A5012981169- Advanced Fluorescence Microscopy Techniques
- Genomics and Chromatin Dynamics
- Advanced Electron Microscopy Techniques and Applications
- RNA Research and Splicing
- Advanced Biosensing Techniques and Applications
- Near-Field Optical Microscopy
- Photoacoustic and Ultrasonic Imaging
- Advanced biosensing and bioanalysis techniques
- Immunotherapy and Immune Responses
- Nuclear Structure and Function
- Image Retrieval and Classification Techniques
- Monoclonal and Polyclonal Antibodies Research
- DNA and Nucleic Acid Chemistry
- Microtubule and mitosis dynamics
- Chromosomal and Genetic Variations
- Advanced Image and Video Retrieval Techniques
- Spectroscopy Techniques in Biomedical and Chemical Research
- Face and Expression Recognition
- Nanopore and Nanochannel Transport Studies
- Cancer Cells and Metastasis
- Single-cell and spatial transcriptomics
- Force Microscopy Techniques and Applications
- RNA Interference and Gene Delivery
Northwestern University
2022-2025
Guangdong University of Technology
2024
Disrupted nuclear shape is associated with multiple pathological processes including premature aging disorders, cancer-relevant chromosomal rearrangements, and DNA damage. Nuclear blebs (i.e., herniations of the envelope) have been induced by (1) compression, (2) migration (e.g., cancer metastasis), (3) actin contraction, (4) lamin mutation or depletion, (5) heterochromatin enzyme inhibition. Recent work has shown that chromatin transformation a hallmark bleb formation, but higher-order...
Understanding chromatin organization requires integrating measurements of genome connectivity and physical structure. It is well established that cohesin essential for TAD loop features in Hi-C, but the corresponding change structure has not been studied using electron microscopy. Pairing scanning transmission tomography with multiomic analysis single-molecule localization microscopy, we study role regulating conformationally defined nanoscopic packing domains. Our results indicate domains...
SignificanceSpectroscopic single-molecule localization microscopy (sSMLM) takes advantage of nanoscopy and spectroscopy, enabling sub-10 nm resolution as well simultaneous multicolor imaging multi-labeled samples. Reconstruction raw sSMLM data using deep learning is a promising approach for visualizing the subcellular structures at nanoscale.AimDevelop novel computational leveraging to reconstruct both label-free fluorescence-labeled data.ApproachWe developed two-network-model based...
In single cells, variably sized nanoscale chromatin structures are observed, but it is unknown whether these form a cohesive framework that regulates RNA transcription. Here, we demonstrate the human genome an emergent, self-assembling, reinforcement learning system. Conformationally defined heterogeneous, nanoscopic packing domains by interplay of transcription, nucleosome remodeling, and loop extrusion. We show not topologically associated domains. Instead, exist across structure-function...
Chromatin organization regulates transcription to influence cellular plasticity and cell fate. We explored whether chromatin nanoscale packing domains are involved in stemness response chemotherapy. Using an optical spectroscopic nanosensing technology we show that ovarian cancer-derived cancer stem cells (CSCs) display upregulation of compared non-CSCs. Cleavage under targets tagmentation (CUT&Tag) sequencing with antibodies for repressive H3K27me3 active H3K4me3 H3K27ac marks mapped...
Abstract Super-resolution microscopy has revolutionized our ability to visualize structures below the diffraction limit of conventional optical and is particularly useful for investigating complex biological targets like chromatin. Chromatin exhibits a hierarchical organization with structural compartments domains at different length scales, from nanometers micrometers. Single molecule localization (SMLM) methods, such as STORM, are essential studying chromatin supra-nucleosome level due...
Super-resolution microscopy has revolutionized our ability to visualize structures below the diffraction limit of conventional optical and is particularly useful for investigating complex biological targets like chromatin. Chromatin exhibits a hierarchical organization with structural compartments domains at different length scales, from nanometers micrometers. Single molecule localization (SMLM) methods, such as STORM, are essential studying chromatin supra-nucleosome level due their target...
ABSTRACT Disrupted nuclear shape is associated with multiple pathological processes including premature aging disorders, cancer-relevant chromosomal rearrangements, and DNA damage. Nuclear blebs (i.e., herniations of the envelope) have been induced by (1) compression, (2) migration (e.g., cancer metastasis), (3) actin contraction, (4) lamin mutation or depletion, (5) heterochromatin enzyme inhibition. Recent work has shown that chromatin transformation a hallmark bleb formation, but...
With the increasing demand for high-resolution images, handling high-dimensional image data has become a key aspect of intelligence algorithms. One effective approach is to preserve manifold structure and find accurate mappings in lower-dimensional space. However, various non-sparse, high-energy occlusions real-world images can lead erroneous calculations sample relationships, invalidating existing distance-based dimensionality reduction techniques. Many types noise are difficult capture...
The development of super-resolution imaging techniques have extended the resolving power to around 10 - 50 nm. However, most current need exogenous fluorescent dyes as contrast, whose essential weakness labeling includes imprecise spatial localization, and perturbation sample. In 2017, Dong et al., demonstrated that intrinsic fluorescence DNA under visible light excitation has similar photo-switching properties organic used in single-molecule localization microscopy. this paper, we measured...
We developed a protocol on staining and imaging of three-color single-molecule localization microscopy constitutive heterochromatin (H3K9me3), euchromatin (H3K27ac) RNA polymerase II proposed analysis methods to show their functional coupling.
The relationship between gene transcription and chromatin organization is an area of active study. Due to its role in mRNA synthesis, many studies have focused on the regulaton RNA polymerase II (Pol-II) function by supranucleosomal structure vice-versa. In contrast, there little work I (Pol-I) non-nucleolar chromatin. Prior has shown that Pol-I engages with components Pol-II rDNA, but it's global beyond nucleolus largely been ignored. By pairing auxin-inducible degron technology nanoscopic...
We present a deep-learning-based computational approach for multicolor spectroscopic single-molecule localization microscopy. Artificial neural networks trained on simulated data to localize the stochastically blinking single-molecules and enhance corresponding emission spectra show improved simultaneous imaging.
The spectra and photophysical parameters of DNA molecules under visible light illumination different wavelengths are measured for the first time, which may lead to a new label-free super-resolution imaging technique.
We present all machine learning-based reconstruction approach for simultaneous multicolor spectroscopic super-resolution microscopy. Machine learning is used localization and spectral classification. Reconstruction of the two-color imaging nanoruler sample with a mark-to-mark distance 40 nm presented.