A5100437787- Single-cell and spatial transcriptomics
- Neuroinflammation and Neurodegeneration Mechanisms
- Light effects on plants
- Photoreceptor and optogenetics research
- Immune cells in cancer
- Advanced biosensing and bioanalysis techniques
- Photosynthetic Processes and Mechanisms
- Cell Image Analysis Techniques
- Genomics and Chromatin Dynamics
- Receptor Mechanisms and Signaling
- bioluminescence and chemiluminescence research
- Cancer Genomics and Diagnostics
- Neurogenesis and neuroplasticity mechanisms
- Gene expression and cancer classification
- Innovative Microfluidic and Catalytic Techniques Innovation
- DNA and Nucleic Acid Chemistry
- Phytochemical compounds biological activities
- RNA and protein synthesis mechanisms
- Natural product bioactivities and synthesis
- Plant chemical constituents analysis
- Alzheimer's disease research and treatments
- Micro and Nano Robotics
- Gene Regulatory Network Analysis
- Parkinson's Disease Mechanisms and Treatments
- Phytochemicals and Antioxidant Activities
University of California, Berkeley
2021-2025
University of Arizona
2023-2025
Scripps Research Institute
2025
Shandong University of Traditional Chinese Medicine
2024
Harvard University
2011-2023
The Ohio State University
2011-2023
Howard Hughes Medical Institute
2015-2023
Lawrence Berkeley National Laboratory
2021-2022
QB3
2021-2022
Vrije Universiteit Amsterdam
2022
α-Synuclein (aSyn) fibrillar polymorphs have distinct in vitro and vivo seeding activities, contributing differently to synucleinopathies. Despite numerous prior attempts, how polymorphic aSyn fibrils differ atomic structure remains elusive. Here, we present fibril from the full-length recombinant human their capacity cytotoxicity vitro. By cryo-electron microscopy helical reconstruction, determine structures of two predominant species, a rod twister, both at 3.7 Å resolution. Our models...
Charting an organs’ biological atlas requires us to spatially resolve the entire single-cell transcriptome, and relate such cellular features anatomical scale. Single-cell single-nucleus RNA-seq (sc/snRNA-seq) can profile cells comprehensively, but lose spatial information. Spatial transcriptomics allows for measurements, at lower resolution with limited sensitivity. Targeted in situ technologies solve both issues, are gene throughput. To overcome these limitations we present Tangram, a...
Here we report the generation of a multimodal cell census and atlas mammalian primary motor cortex as initial product BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved morphological electrophysiological properties cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance collective knowledge...
The mammalian brain consists of millions to billions cells that are organized into many cell types with specific spatial distribution patterns and structural functional properties1-3. Here we report a comprehensive high-resolution transcriptomic cell-type atlas for the whole adult mouse brain. was created by combining single-cell RNA-sequencing (scRNA-seq) dataset around 7 million profiled (approximately 4.0 passing quality control), approximately 4.3 using multiplexed error-robust...
Abstract A mammalian brain is composed of numerous cell types organized in an intricate manner to form functional neural circuits. Single-cell RNA sequencing allows systematic identification based on their gene expression profiles and has revealed many distinct populations the 1,2 . epigenomic profiling 3,4 further provides information gene-regulatory signatures different types. Understanding how contribute function, however, requires knowledge spatial organization connectivity, which not...
In mammalian brains, millions to billions of cells form complex interaction networks enable a wide range functions. The enormous diversity and intricate organization have impeded our understanding the molecular cellular basis brain function. Recent advances in spatially resolved single-cell transcriptomics enabled systematic mapping spatial molecularly defined cell types tissues1-3, including several regions (for example, refs. 1-11). However, comprehensive atlas whole is still missing. Here...
The human cerebral cortex has tremendous cellular diversity. How different cell types are organized in the and how organization varies across species remain unclear. In this study, we performed spatially resolved single-cell profiling of 4000 genes using multiplexed error-robust fluorescence situ hybridization (MERFISH), identified more than 100 transcriptionally distinct populations, generated a molecularly defined atlas middle superior temporal gyrus. We further explored cell-cell...
The mammalian brain is composed of millions to billions cells that are organized into numerous cell types with specific spatial distribution patterns and structural functional properties. An essential step towards understanding function obtain a parts list, i.e., catalog types, the brain. Here, we report comprehensive high-resolution transcriptomic type atlas for whole adult mouse was created based on combination two single-cell-level, whole-brain-scale datasets: single-cell RNA-sequencing...
In mammalian brains, tens of millions to billions cells form complex interaction networks enable a wide range functions. The enormous diversity and intricate organization in the brain have so far hindered our understanding molecular cellular basis its Recent advances spatially resolved single-cell transcriptomics allowed systematic mapping spatial molecularly defined cell types tissues1-3. However, these approaches only been applied few regions1-11 comprehensive atlas whole is still missing....
Nucleosomes are stable DNA-histone protein complexes that must be unwrapped and disassembled for genome expression, replication, repair. Histone posttranslational modifications (PTMs) major regulatory factors of these nucleosome structural changes, but the molecular mechanisms associated with PTM function remains poorly understood. Here we demonstrate histone PTMs within distinct structured regions directly regulate inherent dynamic properties nucleosome. Precise were introduced into...
Abstract Selective hydrogenation and hydrodeoxygenation (HDO) of biomass to value‐added products play a crucial role in the development renewable energy resources. However, achieving temperature‐controlled selectivity within one catalytic system while retaining excellent HDO performance remains great challenge. Here, nitrogen/oxygen (N/O) co‐doped porous carbon nanosphere derived from resin polymer spheres is synthesized as host matrix situ encapsulate highly dispersed Pd nanoparticles...
Spatial transcriptomics is a state-of-art technique that allows researchers to study gene expression patterns in tissues over the spatial domain. As result of technical limitations, majority techniques provide bulk data for each sequencing spot. Consequently, order obtain high-resolution data, performing deconvolution becomes essential. Most existing methods rely on reference (e.g., single-cell data), which may not be available real applications. Current reference-free encounter limitations...
Epithelial cell death plays a critical role in hyperoxia-induced lung injury. We investigated the involvement of autophagic marker microtubule-associated protein-1 light chain-3B (LC3B) epithelial apoptosis after hyperoxia. Prolonged hyperoxia (>95% O(2)), which causes characteristic injury mice, activated morphological and biochemical markers autophagy. Hyperoxia induced time-dependent expression conversion LC3B-I to LC3B-II mouse vivo cultured cells (Beas-2B, human bronchial cells) vitro....
Nucleosome DNA unwrapping and its disassembly into hexasomes tetrasomes is necessary for genomic access plays an important role in transcription regulation. Previous single-molecule mechanical nucleosome revealed a low- high-force transitions, force-FRET pulling experiments showed that asymmetric, occurring always first from one side before the other. However, assignment of segments involved these transitions remains controversial. Here, using high-resolution optical tweezers with...
Biomimetic artificial surfaces that enable the manipulation of gas bubble mobility have been explored in a wide range applications nanomaterial synthesis, surface defouling, biomedical diagnostics, and therapeutics. Although many superhydrophobic isotropic-lubricant-infused porous developed to manipulate bubbles, simultaneous control over adhesion transport bubbles underwater remains challenge. Thermotropic liquid crystals (LCs), class structured fluids, provide an opportunity tune behavior...
Significance The Trp triad-dependent photoreduction of the flavin chromophore has been widely accepted as photoexcitation mechanism cryptochrome photoreceptors. However, experimental evidence supporting this hypothesis derived primarily from biophysical studies in vitro, except for one genetics study Arabidopsis 1 (CRY1). In contrast to previous report, we found that all Trp-triad mutations CRY1 remained physiologically active plants, and result cannot be readily explained by ATP-dependent...
Photolyase is a blue-light-activated enzyme that repairs ultraviolet-induced DNA damage occurs in the form of cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts. Previous studies on microbial photolyases have revealed an electron-tunneling pathway critical for repair mechanism. In this study, we used femtosecond spectroscopy to deconvolute seven electron-transfer reactions 10 elementary steps all classes CPD photolyases. We report unified through conserved...
Abstract Single-cell genomic analysis has grown rapidly in recent years and finds widespread applications various fields of biology, including cancer development, immunology, pre-implantation genetic diagnosis neurobiology. To date, the amplification bias, uniformity reproducibility three major single cell whole genome methods (GenomePlex WGA4, MDA MALBAC) have not been systematically investigated using mammalian cells. In this study, we amplified DNA from individual hippocampal neurons...
Abstract A mammalian brain is comprised of numerous cell types organized in an intricate manner to form functional neural circuits. Single-cell RNA sequencing provides a powerful approach identify based on their gene expression profiles and has revealed many distinct populations the 1-3 . epigenomic profiling 4,5 further information gene-regulatory signatures different types. Understanding how contribute function, however, requires knowledge spatial organization connectivity, which not...
Abstract Neuronal nitric oxide synthase (nNOS, gene name Nos1) orchestrates the synthesis of (NO) within neurons, pivotal for diverse neural processes encompassing synaptic transmission, plasticity, neuronal excitability, learning, memory, and neurogenesis. Despite its significance, precise regulation nNOS activity across distinct types remains incompletely understood. Erb-b2 receptor tyrosine kinase 4 (ErbB4), selectively expressed in GABAergic interneurons activated by ligand neuregulin 1...
The flavin adenine dinucleotide cofactor has an unusual bent configuration in photolyase and cryptochrome, such a folded structure may have functional role initial photochemistry. Using femtosecond spectroscopy, we report here our systematic characterization of cyclic intramolecular electron transfer (ET) dynamics between the moieties four redox forms oxidized, neutral, anionic semiquinone, hydroquinone states. By comparing wild-type mutant enzymes, determined that excited neutral oxidized...