribution of hopping rates. We develop a continuous-time rand...

The rice cellulose synthase-like D4 gene ( OsCSLD4 ) is required for resistance to Xanthomonas pv. oryzae

Plant cell walls serve as a physical support and a barrier to pathogen invasion. Cellulose is the main component of cell walls. The cellulose synthase-like D ( CSLD ) subfamily genes are required for plant normal development. In rice, Oscsld4 mutant plants are dwarfed and have na...

Multi-omics analysis reveals Protein Kinase A-associated regulatory remodeling during adaptation of Trichoderma reesei to lignocellulosic substrate

The filamentous fungus Trichoderma reesei is a major industrial source of holocellulolytic enzymes, and its response to complex carbon sources is regulated by nutrient-sensing mechanisms, including the cyclic adenosine monophosphate (cAMP)-protein kinase A (PKA) signaling pathway...

Ambient Alkaline Pretreatment Enables Isoprenol Fermentation from Lignocellulosic Biomass for Sustainable Aviation Fuel Production

Abstract Mitigating aviation’s carbon emissions remains challenging because air travel relies on energy-dense liquid fuels with limited substitutes. Here, we report a fermentation-based bioconversion process for producing isoprenol, a precursor to 1,4-dimethylcyclooctane (DMCO),...

Layer-Controlled Intermolecular Coupling and Many-Body Effects in C60 Films

Abstract Crystalline C60 is a molecular solid whose electronic properties emerge from the interplay of intermolecular hopping, electron correlations, and electron–vibration coupling. Unlike moiré van der Waals heterostructures, where the interaction strength is commonly tuned by...

Het-node2vec: second-order random walk sampling for heterogeneous graph embedding

Abstract Many real-world problems are naturally modeled as heterogeneous graphs, where nodes and edges represent multiple types of entities and relations. Existing learning models for heterogeneous graph representation usually depend on the computation of specific, user-defined h...

Mapping the nuclear environments of extreme coronal line emitting galaxies

Abstract Extreme coronal line emitters (ECLEs) are a rare class of galactic nuclei exhibiting unusually strong high-ionisation forbidden emission lines, and several ECLEs have been linked to tidal disruption events (TDEs). In this work, we compile and analyse optical spectra of 3...

Effect of Substrate Miscut on the Epitaxial Growth of MoS2 on Sapphire

Abstract The combined effects of substrate miscut angle and growth temperature on the epitaxial growth and properties of MoS2 monolayers synthesized by metalorganic chemical vapor deposition (MOCVD) on c-plane sapphire substrates were investigated. Increasing the miscut angle tow...

Quantum Light Spectroscopy

Abstract Spectroscopy based on individual-photon-level light sources brings new variables to both spectroscopy and imaging. We refer to this approach as quantum-light spectroscopy (QLS). The photon statistics of different types of photon sources and photon entanglements are brief...

Mechanical cues of an interpenetrating polysaccharide matrix regulate self-assembly of collagen fibers

Collagen molecules self-assemble into supramolecular fibers within a molecularly crowded, polysaccharide-rich extracellular matrix (ECM). The ECM typically has fluid-like, viscoelastic properties that can be quantified rheologically. Here, we determine that the viscoelasticity of...

Reimagining biomedical science workflows in the age of large language models

Abstract Large language models (LLMs) are generative artificial intelligence (AI) models that are rapidly reshaping the practice of biomedical science. Their ability to synthesize literature, generate analytical code, and interface with multimodal data offers a new framework for...

Semi-supervised Retrieval of Functional Residues Through the Integration of Protein Language Models and Gene Ontology Data

Abstract Motivation Experimental studies of protein function often focus on mechanistic descriptions, characterizing how specific sites and residues contribute to activity. Abstractions such as domains and active sites enable quantitative descriptions of how protein features act...

A genomic catalog of Earth’s bacterial and archaeal symbionts

1 SUMMARY Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth, yet remains underexplored due to culturing challenges. This study employed machine learning (ML) to predict symbiotic lifestyles in hundreds of thousands of microbial genomes fr...

Zero-copy interoperability between PETSc device sparse operators and PyTorch autograd: paper, code, and measurement data

Everything behind the paper Zero-copy interoperability between PETSc device sparse operators and PyTorch autograd: the bridge library, its correctness gates, the benchmark scripts, the measurement data behind every table and figure, and the paper source and PDF. The bridge expose...