A5100387866- Genomics and Chromatin Dynamics
- Plant Molecular Biology Research
- Advanced Electron Microscopy Techniques and Applications
- RNA and protein synthesis mechanisms
- Gene expression and cancer classification
- Electron and X-Ray Spectroscopy Techniques
- RNA Research and Splicing
- RNA modifications and cancer
- Plant Reproductive Biology
- Ubiquitin and proteasome pathways
- Advanced Fluorescence Microscopy Techniques
- Cellular Mechanics and Interactions
- Horticultural and Viticultural Research
- Near-Field Optical Microscopy
- Genomics and Phylogenetic Studies
- Spectroscopy Techniques in Biomedical and Chemical Research
- Integrated Circuits and Semiconductor Failure Analysis
- Pluripotent Stem Cells Research
- Advanced Biosensing Techniques and Applications
- Cancer-related molecular mechanisms research
- Advanced biosensing and bioanalysis techniques
- Histone Deacetylase Inhibitors Research
- Protein Degradation and Inhibitors
- Plant tissue culture and regeneration
- Phytoplasmas and Hemiptera pathogens
Heilongjiang Bayi Agricultural University
2025
The University of Texas Health Science Center at Houston
2024
Northwestern University
1999-2023
First Affiliated Hospital of Jinan University
2023
Soochow University
2023
Scripps Research Institute
2022
South China Agricultural University
2022
Wuhan University
2021
Renmin Hospital of Wuhan University
2021
Beijing Forestry University
2019-2021
Abstract Epigenomic modifications are instrumental for transcriptional regulation, but comprehensive reference epigenomes remain unexplored in rice. Here, we develop an enhanced chromatin immunoprecipitation (eChIP) approach plants, and generate genome-wide profiling of five histone RNA polymerase II occupancy with it. By integrating accessibility, DNA methylation, transcriptome datasets, construct epigenome landscapes across various tissues 20 representative rice varieties. Approximately...
Abstract As x-ray and electron tomography is pushed further into the nanoscale, limitations of rotation stages become more apparent, leading to challenges in alignment acquired projection images. Here we present an approach for rapid post-acquisition these projections obtain high quality three-dimensional Our based on a joint estimation errors, object, using iterative refinement procedure. With simulated data where know error each image, our shows residual that factor thousand smaller, it...
nano-ChIA combines multiple nanoimaging modalities to uncover 4D chromatin organization and its relationship molecular function.
Chromatin organization over multiple length scales plays a critical role in the regulation of transcription. Deciphering interplay these processes requires high-resolution, three-dimensional, quantitative imaging chromatin structure vitro. Herein, we introduce ChromSTEM, method that utilizes high-angle annular dark-field and tomography scanning transmission electron microscopy combined with DNA-specific staining for microscopy. We utilized ChromSTEM an in-depth quantification 3D conformation...
Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of protein in comprehensive and unbiased manner. A typical PBM experiment binding signal intensities to all possible DNA k-mers (k = 8 ∼10); such affinity data usually need be reduced represented as motif models before they further analyzed applied. Since proteins often bind multiple modes, one major challenges decompose into multimodal representations. Here, we describe new algorithm...
We report the development of potential theranostic agents for cardiovascular disease that are based on high-density lipoprotein-like magnetic nanostructures (HDL-MNS). The HDL-MNS offer prospects diagnosis via noninvasive resonance imaging anatomic detection and also serve as effective cholesterol efflux to address atherosclerotic vascular lesions. synthesized by adding phospholipids HDL-defining apolipoprotein A1 surface (MNS) mimic some aspects natural HDL particles. From a diagnostic...
In many human diseases, associated genetic changes tend to occur within noncoding regions, whose effect might be related transcriptional control. A central goal in genetics is understand the function of such regions: given a region that statistically with gene expression (expression quantitative trait locus [eQTL]), does it fact play regulatory role? And if so, how this role "coded" its sequence? These questions were subject Critical Assessment Genome Interpretation eQTL challenge....
The CPMC model demonstrates the regulatory role of chromatin’s physical structure on transcription and phenotypic plasticity.
With the textbook view of chromatin folding based on 30-nm fiber being challenged, it has been proposed that interphase DNA an irregular 10-nm nucleosome polymer structure whose philosophy is unknown. Nevertheless, experimental advances suggest this packing associated with many nontrivial physical properties are puzzling from a physics point view. Here, we show reconciliation these exotic necessitates modularizing three-dimensional genome into tree data structures top of, and in striking...
Enhanced expression of genes involved in nucleotide biosynthesis, such as dihydrofolate reductase (DHFR), is a hallmark entrance into the DNA synthesis (S) phase mammalian cell cycle. To investigate regulated DHFR gene, we stimulated serum-starved NIH 3T3 cells to synchronously reenter Our previous results show that cis-acting element at site transcription initiation necessary for serum regulation. Recently, this has been demonstrated bind cloned factor E2F. In study, focused on role E2F...
A conserved transcriptional feedback loop underlies animal circadian rhythms. In Drosophila , the transcription factors CLOCK (CLK) and CYCLE (CYC) activate of direct target genes like period ( per ) timeless tim ). They encode proteins PER TIM, respectively, which repress CLK/CYC activity. Previous work indicates that repression is due to a PER–CLK/CYC interaction as well phosphorylation. We describe here role ubiquitin-specific protease 8 (USP8) in importance CLK ubiquitylation usp8 loss...
Chromatin is the macromolecular assembly containing cell’s genetic information, and its architectural conformation facilitates accessibility to activation sites thus gene expression. We have developed an analytical framework quantify chromatin structure with spectral microscopy. can be described as a mass fractal, packing scaling <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mi>D</mml:mi> </mml:math> up specific genomic length scales. Considering various...
RNA is challenging to target with bioactive small molecules, particularly those of low molecular weight that bind sufficient affinity and specificity. In this report, we developed a platform address challenge, affording novel interaction. An RNA-focused small-molecule fragment collection (n = 2500) was constructed by analyzing features in all publicly reported compounds RNA, the largest fragments date. The RNA-binding landscape for each studied using library-versus-library selection an...
Adzuki bean (Vigna angularis) rust, caused by the fungus Uromyces vignae, is an important disease affecting adzuki yield and quality. Previously, several NAC transcription factors (TFs) were induced rust infection in a resistant variety, suggesting that TF members may play roles resistance. To further explore functions of TFs resistance to provide reference for varietal breeding, 101 identified from genome. The synteny analysis revealed 25 pairs VaNACs genome, which exhibited...
Abstract Motivation: Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-Seq) measures the genome-wide occupancy of transcription factors in vivo . Different combinations DNA-binding protein occupancies may result a gene being expressed different tissues or at developmental stages. To fully understand functions genes, it is essential to develop probabilistic models on multiple ChIP-Seq profiles decipher combinatorial regulatory mechanisms factors. Results: In...
ATR-X (α-thalassemia/mental retardation X-linked) syndrome is caused by mutations in chromatin remodeler ATRX. ATRX can bind the variable number of tandem repeats (VNTR) sequence promoter region α-globin gene cluster. The VNTR sequence, which contains potential G-quadruplex-forming CGC(GGGGCGGGG)n , involved downregulation expression. We investigated G-quadruplex and i-motif formation single-stranded DNA long double-stranded DNA. without showed approximately twofold higher luciferase...
The system optimum dynamic traffic assignment problem, in which drivers fix their arrival rather than departure times, is examined. A model formulated as a linear program that simultaneously optimizes time and route choice. applies to multiorigin/multidestination problems, the first-in-first-out condition generally observed on links nodes of network. An extension discussed accounts for combined time– time–based demand same models are tested an example network, results discussed.
A novel magnetic nanostructures (MNS) stabilized lipid nanoconstruct is reported that shows superior structural stability and theranostic functionality than conventional based nanocarriers.
Abstract Electron microscopy of biological, polymeric, and other beam-sensitive structures is often hampered by deleterious electron beam interactions. In fact, imaging such materials limited the allowable radiation dosage rather that capabilities microscope itself, which has been compounded availability high brightness sources. Reducing dwell times to overcome dose-related artifacts, as radiolysis electrostatic charging, challenging due inherently low contrast in many materials. These...
Transcription factor binding sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, protein microarray (PBM) high-throughput platform that can measure the DNA preference of in comprehensive unbiased manner; for instance, typical PBM experiment signal intensities to all possible k-mers (k = 8∼10). Since proteins often bind with different intensities, one major challenges build TFBS (also known as motif) models which...
Recently, N 6 -methyladenosine (m A) RNA methylation in eukaryotic mRNA has become increasingly obvious the pathogenesis and prognosis of cancer. Moreover, tumor microenvironment is involved regulation tumorigenesis. In our research, clinical data, including 374 50 normal patients, were obtained from The Cancer Genome Atlas (TCGA). Then 19 m A regulators selected other studies. Hepatocellular carcinoma (HCC) patients clustered cluster1/2, according to consensus clustering for regulators. We...