A5035856815- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Gear and Bearing Dynamics Analysis
- Redox biology and oxidative stress
- Gene expression and cancer classification
- Tribology and Lubrication Engineering
- RNA modifications and cancer
- Gene Regulatory Network Analysis
- COVID-19 diagnosis using AI
- Endoplasmic Reticulum Stress and Disease
- Signaling Pathways in Disease
- Machine Learning in Healthcare
- Artificial Intelligence in Healthcare
- Pancreatic and Hepatic Oncology Research
- Cancer-related molecular mechanisms research
- Sulfur Compounds in Biology
- Renal Transplantation Outcomes and Treatments
- Lubricants and Their Additives
- Photosynthetic Processes and Mechanisms
- Pancreatic function and diabetes
- Macrophage Migration Inhibitory Factor
- Metalloenzymes and iron-sulfur proteins
- RNA regulation and disease
Second Affiliated Hospital of Nanjing Medical University
2025
Zhengzhou University
2025
Massachusetts Institute of Technology
2019-2024
Whitehead Institute for Biomedical Research
2022-2024
Hunan University
2018-2024
Jiangsu Province Hospital
2019-2023
Nanjing Medical University
2017-2023
Peking University
2016-2022
First Affiliated Hospital of Jinan University
2020
ETH Zurich
2017
The OxyR transcription factor is sensitive to oxidation and activates the expression of antioxidant genes in response hydrogen peroxide Escherichia coli . Genetic biochemical studies revealed that activated through formation a disulfide bond deactivated by enzymatic reduction with glutaredoxin 1 (Grx1). gene encoding Grx1 regulated OxyR, thus providing mechanism for autoregulation. redox potential was determined be –185 millivolts, ensuring reduced absence stress. These results represent an...
ABSTRACT The genome-wide transcription profile of Escherichia coli cells treated with hydrogen peroxide was examined a DNA microarray composed 4,169 E. open reading frames. By measuring gene expression in isogenic wild-type and oxyR deletion strains, we confirmed that the response regulator OxyR activates most highly peroxide-inducible genes. measurements allowed identification several new OxyR-activated genes, including hemH heme biosynthetic gene; six-gene suf operon, which may participate...
The Escherichia coli transcription factor OxyR is activated by the formation of an intramolecular disulfide bond and subsequently deactivated enzymatic reduction bond. Here we show that can be two possible pathways. In mutants defective in cellular disulfide-reducing systems, constitutively a change thiol—disulfide redox status absence added oxidants. wild-type cells, hydrogen peroxide. By monitoring presence after exposure to peroxide vivo vitro , also kinetics oxidation low concentrations...
ABSTRACT The cytotoxic effects of reactive oxygen species are largely mediated by iron. Hydrogen peroxide reacts with iron to form the extremely and damaging hydroxyl radical via Fenton reaction. Superoxide anion accelerates this reaction because dismutation superoxide leads increased levels hydrogen elevates intracellular concentration attacking iron-sulfur proteins. We found that regulators Escherichia coli responses oxidative stress, OxyR SoxRS, activate expression Fur, global repressor...
We examined the genomewide transcriptional responses of Escherichia coli treated with nitrosylated glutathione or nitric oxide (NO)-generator acidified sodium nitrite (NaNO(2)) during aerobic growth. These assays showed that NorR, a homolog NO-responsive transcription factors in Ralstonia eutrophus, and Fur, global repressor ferric ion uptake, are major regulators response to reactive nitrogen species. In contrast, SoxR OxyR, E. defenses against superoxide-generating compounds hydrogen...
Two genes encoding thioredoxin are found on the<i>Escherichia coli</i> genome. Both of them capable reducing protein disulfide bonds <i>in vivo</i> and vitro</i>. The catalytic site contains a Cys-<i>X</i> <sub>1</sub>-<i>X</i> <sub>2</sub>-Cys motif in so-called fold. Thioredoxin 2 has two additional pairs cysteines non-conserved N-terminal domain. This domain does not appear to be important for the function donating electrons ribonucleotide reductase, 3′-phosphoadenylsulfate-reductase, or...
// Jian-Zhong Lin 1 , Zeng-Jun Wang 2 Wei De 3 Ming Zheng Wei-Zhang Xu 4 Hong-Fei Wu Alex Armstrong 5 and Jia-Geng Zhu 6 Department of Urology, BenQ Medical Center, Nanjing University, Nanjing, China The First Clinical College Biochemistry Molecular biology, Jiangsu Key Laboratory Translational Cancer Research, Institute Province, Pharmacology, University Manchester, England Hospital, Correspondence to: Lin, email: linjianzhong82@126.com Zhu, zhujiageng1972@sina.com Keywords: AXL, docetaxel...
ABSTRACT A computational search was carried out to identify additional targets for the Escherichia coli OxyR transcription factor. This approach predicted binding sites upstream of dsbG , encoding a periplasmic disulfide bond chaperone-isomerase; fhuF protein required iron uptake; and within yfdI . DNase I footprinting assays confirmed that oxidized bound site centered 54 bp gene 238 known in promoter region divergently transcribed ahpC gene. Although new near Northern blotting primer...
Fur is a DNA binding protein that represses bacterial iron uptake systems. Eleven footprinted Escherichia coli sites were used to create an initial information theory model of binding, which was then refined by adding 13 experimentally confirmed sites. When the scanned across all available sequences, sequence walkers, are visual depictions predicted sites, frequently appeared in clusters fit footprints ( ∼ 83% coverage). This indicated can accurately predict binding. Within clusters,...
ChIP-chip (or ChIP-on-chip) is a technology for isolation and identification of genomic sites occupied by specific DNA-binding proteins in living cells. The signals can be obtained over the whole genome tiling arrays, where peak shape generally observed around protein-binding site. In this article, we describe process present probability model data. We then propose model-based method recognizing shapes purpose detecting sites. also investigate issue bandwidth nonparametric kernel smoothing method.
Abstract Insulin receptor (IR) signaling is central to normal metabolic control and dysregulated in diseases such as type 2 diabetes. We report here that IR incorporated into dynamic clusters at the plasma membrane, cytoplasm nucleus of human hepatocytes adipocytes. stimulation promotes further incorporation these insulin-sensitive cells but not insulin-resistant cells, where both accumulation behavior are reduced. Treatment with metformin, a first-line drug used treat diabetes, can rescue...
Background Chronic allograft dysfunction (CAD) stands as a critical factor that limits the long-term viability of transplanted kidneys. Ferroptosis is an iron-dependent form programmed cell death increasingly linked to chronic fibrosis. However, mechanism by which ferroptosis contributes onset and progression CAD remains unclear. Methods This study analyzed transcriptome data from renal transplant biopsy samples in Gene Expression Omnibus (GEO), through clinical samples, animal models,...
Nanoscale spatiotemporal clustering of RNA polymerase II (Pol II) plays an important role in transcription regulation. However, dynamics individual Pol clusters live-cell nuclei has not been measured directly, prohibiting in-depth understanding their working mechanisms. In this work, we studied the using Bayesian nanoscopy live mammalian cell nuclei. With 50 nm spatial resolution and 4 s temporal resolution, allows direct observation assembly disassembly clusters. The results only provide...
Alcoholic liver disease (ALD) causes insulin resistance, lipid metabolism dysfunction, and inflammation. We investigated the protective effects direct regulating target of S-allylmercaptocysteine (SAMC) from aged garlic on cell injury. A chronic ethanol-fed ALD in vivo model (the NIAAA model) was used to test functions SAMC. It observed that SAMC (300 mg/kg, by gavage method) effectively ameliorated ALD-induced body weight reduction, steatosis, inflammation without affecting health status...
Biomolecular condensates are membraneless compartments that organize biochemical processes in cells. In contrast to well-understood mechanisms describing how form and dissolve, the principles underlying condensate patterning - including their size, number spacing cell remain largely unknown. We hypothesized RNA, a key regulator of formation dissolution, influences patterning. Using nucleolar fibrillar centers (FCs) as model condensate, we found inhibiting ribosomal RNA synthesis...