64 results on '"Fang, X."'
Search Results
2. The rate-limiting step in the folding of a large ribozyme without kinetic traps.
- Author
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Fang, X.-W., Thiyagarajan, P., Sosnick, T.R., and Pan, T.
- Subjects
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CATALYTIC RNA , *KINETIC theory of matter , *METAL ions - Abstract
Investigates the rate-limiting step in the folding of a large ribozyme in the absence of kinetic traps. Use of Chevron analysis; List of the folding parameters of C-domain; Dependence of the metal ion on the limiting step.
- Published
- 2002
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3. The thermodynamic origin of the stability of a thermophilic ribozyme.
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Fang, X.-W., Golden, B.L., Littrell, K., Shelton, V., Thiyagarajan, P., Pan, T., and Sosnick, T.R.
- Subjects
- *
CATALYTIC RNA , *THERMOPHILIC microorganisms - Abstract
Investigates the equilibrium folding of a thermophilic ribozyme and its mesophilic homologue using hydroxyl radical protection, small-angle x-ray scattering and circular dichroism. Analysis of the RNA structure; Thermodynamic origin of functional stability.
- Published
- 2001
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4. A family of erythrocyte binding proteins of malaria parasites.
- Author
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Adams, J H, Sim, B K, Dolan, S A, Fang, X, Kaslow, D C, and Miller, L H
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Malaria erythrocyte binding proteins use the Duffy blood group antigen (Plasmodium vivax and Plasmodium knowlesi) and sialic acid (Plasmodium falciparum) on the erythrocyte surface as receptors. We had previously cloned the one P. vivax gene, the one P. falciparum gene, and part of one of the three P. knowlesi genes encoding these erythrocyte binding proteins and described the homology between the P. knowlesi and P. vivax genes. We have completed the cloning and sequencing of the three P. knowlesi genes and identified introns in the P. vivax and P. falciparum genes that correct the previously published deduced amino acid sequences. All have similar structures, with one or two exons encoding the signal sequence and the erythrocyte binding domain, an exon encoding the transmembrane domain, and two exons encoding the cytoplasmic domain with the exception of the P. knowlesi beta gene. The regions of amino acid sequence homology among all the genes are the 5' and 3' cysteine-rich regions of the erythrocyte binding domain. On the basis of gene structure and amino acid homology, we propose that the Duffy binding proteins and the sialic acid binding protein are members of a gene family. The level of conservation (approximately 70%) of the deduced amino acid sequences in the 5' cysteine-rich region between the P. vivax protein and the three P. knowlesi proteins is as great as between the three P. knowlesi proteins themselves; the P. knowlesi beta protein just 3' to this cysteine-rich region is homologous to the P. vivax protein but not to the other P. knowlesi proteins. Conservation of amino acid sequences among these organisms, separated in evolution, may indicate the regions where the adhesin function resides.
- Published
- 1992
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5. dOct2, a Drosophila Oct transcription factor that functions in yeast.
- Author
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Prakash, K, Fang, X D, Engelberg, D, Behal, A, and Parker, C S
- Abstract
Oct factors are members of the POU family of transcription factors that are shown to play important roles during development in mammals. Here we report the cDNA cloning and expression of a Drosophila Oct transcription factor. Whole mount in situ hybridization experiments revealed that the spatial expression patterns of this gene during embryonic development have not yet been observed for any other gene. In early embryogenesis, its transcripts are transiently expressed as a wide uniform band from 20% to 40% of the egg length, very similar to that of gap genes. This pattern progressively resolves into a series of narrower stripes followed by expression in 14 stripes. Subsequently, transcripts from this gene are expressed in the central nervous system and the brain. When expressed in the yeast Saccharomyces cerevisiae, this Drosophila factor functions as a strong, octamer-dependent activator of transcription. Our data strongly suggest possible functions for the Oct factor in pattern formation in Drosophila that might transcend the boundaries of genetically defined segmentation genes.
- Published
- 1992
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6. Uncovering underlying physical principles and driving forces of cell differentiation and reprogramming from single-cell transcriptomics.
- Author
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Zhu L, Yang S, Zhang K, Wang H, Fang X, and Wang J
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- Animals, Humans, Gene Expression Profiling methods, Single-Cell Analysis methods, Cell Differentiation, Cellular Reprogramming genetics, Transcriptome
- Abstract
Recent advances in single-cell sequencing technology have revolutionized our ability to acquire whole transcriptome data. However, uncovering the underlying transcriptional drivers and nonequilibrium driving forces of cell function directly from these data remains challenging. We address this by learning cell state vector fields from discrete single-cell RNA velocity to quantify the single-cell global nonequilibrium driving forces as landscape and flux. From single-cell data, we quantified the Waddington landscape, showing that optimal paths for differentiation and reprogramming deviate from the naively expected landscape gradient paths and may not pass through landscape saddles at finite fluctuations, challenging conventional transition state estimation of kinetic rate for cell fate decisions due to the presence of the flux. A key insight from our study is that stem/progenitor cells necessitate greater energy dissipation for rapid cell cycles and self-renewal, maintaining pluripotency. We predict optimal developmental pathways and elucidate the nucleation mechanism of cell fate decisions, with transition states as nucleation sites and pioneer genes as nucleation seeds. The concept of loop flux quantifies the contributions of each cycle flux to cell state transitions, facilitating the understanding of cell dynamics and thermodynamic cost, and providing insights into optimizing biological functions. We also infer cell-cell interactions and cell-type-specific gene regulatory networks, encompassing feedback mechanisms and interaction intensities, predicting genetic perturbation effects on cell fate decisions from single-cell omics data. Essentially, our methodology validates the landscape and flux theory, along with its associated quantifications, offering a framework for exploring the physical principles underlying cellular differentiation and reprogramming and broader biological processes through high-throughput single-cell sequencing experiments., Competing Interests: Competing interests statement:The authors declare no competing interest.
- Published
- 2024
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7. Rapid detection of IDH mutations in gliomas by intraoperative mass spectrometry.
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Hua W, Zhang W, Brown H, Wu J, Fang X, Shahi M, Chen R, Zhang H, Jiao B, Wang N, Xu H, Fu M, Wang X, Zhang J, Zhang X, Wang Q, Zhu W, Ye D, Garcia DM, Chaichana K, Cooks RG, Ouyang Z, Mao Y, and Quinones-Hinojosa A
- Subjects
- Humans, Tandem Mass Spectrometry methods, Glutarates metabolism, Mass Spectrometry methods, Glutamic Acid metabolism, Glutamic Acid genetics, Glioma genetics, Glioma surgery, Glioma pathology, Isocitrate Dehydrogenase genetics, Mutation, Brain Neoplasms genetics, Brain Neoplasms surgery, Brain Neoplasms pathology
- Abstract
The development and performance of two mass spectrometry (MS) workflows for the intraoperative diagnosis of isocitrate dehydrogenase (IDH) mutations in glioma is implemented by independent teams at Mayo Clinic, Jacksonville, and Huashan Hospital, Shanghai. The infiltrative nature of gliomas makes rapid diagnosis necessary to guide the extent of surgical resection of central nervous system (CNS) tumors. The combination of tissue biopsy and MS analysis used here satisfies this requirement. The key feature of both described methods is the use of tandem MS to measure the oncometabolite 2-hydroxyglutarate (2HG) relative to endogenous glutamate (Glu) to characterize the presence of mutant tumor. The experiments i) provide IDH mutation status for individual patients and ii) demonstrate a strong correlation of 2HG signals with tumor infiltration. The measured ratio of 2HG to Glu correlates with IDH-mutant (IDH-mut) glioma ( P < 0.0001) in the tumor core data of both teams. Despite using different ionization methods and different mass spectrometers, comparable performance in determining IDH mutations from core tumor biopsies was achieved with sensitivities, specificities, and accuracies all at 100%. None of the 31 patients at Mayo Clinic or the 74 patients at Huashan Hospital were misclassified when analyzing tumor core biopsies. Robustness of the methodology was evaluated by postoperative re-examination of samples. Both teams noted the presence of high concentrations of 2HG at surgical margins, supporting future use of intraoperative MS to monitor for clean surgical margins. The power of MS diagnostics is shown in resolving contradictory clinical features, e.g., in distinguishing gliosis from IDH-mut glioma., Competing Interests: Competing interests statement:Z.O. is the founder of PurSpec Technologies, which is developing miniature mass spectrometry systems.
- Published
- 2024
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8. Targeting MFGE8 secreted by cancer-associated fibroblasts blocks angiogenesis and metastasis in esophageal squamous cell carcinoma.
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Liu B, Zhang B, Qi J, Zhou H, Tan L, Huang J, Huang J, Fang X, Gong L, Luo J, Liu S, Fu L, Ling F, Ma S, Lai-Wan Kwong D, Wang X, and Guan XY
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- Humans, Proto-Oncogene Proteins c-akt metabolism, Phosphatidylinositol 3-Kinases metabolism, Cell Line, Tumor, Cell Proliferation, Fibroblasts metabolism, Tumor Microenvironment, Antigens, Surface metabolism, Milk Proteins metabolism, Esophageal Squamous Cell Carcinoma pathology, Cancer-Associated Fibroblasts metabolism, Esophageal Neoplasms genetics, Esophageal Neoplasms metabolism
- Abstract
Cancer-associated fibroblasts (CAFs) play vital roles in establishing a suitable tumor microenvironment. In this study, RNA sequencing data revealed that CAFs could promote cell proliferation, angiogenesis, and ECM reconstitution by binding to integrin families and activating PI3K/AKT pathways in esophageal squamous cell carcinoma (ESCC). The secretions of CAFs play an important role in regulating these biological activities. Among these secretions, we found that MFGE8 is specifically secreted by CAFs in ESCC. Additionally, the secreted MFGE8 protein is essential in CAF-regulated vascularization, tumor proliferation, drug resistance, and metastasis. By binding to Integrin αVβ3/αVβ5 receptors, MFGE8 promotes tumor progression by activating both the PI3K/AKT and ERK/AKT pathways. Interestingly, the biological function of MFGE8 secreted by CAFs fully demonstrated the major role of CAFs in ESCC and its mode of mechanism, showing that MFGE8 could be a driver factor of CAFs in remodeling the tumor environment. In vivo treatment targeting CAFs-secreting MFGE8 or its receptor produced significant inhibitory effects on ESCC growth and metastasis, which provides an approach for the treatment of ESCC.
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- 2023
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9. CPT1A-mediated fatty acid oxidation confers cancer cell resistance to immune-mediated cytolytic killing.
- Author
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Liu Z, Liu W, Wang W, Ma Y, Wang Y, Drum DL, Cai J, Blevins H, Lee E, Shah S, Fisher PB, Wang X, Fang X, Guo C, and Wang XY
- Subjects
- Humans, Cytotoxicity, Immunologic, Fatty Acids, Lipid Metabolism, T-Lymphocytes, Cytotoxic, Carnitine O-Palmitoyltransferase genetics, Neoplasms therapy
- Abstract
Although tumor-intrinsic fatty acid β-oxidation (FAO) is implicated in multiple aspects of tumorigenesis and progression, the impact of this metabolic pathway on cancer cell susceptibility to immunotherapy remains unknown. Here, we report that cytotoxicity of killer T cells induces activation of FAO and upregulation of carnitine palmitoyltransferase 1A (CPT1A), the rate-limiting enzyme of FAO in cancer cells. The repression of CPT1A activity or expression renders cancer cells more susceptible to destruction by cytotoxic T lymphocytes. Our mechanistic studies reveal that FAO deficiency abrogates the prosurvival signaling in cancer cells under immune cytolytic stress. Furthermore, we identify T cell-derived IFN-γ as a major factor responsible for induction of CPT1A and FAO in an AMPK-dependent manner, indicating a dynamic interplay between immune effector cells and tumor targets. While cancer growth in the absence of CPT1A remains largely unaffected, established tumors upon FAO inhibition become significantly more responsive to cellular immunotherapies including chimeric antigen receptor-engineered human T cells. Together, these findings uncover a mode of cancer resistance and immune editing that can facilitate immune escape and limit the benefits of immunotherapies.
- Published
- 2023
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10. Mid-Pleistocene links between Asian dust, Tibetan glaciers, and Pacific iron fertilization.
- Author
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Zan J, Maher BA, Yamazaki T, Fang X, Han W, Kang J, and Hu Z
- Abstract
Increasing Asian dust fluxes, associated with late Cenozoic cooling and intensified glaciations, are conventionally thought to drive iron fertilization of phytoplankton productivity in the North Pacific, contributing to ocean carbon storage and drawdown of atmospheric CO
2 . During the early Pleistocene glaciations, however, productivity remained low despite higher Asian dust fluxes, only displaying glacial stage increases after the mid-Pleistocene climate transition (~800 ka B.P.). We solve this paradox by analyzing an Asian dust sequence, spanning the last 3.6 My, from the Tarim Basin, identifying a major switch in the iron composition of the dust at ~800 ka, associated with expansion of Tibetan glaciers and enhanced production of freshly ground rock minerals. This compositional shift in the Asian dust was recorded synchronously in the downwind, deep sea sediments of the central North Pacific. The switch from desert dust, containing stable, highly oxidized iron, to glacial dust, richer in reactive reduced iron, coincided with increased populations of silica-producing phytoplankton in the equatorial North Pacific and increased primary productivity in more northerly locations, such as the South China Sea. We calculate that potentially bioavailable Fe2+ flux to the North Pacific was more than doubled after the switch to glacially- sourced dust. These findings indicate a positive feedback between Tibetan glaciations, glaciogenic production of dust with enhanced iron bioavailability, and changes in North Pacific iron fertilization. Notably, this strengthened link between climate and eolian dust coincided with the mid-Pleistocene transition to increased storage of C in the glacial North Pacific and more intense northern hemisphere glaciations.- Published
- 2023
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11. Proline hydroxylation of CREB-regulated transcriptional coactivator 2 controls hepatic glucose metabolism.
- Author
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Xue Y, Cui A, Wei S, Ma F, Liu Z, Fang X, Huo S, Sun X, Li W, Hu Z, Liu Y, Cai G, Su W, Zhao J, Yan X, Gao C, Wen J, Zhang H, Li H, Liu Y, Lin X, Xu Y, Fu W, Fang J, and Li Y
- Subjects
- Humans, Mice, Animals, Proline metabolism, Hydroxylation, Liver metabolism, Cyclic AMP Response Element-Binding Protein genetics, Cyclic AMP Response Element-Binding Protein metabolism, Gluconeogenesis physiology, Prolyl Hydroxylases metabolism, Hepatocytes metabolism, Mice, Inbred C57BL, Glucose metabolism, Diabetes Mellitus, Type 2 metabolism
- Abstract
Prolyl hydroxylase domain (PHD) enzymes change HIF activity according to oxygen signal; whether it is regulated by other physiological conditions remains largely unknown. Here, we report that PHD3 is induced by fasting and regulates hepatic gluconeogenesis through interaction and hydroxylation of CRTC2. Pro129 and Pro615 hydroxylation of CRTC2 following PHD3 activation is necessary for its association with cAMP-response element binding protein (CREB) and nuclear translocation, and enhanced binding to promoters of gluconeogenic genes by fasting or forskolin. CRTC2 hydroxylation-stimulated gluconeogenic gene expression is independent of SIK-mediated phosphorylation of CRTC2. Liver-specific knockout of PHD3 (PHD3 LKO) or prolyl hydroxylase-deficient knockin mice (PHD3 KI) show attenuated fasting gluconeogenic genes, glycemia, and hepatic capacity to produce glucose during fasting or fed with high-fat, high-sucrose diet. Importantly, Pro615 hydroxylation of CRTC2 by PHD3 is increased in livers of fasted mice, diet-induced insulin resistance or genetically obese ob/ob mice, and humans with diabetes. These findings increase our understanding of molecular mechanisms linking protein hydroxylation to gluconeogenesis and may offer therapeutic potential for treating excessive gluconeogenesis, hyperglycemia, and type 2 diabetes.
- Published
- 2023
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12. Knowledge gaps are making it harder to formulate national climate policies.
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Feng R, Hu L, Hu X, and Fang X
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- 2023
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13. Human defensin-inspired discovery of peptidomimetic antibiotics.
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Luo G, Zhang J, Wang H, Sun Y, Cheng B, Xu Z, Zhang Y, Li H, Lu W, Nemeth E, Ganz T, and Fang X
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- Anti-Bacterial Agents pharmacology, Defensins pharmacology, Gram-Negative Bacteria drug effects, Humans, Microbial Sensitivity Tests, Molecular Structure, Peptidomimetics pharmacology, Structure-Activity Relationship, Anti-Bacterial Agents chemistry, Defensins chemistry, Drug Discovery methods, Peptidomimetics chemistry
- Abstract
SignificanceWe report the development of peptidomimetic antibiotics derived from a natural antimicrobial peptide, human α-defensin 5. By engaging multiple bacterial targets, the lead compound is efficacious in vitro and in vivo against bacteria with highly inducible antibiotic resistance, promising a useful therapeutic agent for the treatment of infections caused by antibiotic-resistant bacteria.
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- 2022
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14. Antagonistic cotranscriptional regulation through ARGONAUTE1 and the THO/TREX complex orchestrates FLC transcriptional output.
- Author
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Xu C, Fang X, Lu T, and Dean C
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- Cell Nucleus metabolism, Chromatin metabolism, Flowers genetics, Gene Expression Regulation, Plant, Gene Silencing, Histone Deacetylases genetics, Histone-Lysine N-Methyltransferase metabolism, Histones metabolism, MADS Domain Proteins genetics, Proteomics, RNA Polymerase II metabolism, RNA Splicing, RNA, Antisense genetics, Arabidopsis genetics, Arabidopsis metabolism, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism, Argonaute Proteins genetics, Argonaute Proteins metabolism, Histone Deacetylases metabolism, MADS Domain Proteins metabolism
- Abstract
Quantitative transcriptional control is essential for physiological and developmental processes in many organisms. Transcriptional output is influenced by cotranscriptional processes interconnected to chromatin regulation, but how the functions of different cotranscriptional regulators are integrated is poorly understood. The Arabidopsis floral repressor locus FLOWERING LOCUS C ( FLC ) is cotranscriptionally repressed by alternative processing of the antisense transcript COOLAIR. Proximal 3'-end processing of COOLAIR resolves a cotranscriptionally formed R-loop, and this process physically links to a histone-modifying complex FLD/SDG26/LD. This induces a chromatin environment locally that determines low transcription initiation and a slow elongation rate to both sense and antisense strands. Here, we show that ARGONAUTE1 (AGO1) genetically functions in this cotranscriptional repression mechanism. AGO1 associates with COOLAIR and influences COOLAIR splicing dynamics to promote proximal COOLAIR , R-loop resolution, and chromatin silencing. Proteomic analyses revealed physical associations between AGO1, subunits of RNA Polymerase II (Pol II), the splicing-related proteins-the spliceosome NineTeen Complex (NTC) and related proteins (NTR)-and the THO/TREX complex. We connect these activities by demonstrating that the THO/TREX complex activates FLC expression acting antagonistically to AGO1 in COOLAIR processing. Together these data reveal that antagonistic cotranscriptional regulation through AGO1 or THO/TREX influences COOLAIR processing to deliver a local chromatin environment that determines FLC transcriptional output. The involvement of these conserved cotranscriptional regulators suggests similar mechanisms may underpin quantitative transcriptional regulation generally., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)
- Published
- 2021
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15. Ciliopathy genes are required for apical secretion of Cochlin, an otolith crystallization factor.
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Leventea E, Zhu Z, Fang X, Nikolaeva Y, Markham E, Hirst RA, van Eeden FJM, and Malicki JJ
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- Amino Acid Sequence, Animals, Bardet-Biedl Syndrome genetics, Base Sequence, Cilia metabolism, Crystallization, Epistasis, Genetic, Extracellular Matrix Proteins genetics, Gene Expression Regulation, Developmental, Homozygote, Mutation genetics, Phenotype, Zebrafish Proteins genetics, Ciliopathies genetics, Otolithic Membrane metabolism, Zebrafish genetics, Zebrafish Proteins metabolism
- Abstract
Here, we report that important regulators of cilia formation and ciliary compartment-directed protein transport function in secretion polarity. Mutations in cilia genes cep290 and bbs2 , involved in human ciliopathies, affect apical secretion of Cochlin, a major otolith component and a determinant of calcium carbonate crystallization form. We show that Cochlin, defective in human auditory and vestibular disorder, DFNA9, is secreted from small specialized regions of vestibular system epithelia. Cells of these regions secrete Cochlin both apically into the ear lumen and basally into the basal lamina. Basally secreted Cochlin diffuses along the basal surface of vestibular epithelia, while apically secreted Cochlin is incorporated into the otolith. Mutations in a subset of ciliopathy genes lead to defects in Cochlin apical secretion, causing abnormal otolith crystallization and behavioral defects. This study reveals a class of ciliary proteins that are important for the polarity of secretion and delineate a secretory pathway that regulates biomineralization., Competing Interests: The authors declare no competing interest.
- Published
- 2021
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16. Chemical mutagenesis of a GPCR ligand: Detoxifying "inflammo-attraction" to direct therapeutic stem cell migration.
- Author
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Lee JP, Zhang R, Yan M, Duggineni S, Wakeman DR, Niles WL, Feng Y, Chen J, Hamblin MH, Han EB, Gonzalez R, Fang X, Zhu Y, Wang J, Xu Y, Wenger DA, Seyfried TN, An J, Sidman RL, Huang Z, and Snyder EY
- Subjects
- Astrocytes metabolism, Astrocytes pathology, Cell Movement genetics, Central Nervous System metabolism, Central Nervous System pathology, Humans, Induced Pluripotent Stem Cells, Inflammation genetics, Ligands, Mutagenesis genetics, Neural Stem Cells metabolism, Neural Stem Cells transplantation, Neurodegenerative Diseases genetics, Neurodegenerative Diseases therapy, Neurons pathology, Chemokine CXCL12 genetics, Neurons metabolism, Protein Binding genetics, Receptors, CXCR4 genetics
- Abstract
A transplanted stem cell's engagement with a pathologic niche is the first step in its restoring homeostasis to that site. Inflammatory chemokines are constitutively produced in such a niche; their binding to receptors on the stem cell helps direct that cell's "pathotropism." Neural stem cells (NSCs), which express CXCR4, migrate to sites of CNS injury or degeneration in part because astrocytes and vasculature produce the inflammatory chemokine CXCL12. Binding of CXCL12 to CXCR4 (a G protein-coupled receptor, GPCR) triggers repair processes within the NSC. Although a tool directing NSCs to where needed has been long-sought, one would not inject this chemokine in vivo because undesirable inflammation also follows CXCL12-CXCR4 coupling. Alternatively, we chemically "mutated" CXCL12, creating a CXCR4 agonist that contained a strong pure binding motif linked to a signaling motif devoid of sequences responsible for synthetic functions. This synthetic dual-moity CXCR4 agonist not only elicited more extensive and persistent human NSC migration and distribution than did native CXCL 12, but induced no host inflammation (or other adverse effects); rather, there was predominantly reparative gene expression. When co-administered with transplanted human induced pluripotent stem cell-derived hNSCs in a mouse model of a prototypical neurodegenerative disease, the agonist enhanced migration, dissemination, and integration of donor-derived cells into the diseased cerebral cortex (including as electrophysiologically-active cortical neurons) where their secreted cross-corrective enzyme mediated a therapeutic impact unachieved by cells alone. Such a "designer" cytokine receptor-agonist peptide illustrates that treatments can be controlled and optimized by exploiting fundamental stem cell properties (e.g., "inflammo-attraction")., Competing Interests: Competing interest statement: J.R.S. was one of 17 coauthors with R.G. and E.Y.S. on a 2016 research article. He did not collaborate directly with them., (Copyright © 2020 the Author(s). Published by PNAS.)
- Published
- 2020
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17. The 3.6-Ma aridity and westerlies history over midlatitude Asia linked with global climatic cooling.
- Author
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Fang X, An Z, Clemens SC, Zan J, Shi Z, Yang S, and Han W
- Abstract
Midlatitude Asia (MLA), strongly influenced by westerlies-controlled climate, is a key source of global atmospheric dust, and plays a significant role in Earth's climate system . However, it remains unclear how the westerlies, MLA aridity, and dust flux from this region evolved over time. Here, we report a unique high-resolution eolian dust record covering the past 3.6 Ma, retrieved from the thickest loess borehole sequence (671 m) recovered to date, at the southern margin of the Taklimakan desert in the MLA interior. The results show that eolian dust accumulation, which is closely related to aridity and the westerlies, indicates existence of a dry climate, desert area, and stable land surface, promoting continuous loess deposition since at least ∼3.6 Ma. This region experienced long-term stepwise drying at ∼2.7, 1.1, and 0.5 Ma, coeval with a dominant periodicity shift from 41-ka cyclicity to 100-ka cyclicity between 1.1 Ma and 0.5 Ma. These features match well with global ice volume variability both in the time and frequency domains (including the Mid-Pleistocene Transition), highlighting global cooling-forced aridity and westerlies climate changes on these timescales. Numerical modeling demonstrates that global cooling can dry MLA and intensify the westerlies, which facilitates dust emission and transport, providing an interpretive framework. Increased dust may have promoted positive feedbacks (e.g., decreasing atmospheric CO
2 concentrations and modulating radiation budgets), contributing to further cooling. Unraveling the long-term evolution of MLA aridity and westerlies climate is an indispensable component of the unfolding mystery of global climate change., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)- Published
- 2020
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18. Site-specific covalent labeling of large RNAs with nanoparticles empowered by expanded genetic alphabet transcription.
- Author
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Wang Y, Chen Y, Hu Y, and Fang X
- Subjects
- Dengue Virus chemistry, Scattering, Small Angle, Transcription, Genetic, Dengue Virus genetics, Gold chemistry, Metal Nanoparticles chemistry, RNA, Viral chemistry, RNA, Viral genetics
- Abstract
Conjugation of RNAs with nanoparticles (NPs) is of significant importance because of numerous applications in biology and medicine, which, however, remains challenging especially for large ones. So far, the majority of RNA labeling relies on solid-phase chemical synthesis, which is generally limited to RNAs smaller than 100 nucleotides (nts). We, here, present an efficient and generally applicable labeling strategy for site-specific covalent conjugation of large RNAs with a gold nanoparticle (Nanogold) empowered by transcription of an expanded genetic alphabet containing the A-T/U and G-C natural base pairs (bps) and the TPT3-NaM unnatural base pair (UBP). We synthesize an amine-derivatized TPT3 (TPT3
A ), which is site specifically incorporated into a 97-nt 3'SL RNA and a 719-nt minigenomic RNA (DENV-mini) from Dengue virus serotype 2 (DENV2) by in vitro T7 transcription. The TPT3A -modified RNAs are covalently conjugated with mono- Sulfo - N -hydroxysuccinimidyl (NHS)-Nanogold NPs via an amine and NHS ester reaction and further purified under nondenaturing conditions. TPT3 modification and Nanogold labeling cause minimal structural perturbations to the RNAs by circular dichroism, small angle X-ray scattering (SAXS), and binding activity assay. We demonstrate the application of the Nanogold-RNA conjugates in large RNA structural biology by an emerging molecular ruler, X-ray scattering interferometry (XSI). The internanoparticle distance distributions in the 3'SL and DENV-mini RNAs derived from XSI measurements support the hypothetical model of flavivirus genome circularization, thus, validate the applicability of this labeling strategy. The presented strategy overcomes the size constraints in conventional RNA labeling strategies and is expected to have wide applications in large RNA structural biology and RNA nanotechnology., Competing Interests: The authors declare no competing interest.- Published
- 2020
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19. The Arabidopsis epigenetic regulator ICU11 as an accessory protein of Polycomb Repressive Complex 2.
- Author
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Bloomer RH, Hutchison CE, Bäurle I, Walker J, Fang X, Perera P, Velanis CN, Gümüs S, Spanos C, Rappsilber J, Feng X, Goodrich J, and Dean C
- Subjects
- Arabidopsis genetics, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism, Histones genetics, Histones metabolism, Methylation, Protein Binding, Transcription Factors genetics, Transcription Factors metabolism, Arabidopsis metabolism, Epigenesis, Genetic, Polycomb Repressive Complex 2 genetics, Polycomb Repressive Complex 2 metabolism
- Abstract
Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular function we identified the Arabidopsis FLOWERING LOCUS C ( FLC ) as a direct target and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site in FLC , and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states at FLC , from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)
- Published
- 2020
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20. The 3' processing of antisense RNAs physically links to chromatin-based transcriptional control.
- Author
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Fang X, Wu Z, Raitskin O, Webb K, Voigt P, Lu T, Howard M, and Dean C
- Subjects
- Arabidopsis Proteins genetics, Chromatin, RNA, Plant genetics, Arabidopsis metabolism, Arabidopsis Proteins metabolism, Gene Expression Regulation, Plant physiology, RNA, Antisense, RNA, Plant metabolism, Transcription, Genetic physiology
- Abstract
Noncoding RNA plays essential roles in transcriptional control and chromatin silencing. At Arabidopsis thaliana FLC, antisense transcription quantitatively influences transcriptional output, but the mechanism by which this occurs is still unclear. Proximal polyadenylation of the antisense transcripts by FCA, an RNA-binding protein that physically interacts with RNA 3' processing factors, reduces FLC transcription. This process genetically requires FLD, a homolog of the H3K4 demethylase LSD1. However, the mechanism linking RNA processing to FLD function had not been established. Here, we show that FLD tightly associates with LUMINIDEPENDENS (LD) and SET DOMAIN GROUP 26 (SDG26) in vivo, and, together, they prevent accumulation of monomethylated H3K4 (H3K4me1) over the FLC gene body. SDG26 interacts with the RNA 3' processing factor FY (WDR33), thus linking activities for proximal polyadenylation of the antisense transcripts to FLD/LD/SDG26-associated H3K4 demethylation. We propose this demethylation antagonizes an active transcription module, thus reducing H3K36me3 accumulation and increasing H3K27me3. Consistent with this view, we show that Polycomb Repressive Complex 2 (PRC2) silencing is genetically required by FCA to repress FLC Overall, our work provides insights into RNA-mediated chromatin silencing., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)
- Published
- 2020
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21. Sympatric speciation of wild emmer wheat driven by ecology and chromosomal rearrangements.
- Author
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Wang H, Yin H, Jiao C, Fang X, Wang G, Li G, Ni F, Li P, Su P, Ge W, Lyu Z, Xu S, Yang Y, Hao Y, Cheng X, Zhao J, Liu C, Xu F, Ma X, Sun S, Zhao Y, Bao Y, Liu C, Zhang J, Pavlicek T, Li A, Yang Z, Nevo E, and Kong L
- Subjects
- Ascomycota, Basidiomycota, Chromosomes, Plant, Gene Flow, Genes, Plant genetics, Homozygote, Israel, Karyotyping, Plant Diseases microbiology, Stress, Physiological, Disease Resistance genetics, Sympatry genetics, Triticum genetics
- Abstract
In plants, the mechanism for ecological sympatric speciation (SS) is little known. Here, after ruling out the possibility of secondary contact, we show that wild emmer wheat, at the microclimatically divergent microsite of "Evolution Canyon" (EC), Mt. Carmel, Israel, underwent triple SS. Initially, it split following a bottleneck of an ancestral population, and further diversified to three isolated populations driven by disruptive ecological selection. Remarkably, two postzygotically isolated populations (SFS1 and SFS2) sympatrically branched within an area less than 30 m at the tropical hot and dry savannoid south-facing slope (SFS). A series of homozygous chromosomal rearrangements in the SFS1 population caused hybrid sterility with the SFS2 population. We demonstrate that these two populations developed divergent adaptive mechanisms against severe abiotic stresses on the tropical SFS. The SFS2 population evolved very early flowering, while the SFS1 population alternatively evolved a direct tolerance to irradiance by improved ROS scavenging activity that potentially accounts for its evolutionary fate with unstable chromosome status. Moreover, a third prezygotically isolated sympatric population adapted on the abutting temperate, humid, cool, and forested north-facing slope (NFS), separated by 250 m from the SFS wild emmer wheat populations. The NFS population evolved multiple resistant loci to fungal diseases, including powdery mildew and stripe rust. Our study illustrates how plants sympatrically adapt and speciate under disruptive ecological selection of abiotic and biotic stresses., Competing Interests: The authors declare no competing interest.
- Published
- 2020
- Full Text
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22. A three-dimensional hybrid electrode with electroactive microbes for efficient electrogenesis and chemical synthesis.
- Author
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Fang X, Kalathil S, Divitini G, Wang Q, and Reisner E
- Abstract
Integration of electroactive bacteria into electrodes combines strengths of intracellular biochemistry with electrochemistry for energy conversion and chemical synthesis. However, such biohybrid systems are often plagued with suboptimal electrodes, which limits the incorporation and productivity of the bacterial colony. Here, we show that an inverse opal-indium tin oxide electrode hosts a large population of current-producing Geobacter and attains a current density of 3 mA cm
-2 stemming from bacterial respiration. Differential gene expression analysis revealed Geobacter 's transcriptional regulations to express more electron-relaying proteins when interfaced with electrodes. The electrode also allows coculturing with Shewanella for syntrophic electrogenesis, which grants the system additional flexibility in converting electron donors. The biohybrid electrode containing Geobacter can also catalyze the reduction of soluble fumarate and heterogenous graphene oxide, with electrons from an external power source or an irradiated photoanode. This biohybrid electrode represents a platform to employ live cells for sustainable power generation and biosynthesis., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)- Published
- 2020
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23. Remarkable nucleation and growth of ultrafine particles from vehicular exhaust.
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Guo S, Hu M, Peng J, Wu Z, Zamora ML, Shang D, Du Z, Zheng J, Fang X, Tang R, Wu Y, Zeng L, Shuai S, Zhang W, Wang Y, Ji Y, Li Y, Zhang AL, Wang W, Zhang F, Zhao J, Gong X, Wang C, Molina MJ, and Zhang R
- Subjects
- Air Pollutants chemistry, Oxidation-Reduction, Particle Size, Temperature, Particulate Matter chemistry, Vehicle Emissions analysis
- Abstract
High levels of ultrafine particles (UFPs; diameter of less than 50 nm) are frequently produced from new particle formation under urban conditions, with profound implications on human health, weather, and climate. However, the fundamental mechanisms of new particle formation remain elusive, and few experimental studies have realistically replicated the relevant atmospheric conditions. Previous experimental studies simulated oxidation of one compound or a mixture of a few compounds, and extrapolation of the laboratory results to chemically complex air was uncertain. Here, we show striking formation of UFPs in urban air from combining ambient and chamber measurements. By capturing the ambient conditions (i.e., temperature, relative humidity, sunlight, and the types and abundances of chemical species), we elucidate the roles of existing particles, photochemistry, and synergy of multipollutants in new particle formation. Aerosol nucleation in urban air is limited by existing particles but negligibly by nitrogen oxides. Photooxidation of vehicular exhaust yields abundant precursors, and organics, rather than sulfuric acid or base species, dominate formation of UFPs under urban conditions. Recognition of this source of UFPs is essential to assessing their impacts and developing mitigation policies. Our results imply that reduction of primary particles or removal of existing particles without simultaneously limiting organics from automobile emissions is ineffective and can even exacerbate this problem., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)
- Published
- 2020
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24. What music makes us feel: At least 13 dimensions organize subjective experiences associated with music across different cultures.
- Author
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Cowen AS, Fang X, Sauter D, and Keltner D
- Subjects
- Auditory Perception, China, Cross-Cultural Comparison, Humans, United States, Affect physiology, Arousal physiology, Cultural Evolution, Emotions physiology, Models, Theoretical, Music psychology
- Abstract
What is the nature of the feelings evoked by music? We investigated how people represent the subjective experiences associated with Western and Chinese music and the form in which these representational processes are preserved across different cultural groups. US ( n = 1,591) and Chinese ( n = 1,258) participants listened to 2,168 music samples and reported on the specific feelings (e.g., "angry," "dreamy") or broad affective features (e.g., valence, arousal) that they made individuals feel. Using large-scale statistical tools, we uncovered 13 distinct types of subjective experience associated with music in both cultures. Specific feelings such as "triumphant" were better preserved across the 2 cultures than levels of valence and arousal, contrasting with theoretical claims that valence and arousal are building blocks of subjective experience. This held true even for music selected on the basis of its valence and arousal levels and for traditional Chinese music. Furthermore, the feelings associated with music were found to occupy continuous gradients, contradicting discrete emotion theories. Our findings, visualized within an interactive map (https://www.ocf.berkeley.edu/∼acowen/music.html) reveal a complex, high-dimensional space of subjective experience associated with music in multiple cultures. These findings can inform inquiries ranging from the etiology of affective disorders to the neurological basis of emotion., Competing Interests: The authors declare no competing interest.
- Published
- 2020
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25. Structure and regulation of human epithelial cell transforming 2 protein.
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Chen M, Pan H, Sun L, Shi P, Zhang Y, Li L, Huang Y, Chen J, Jiang P, Fang X, Wu C, and Chen Z
- Subjects
- Binding Sites, Cytokinesis physiology, Fluorescence Resonance Energy Transfer, Gene Knockdown Techniques, Humans, Mutation, Neoplasms genetics, Neoplasms metabolism, Protein Conformation, Protein Domains, Proto-Oncogene Proteins genetics, Signal Transduction, rhoA GTP-Binding Protein chemistry, rhoA GTP-Binding Protein metabolism, Epithelial Cells metabolism, Proto-Oncogene Proteins chemistry, Proto-Oncogene Proteins metabolism
- Abstract
Epithelial cell transforming 2 (Ect2) protein activates Rho GTPases and controls cytokinesis and many other cellular processes. Dysregulation of Ect2 is associated with various cancers. Here, we report the crystal structure of human Ect2 and complementary mechanistic analyses. The data show the C-terminal PH domain of Ect2 folds back and blocks the canonical RhoA-binding site at the catalytic center of the DH domain, providing a mechanism of Ect2 autoinhibition. Ect2 is activated by binding of GTP-bound RhoA to the PH domain, which suggests an allosteric mechanism of Ect2 activation and a positive-feedback loop reinforcing RhoA signaling. This bimodal RhoA binding of Ect2 is unusual and was confirmed with Förster resonance energy transfer (FRET) and hydrogen-deuterium exchange mass spectrometry (HDX-MS) analyses. Several recurrent cancer-associated mutations map to the catalytic and regulatory interfaces, and dysregulate Ect2 in vitro and in vivo. Together, our findings provide mechanistic insights into Ect2 regulation in normal cells and under disease conditions., Competing Interests: The authors declare no competing interest.
- Published
- 2020
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26. Increased gene copy number of DEFA1/DEFA3 worsens sepsis by inducing endothelial pyroptosis.
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Chen Q, Yang Y, Hou J, Shu Q, Yin Y, Fu W, Han F, Hou T, Zeng C, Nemeth E, Linzmeier R, Ganz T, and Fang X
- Subjects
- Alleles, Animals, Antibodies, Monoclonal genetics, Antibodies, Monoclonal immunology, DNA Copy Number Variations genetics, Disease Models, Animal, Endothelial Cells metabolism, Endothelial Cells pathology, Humans, Inflammasomes genetics, Inflammasomes immunology, Mice, Mice, Transgenic, NLR Family, Pyrin Domain-Containing 3 Protein genetics, Pyroptosis genetics, Pyroptosis immunology, Receptors, Purinergic P2X7 genetics, Risk Factors, Sepsis blood, Sepsis pathology, alpha-Defensins antagonists & inhibitors, alpha-Defensins immunology, Genetic Predisposition to Disease, Sepsis genetics, alpha-Defensins genetics
- Abstract
Sepsis claims an estimated 30 million episodes and 6 million deaths per year, and treatment options are rather limited. Human neutrophil peptides 1-3 (HNP1-3) are the most abundant neutrophil granule proteins but their neutrophil content varies because of unusually extensive gene copy number polymorphism. A genetic association study found that increased copy number of the HNP-encoding gene DEFA1/DEFA3 is a risk factor for organ dysfunction during sepsis development. However, direct experimental evidence demonstrating that these risk alleles are pathogenic for sepsis is lacking because the genes are present only in some primates and humans. Here, we generate DEFA1/DEFA3 transgenic mice with neutrophil-specific expression of the peptides. We show that mice with high copy number of DEFA1/DEFA3 genes have more severe sepsis-related vital organ damage and mortality than mice with low copy number of DEFA1/DEFA3 or wild-type mice, resulting from more severe endothelial barrier dysfunction and endothelial cell pyroptosis after sepsis challenge. Mechanistically, HNP-1 induces endothelial cell pyroptosis via P2X7 receptor-mediating canonical caspase-1 activation in a NLRP3 inflammasome-dependent manner. Based on these findings, we engineered a monoclonal antibody against HNP-1 to block the interaction with P2X7 and found that the blocking antibody protected mice carrying high copy number of DEFA1/DEFA3 from lethal sepsis. We thus demonstrate that DEFA1/DEFA3 copy number variation strongly modulates sepsis development in vivo and explore a paradigm for the precision treatment of sepsis tailored by individual genetic information., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)
- Published
- 2019
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27. Ferroptosis as a target for protection against cardiomyopathy.
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Fang X, Wang H, Han D, Xie E, Yang X, Wei J, Gu S, Gao F, Zhu N, Yin X, Cheng Q, Zhang P, Dai W, Chen J, Yang F, Yang HT, Linkermann A, Gu W, Min J, and Wang F
- Subjects
- Animals, Cardiomyopathies chemically induced, Doxorubicin pharmacology, Doxorubicin toxicity, Heme metabolism, Heme Oxygenase-1 genetics, Heme Oxygenase-1 metabolism, Lipid Peroxidation, Mice, Mice, Knockout, Mitochondria, Heart drug effects, Mitochondria, Heart enzymology, Mitochondria, Heart metabolism, Myocytes, Cardiac metabolism, NF-E2-Related Factor 2 genetics, Reperfusion Injury prevention & control, Up-Regulation, Apoptosis, Cardiomyopathies prevention & control, Iron metabolism
- Abstract
Heart disease is the leading cause of death worldwide. A key pathogenic factor in the development of lethal heart failure is loss of terminally differentiated cardiomyocytes. However, mechanisms of cardiomyocyte death remain unclear. Here, we discovered and demonstrated that ferroptosis, a programmed iron-dependent cell death, as a mechanism in murine models of doxorubicin (DOX)- and ischemia/reperfusion (I/R)-induced cardiomyopathy. In canonical apoptosis and/or necroptosis-defective Ripk3
-/- , Mlkl-/- , or Fadd-/- Mlkl-/- mice, DOX-treated cardiomyocytes showed features of typical ferroptotic cell death. Consistently, compared with dexrazoxane, the only FDA-approved drug for treating DOX-induced cardiotoxicity, inhibition of ferroptosis by ferrostatin-1 significantly reduced DOX cardiomyopathy. RNA-sequencing results revealed that heme oxygenase-1 ( Hmox1 ) was significantly up-regulated in DOX-treated murine hearts. Administering DOX to mice induced cardiomyopathy with a rapid, systemic accumulation of nonheme iron via heme degradation by Nrf2-mediated up-regulation of Hmox1, which effect was abolished in Nrf2 -deficent mice. Conversely, zinc protoporphyrin IX, an Hmox1 antagonist, protected the DOX-treated mice, suggesting free iron released on heme degradation is necessary and sufficient to induce cardiac injury. Given that ferroptosis is driven by damage to lipid membranes, we further investigated and found that excess free iron accumulated in mitochondria and caused lipid peroxidation on its membrane. Mitochondria-targeted antioxidant MitoTEMPO significantly rescued DOX cardiomyopathy, supporting oxidative damage of mitochondria as a major mechanism in ferroptosis-induced heart damage. Importantly, ferrostatin-1 and iron chelation also ameliorated heart failure induced by both acute and chronic I/R in mice. These findings highlight that targeting ferroptosis serves as a cardioprotective strategy for cardiomyopathy prevention., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)- Published
- 2019
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28. Characterization of gossypol biosynthetic pathway.
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Tian X, Ruan JX, Huang JQ, Yang CQ, Fang X, Chen ZW, Hong H, Wang LJ, Mao YB, Lu S, Zhang TZ, and Chen XY
- Subjects
- Biosynthetic Pathways, Gossypium metabolism, Isomerases biosynthesis, Isomerases metabolism, Plant Leaves metabolism, Polycyclic Sesquiterpenes, Sesquiterpenes metabolism, Transcriptome drug effects, Gossypol biosynthesis, Gossypol metabolism
- Abstract
Gossypol and related sesquiterpene aldehydes in cotton function as defense compounds but are antinutritional in cottonseed products. By transcriptome comparison and coexpression analyses, we identified 146 candidates linked to gossypol biosynthesis. Analysis of metabolites accumulated in plants subjected to virus-induced gene silencing (VIGS) led to the identification of four enzymes and their supposed substrates. In vitro enzymatic assay and reconstitution in tobacco leaves elucidated a series of oxidative reactions of the gossypol biosynthesis pathway. The four functionally characterized enzymes, together with (+)-δ-cadinene synthase and the P450 involved in 7-hydroxy-(+)-δ-cadinene formation, convert farnesyl diphosphate (FPP) to hemigossypol, with two gaps left that each involves aromatization. Of six intermediates identified from the VIGS-treated leaves, 8-hydroxy-7-keto-δ-cadinene exerted a deleterious effect in dampening plant disease resistance if accumulated. Notably, CYP71BE79, the enzyme responsible for converting this phytotoxic intermediate, exhibited the highest catalytic activity among the five enzymes of the pathway assayed. In addition, despite their dispersed distribution in the cotton genome, all of the enzyme genes identified show a tight correlation of expression. Our data suggest that the enzymatic steps in the gossypol pathway are highly coordinated to ensure efficient substrate conversion., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)
- Published
- 2018
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29. HSPB7 is indispensable for heart development by modulating actin filament assembly.
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Wu T, Mu Y, Bogomolovas J, Fang X, Veevers J, Nowak RB, Pappas CT, Gregorio CC, Evans SM, Fowler VM, and Chen J
- Subjects
- Actin Cytoskeleton genetics, Animals, Cytoskeletal Proteins biosynthesis, Cytoskeletal Proteins genetics, Female, Male, Mice, Mice, Inbred C57BL, Mice, Knockout, Muscle Proteins biosynthesis, Muscle Proteins genetics, Myocardium cytology, Myocytes, Cardiac cytology, Organogenesis genetics, Sarcomeres metabolism, Tropomodulin metabolism, Actin Cytoskeleton metabolism, Cardiomyopathies genetics, HSP27 Heat-Shock Proteins genetics, Heart embryology, Heart Defects, Congenital genetics
- Abstract
Small heat shock protein HSPB7 is highly expressed in the heart. Several mutations within HSPB7 are associated with dilated cardiomyopathy and heart failure in human patients. However, the precise role of HSPB7 in the heart is still unclear. In this study, we generated global as well as cardiac-specific HSPB7 KO mouse models and found that loss of HSPB7 globally or specifically in cardiomyocytes resulted in embryonic lethality before embryonic day 12.5. Using biochemical and cell culture assays, we identified HSPB7 as an actin filament length regulator that repressed actin polymerization by binding to monomeric actin. Consistent with HSPB7's inhibitory effects on actin polymerization, HSPB7 KO mice had longer actin/thin filaments and developed abnormal actin filament bundles within sarcomeres that interconnected Z lines and were cross-linked by α-actinin. In addition, loss of HSPB7 resulted in up-regulation of Lmod2 expression and mislocalization of Tmod1. Furthermore, crossing HSPB7 null mice into an Lmod2 null background rescued the elongated thin filament phenotype of HSPB7 KOs, but double KO mice still exhibited formation of abnormal actin bundles and early embryonic lethality. These in vivo findings indicated that abnormal actin bundles, not elongated thin filament length, were the cause of embryonic lethality in HSPB7 KOs. Our findings showed an unsuspected and critical role for a specific small heat shock protein in directly modulating actin thin filament length in cardiac muscle by binding monomeric actin and limiting its availability for polymerization., Competing Interests: The authors declare no conflict of interest., (Published under the PNAS license.)
- Published
- 2017
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30. Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities.
- Author
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Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, and Palsson BO
- Subjects
- Escherichia coli genetics, Transcriptome, Escherichia coli metabolism, Gene Expression Regulation, Bacterial, Gene Regulatory Networks, Transcription Factors metabolism
- Abstract
Transcriptional regulatory networks (TRNs) have been studied intensely for >25 y. Yet, even for the Escherichia coli TRN-probably the best characterized TRN-several questions remain. Here, we address three questions: ( i ) How complete is our knowledge of the E. coli TRN; ( ii ) how well can we predict gene expression using this TRN; and ( iii ) how robust is our understanding of the TRN? First, we reconstructed a high-confidence TRN (hiTRN) consisting of 147 transcription factors (TFs) regulating 1,538 transcription units (TUs) encoding 1,764 genes. The 3,797 high-confidence regulatory interactions were collected from published, validated chromatin immunoprecipitation (ChIP) data and RegulonDB. For 21 different TF knockouts, up to 63% of the differentially expressed genes in the hiTRN were traced to the knocked-out TF through regulatory cascades. Second, we trained supervised machine learning algorithms to predict the expression of 1,364 TUs given TF activities using 441 samples. The algorithms accurately predicted condition-specific expression for 86% (1,174 of 1,364) of the TUs, while 193 TUs (14%) were predicted better than random TRNs. Third, we identified 10 regulatory modules whose definitions were robust against changes to the TRN or expression compendium. Using surrogate variable analysis, we also identified three unmodeled factors that systematically influenced gene expression. Our computational workflow comprehensively characterizes the predictive capabilities and systems-level functions of an organism's TRN from disparate data types., Competing Interests: The authors declare no conflict of interest.
- Published
- 2017
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31. Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax.
- Author
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Li K, Wang L, Knisbacher BA, Xu Q, Levanon EY, Wang H, Frenkel-Morgenstern M, Tagore S, Fang X, Bazak L, Buchumenski I, Zhao Y, Lövy M, Li X, Han L, Frenkel Z, Beiles A, Cao YB, Wang ZL, and Nevo E
- Subjects
- Animals, Calcium Carbonate, Ecosystem, Female, Gene Flow, Male, Silicates, Soil, Spalax metabolism, Genetic Speciation, MicroRNAs metabolism, Spalax genetics, Sympatry, Transcriptome
- Abstract
Incipient sympatric speciation in blind mole rat, Spalax galili, in Israel, caused by sharp ecological divergence of abutting chalk-basalt ecologies, has been proposed previously based on mitochondrial and whole-genome nuclear DNA. Here, we present new evidence, including transcriptome, DNA editing, microRNA, and codon usage, substantiating earlier evidence for adaptive divergence in the abutting chalk and basalt populations. Genetic divergence, based on the previous and new evidence, is ongoing despite restricted gene flow between the two populations. The principal component analysis, neighbor-joining tree, and genetic structure analysis of the transcriptome clearly show the clustered divergent two mole rat populations. Gene-expression level analysis indicates that the population transcriptome divergence is displayed not only by soil divergence but also by sex. Gene ontology enrichment of the differentially expressed genes from the two abutting soil populations highlights reproductive isolation. Alternative splicing variation of the two abutting soil populations displays two distinct splicing patterns. L-shaped FST distribution indicates that the two populations have undergone divergence with gene flow. Transcriptome divergent genes highlight neurogenetics and nutrition characterizing the chalk population, and energetics, metabolism, musculature, and sensory perception characterizing the abutting basalt population. Remarkably, microRNAs also display divergence between the two populations. The GC content is significantly higher in chalk than in basalt, and stress-response genes mostly prefer nonoptimal codons. The multiple lines of evidence of ecological-genomic and genetic divergence highlight that natural selection overrules the gene flow between the two abutting populations, substantiating the sharp ecological chalk-basalt divergence driving sympatric speciation.
- Published
- 2016
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32. Human mesenchymal stromal cells reduce influenza A H5N1-associated acute lung injury in vitro and in vivo.
- Author
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Chan MC, Kuok DI, Leung CY, Hui KP, Valkenburg SA, Lau EH, Nicholls JM, Fang X, Guan Y, Lee JW, Chan RW, Webster RG, Matthay MA, and Peiris JS
- Subjects
- Acute Lung Injury etiology, Acute Lung Injury physiopathology, Angiotensin I biosynthesis, Animals, Body Fluids physiology, Coculture Techniques, Cystic Fibrosis Transmembrane Conductance Regulator metabolism, Cytokines biosynthesis, Female, Fibroblast Growth Factor 7 biosynthesis, Humans, Inflammation Mediators metabolism, Mesenchymal Stem Cell Transplantation, Mice, Mice, Inbred BALB C, Orthomyxoviridae Infections therapy, Permeability, Pulmonary Alveoli physiopathology, Sodium-Potassium-Exchanging ATPase metabolism, Acute Lung Injury prevention & control, Influenza A Virus, H5N1 Subtype pathogenicity, Influenza, Human complications, Mesenchymal Stem Cells physiology, Orthomyxoviridae Infections complications
- Abstract
Influenza can cause acute lung injury. Because immune responses often play a role, antivirals may not ensure a successful outcome. To identify pathogenic mechanisms and potential adjunctive therapeutic options, we compared the extent to which avian influenza A/H5N1 virus and seasonal influenza A/H1N1 virus impair alveolar fluid clearance and protein permeability in an in vitro model of acute lung injury, defined the role of virus-induced soluble mediators in these injury effects, and demonstrated that the effects are prevented or reduced by bone marrow-derived multipotent mesenchymal stromal cells. We verified the in vivo relevance of these findings in mice experimentally infected with influenza A/H5N1. We found that, in vitro, the alveolar epithelium's protein permeability and fluid clearance were dysregulated by soluble immune mediators released upon infection with avian (A/Hong Kong/483/97, H5N1) but not seasonal (A/Hong Kong/54/98, H1N1) influenza virus. The reduced alveolar fluid transport associated with down-regulation of sodium and chloride transporters was prevented or reduced by coculture with mesenchymal stromal cells. In vivo, treatment of aged H5N1-infected mice with mesenchymal stromal cells increased their likelihood of survival. We conclude that mesenchymal stromal cells significantly reduce the impairment of alveolar fluid clearance induced by A/H5N1 infection in vitro and prevent or reduce A/H5N1-associated acute lung injury in vivo. This potential adjunctive therapy for severe influenza-induced lung disease warrants rapid clinical investigation.
- Published
- 2016
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33. Cyclic nucleotide-gated channel 18 is an essential Ca2+ channel in pollen tube tips for pollen tube guidance to ovules in Arabidopsis.
- Author
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Gao QF, Gu LL, Wang HQ, Fei CF, Fang X, Hussain J, Sun SJ, Dong JY, Liu H, and Wang YF
- Subjects
- Arabidopsis genetics, Arabidopsis Proteins chemistry, Arabidopsis Proteins genetics, Calcium Channels physiology, Cyclic GMP analogs & derivatives, Cyclic GMP pharmacology, Cyclic Nucleotide-Gated Cation Channels chemistry, Cyclic Nucleotide-Gated Cation Channels deficiency, Cyclic Nucleotide-Gated Cation Channels genetics, Genes, Reporter, Genetic Complementation Test, HEK293 Cells, Humans, Membrane Potentials, Mutation, Missense, Ovule, Patch-Clamp Techniques, Plant Infertility genetics, Plants, Genetically Modified, Point Mutation, Protein Structure, Tertiary, Recombinant Fusion Proteins metabolism, Second Messenger Systems, Arabidopsis physiology, Arabidopsis Proteins physiology, Calcium metabolism, Cyclic Nucleotide-Gated Cation Channels physiology, Pollen Tube growth & development
- Abstract
In flowering plants, pollen tubes are guided into ovules by multiple attractants from female gametophytes to release paired sperm cells for double fertilization. It has been well-established that Ca(2+) gradients in the pollen tube tips are essential for pollen tube guidance and that plasma membrane Ca(2+) channels in pollen tube tips are core components that regulate Ca(2+) gradients by mediating and regulating external Ca(2+) influx. Therefore, Ca(2+) channels are the core components for pollen tube guidance. However, there is still no genetic evidence for the identification of the putative Ca(2+) channels essential for pollen tube guidance. Here, we report that the point mutations R491Q or R578K in cyclic nucleotide-gated channel 18 (CNGC18) resulted in abnormal Ca(2+) gradients and strong pollen tube guidance defects by impairing the activation of CNGC18 in Arabidopsis. The pollen tube guidance defects of cngc18-17 (R491Q) and of the transfer DNA (T-DNA) insertion mutant cngc18-1 (+/-) were completely rescued by CNGC18. Furthermore, domain-swapping experiments showed that CNGC18's transmembrane domains are indispensable for pollen tube guidance. Additionally, we found that, among eight Ca(2+) channels (including six CNGCs and two glutamate receptor-like channels), CNGC18 was the only one essential for pollen tube guidance. Thus, CNGC18 is the long-sought essential Ca(2+) channel for pollen tube guidance in Arabidopsis.
- Published
- 2016
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34. Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution.
- Author
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Chen XG, Jiang X, Gu J, Xu M, Wu Y, Deng Y, Zhang C, Bonizzoni M, Dermauw W, Vontas J, Armbruster P, Huang X, Yang Y, Zhang H, He W, Peng H, Liu Y, Wu K, Chen J, Lirakis M, Topalis P, Van Leeuwen T, Hall AB, Jiang X, Thorpe C, Mueller RL, Sun C, Waterhouse RM, Yan G, Tu ZJ, Fang X, and James AA
- Subjects
- Aedes classification, Aedes physiology, Animals, Phylogeny, Aedes genetics, Evolution, Molecular, Genome, Insect
- Abstract
The Asian tiger mosquito, Aedes albopictus, is a highly successful invasive species that transmits a number of human viral diseases, including dengue and Chikungunya fevers. This species has a large genome with significant population-based size variation. The complete genome sequence was determined for the Foshan strain, an established laboratory colony derived from wild mosquitoes from southeastern China, a region within the historical range of the origin of the species. The genome comprises 1,967 Mb, the largest mosquito genome sequenced to date, and its size results principally from an abundance of repetitive DNA classes. In addition, expansions of the numbers of members in gene families involved in insecticide-resistance mechanisms, diapause, sex determination, immunity, and olfaction also contribute to the larger size. Portions of integrated flavivirus-like genomes support a shared evolutionary history of association of these viruses with their vector. The large genome repertory may contribute to the adaptability and success of Ae. albopictus as an invasive species.
- Published
- 2015
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35. Refuting the evidence for an earlier birth of the Taklimakan Desert.
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Sun J, Alloway B, Fang X, and Windley BF
- Published
- 2015
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36. The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau.
- Author
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Zeng X, Long H, Wang Z, Zhao S, Tang Y, Huang Z, Wang Y, Xu Q, Mao L, Deng G, Yao X, Li X, Bai L, Yuan H, Pan Z, Liu R, Chen X, WangMu Q, Chen M, Yu L, Liang J, DunZhu D, Zheng Y, Yu S, LuoBu Z, Guang X, Li J, Deng C, Hu W, Chen C, TaBa X, Gao L, Lv X, Abu YB, Fang X, Nevo E, Yu M, Wang J, and Tashi N
- Subjects
- Base Sequence, Molecular Sequence Data, Tibet, Acclimatization physiology, Genetic Variation physiology, Genome, Plant physiology, Hordeum genetics
- Abstract
The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called "Qingke" in Chinese and "Ne" in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The diploid nature and adaptation to diverse environments of the highland give it unique resources for genetic research and crop improvement. Here we produced a 3.89-Gb draft assembly of Tibetan hulless barley with 36,151 predicted protein-coding genes. Comparative analyses revealed the divergence times and synteny between barley and other representative Poaceae genomes. The expansion of the gene family related to stress responses was found in Tibetan hulless barley. Resequencing of 10 barley accessions uncovered high levels of genetic variation in Tibetan wild barley and genetic divergence between Tibetan and non-Tibetan barley genomes. Selective sweep analyses demonstrate adaptive correlations of genes under selection with extensive environmental variables. Our results not only construct a genomic framework for crop improvement but also provide evolutionary insights of highland adaptation of Tibetan hulless barley.
- Published
- 2015
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37. Structural model of an mRNA in complex with the bacterial chaperone Hfq.
- Author
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Peng Y, Curtis JE, Fang X, and Woodson SA
- Subjects
- Escherichia coli Proteins genetics, Escherichia coli Proteins metabolism, Host Factor 1 Protein genetics, Host Factor 1 Protein metabolism, Molecular Dynamics Simulation, Monte Carlo Method, Nucleic Acid Conformation, Protein Binding, Protein Structure, Tertiary, RNA, Bacterial genetics, RNA, Bacterial metabolism, RNA, Messenger genetics, RNA, Messenger metabolism, RNA, Small Untranslated chemistry, RNA, Small Untranslated genetics, RNA, Small Untranslated metabolism, Scattering, Small Angle, Sigma Factor chemistry, Sigma Factor genetics, Sigma Factor metabolism, X-Ray Diffraction, Escherichia coli Proteins chemistry, Host Factor 1 Protein chemistry, RNA, Bacterial chemistry, RNA, Messenger chemistry
- Abstract
The Sm-like protein Hfq (host factor Q-beta phage) facilitates regulation by bacterial small noncoding RNAs (sRNAs) in response to stress and other environmental signals. Here, we present a low-resolution model of Escherichia coli Hfq bound to the rpoS mRNA, a bacterial stress response gene that is targeted by three different sRNAs. Selective 2'-hydroxyl acylation and primer extension, small-angle X-ray scattering, and Monte Carlo molecular dynamics simulations show that the distal face and lateral rim of Hfq interact with three sites in the rpoS leader, folding the RNA into a compact tertiary structure. These interactions are needed for sRNA regulation of rpoS translation and position the sRNA target adjacent to an sRNA binding region on the proximal face of Hfq. Our results show how Hfq specifically distorts the structure of the rpoS mRNA to enable sRNA base pairing and translational control.
- Published
- 2014
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38. Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization.
- Author
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Qin C, Yu C, Shen Y, Fang X, Chen L, Min J, Cheng J, Zhao S, Xu M, Luo Y, Yang Y, Wu Z, Mao L, Wu H, Ling-Hu C, Zhou H, Lin H, González-Morales S, Trejo-Saavedra DL, Tian H, Tang X, Zhao M, Huang Z, Zhou A, Yao X, Cui J, Li W, Chen Z, Feng Y, Niu Y, Bi S, Yang X, Li W, Cai H, Luo X, Montes-Hernández S, Leyva-González MA, Xiong Z, He X, Bai L, Tan S, Tang X, Liu D, Liu J, Zhang S, Chen M, Zhang L, Zhang L, Zhang Y, Liao W, Zhang Y, Wang M, Lv X, Wen B, Liu H, Luan H, Zhang Y, Yang S, Wang X, Xu J, Li X, Li S, Wang J, Palloix A, Bosland PW, Li Y, Krogh A, Rivera-Bustamante RF, Herrera-Estrella L, Yin Y, Yu J, Hu K, and Zhang Z
- Subjects
- DNA Transposable Elements, Molecular Sequence Data, Plant Proteins genetics, Retroelements, Selection, Genetic, Transcription, Genetic, Capsicum genetics, Genome, Plant
- Abstract
As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.
- Published
- 2014
- Full Text
- View/download PDF
39. Interplay of mevalonate and Hippo pathways regulates RHAMM transcription via YAP to modulate breast cancer cell motility.
- Author
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Wang Z, Wu Y, Wang H, Zhang Y, Mei L, Fang X, Zhang X, Zhang F, Chen H, Liu Y, Jiang Y, Sun S, Zheng Y, Li N, and Huang L
- Subjects
- Actins chemistry, Animals, Base Sequence, Cell Line, Tumor, Cell Movement, Extracellular Signal-Regulated MAP Kinases metabolism, Female, HEK293 Cells, Hippo Signaling Pathway, Humans, Mice, Mice, Inbred BALB C, Molecular Sequence Data, Neoplasm Metastasis, Neoplasm Transplantation, Phosphorylation, Signal Transduction physiology, Simvastatin chemistry, Transcription Factors, YAP-Signaling Proteins, Adaptor Proteins, Signal Transducing metabolism, Breast Neoplasms metabolism, Extracellular Matrix Proteins metabolism, Gene Expression Regulation, Neoplastic, Hyaluronan Receptors metabolism, Mevalonic Acid metabolism, Phosphoproteins metabolism, Protein Serine-Threonine Kinases metabolism
- Abstract
Expression of receptor for hyaluronan-mediated motility (RHAMM), a breast cancer susceptibility gene, is tightly controlled in normal tissues but elevated in many tumors, contributing to tumorigenesis and metastases. However, how the expression of RHAMM is regulated remains elusive. Statins, inhibitors of mevalonate metabolic pathway widely used for hypercholesterolemia, have been found to also have antitumor effects, but little is known of the specific targets and mechanisms. Moreover, Hippo signaling pathway plays crucial roles in organ size control and cancer development, yet its downstream transcriptional targets remain obscure. Here we show that RHAMM expression is regulated by mevalonate and Hippo pathways converging onto Yes-associated protein (YAP)/TEAD, which binds RHAMM promoter at specific sites and controls its transcription and consequently breast cancer cell migration and invasion (BCCMI); and that simvastatin inhibits BCCMI via targeting YAP-mediated RHAMM transcription. Required for ERK phosphorylation and BCCMI, YAP-activated RHAMM transcription is dependent on mevalonate and sensitive to simvastatin, which modulate RHAMM transcription by modulating YAP phosphorylation and nuclear-cytoplasmic localization. Further, modulation by mevalonate/simvastatin of YAP-activated RHAMM transcription requires geranylgeranylation, Rho GTPase activation, and actin cytoskeleton rearrangement, but is largely independent of MST and LATS kinase activity. These findings from in vitro and in vivo investigations link mevalonate and Hippo pathways with RHAMM as a downstream effector, a YAP-transcription and simvastatin-inhibition target, and a cancer metastasis mediator; uncover a mechanism regulating RHAMM expression and cancer metastases; and reveal a mode whereby simvastatin exerts anticancer effects; providing potential targets for cancer therapeutic agents.
- Published
- 2014
- Full Text
- View/download PDF
40. Shear stress activation of nuclear receptor PXR in endothelial detoxification.
- Author
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Wang X, Fang X, Zhou J, Chen Z, Zhao B, Xiao L, Liu A, Li YS, Shyy JY, Guan Y, Chien S, and Wang N
- Subjects
- ATP Binding Cassette Transporter, Subfamily B, Member 1 genetics, ATP Binding Cassette Transporter, Subfamily B, Member 1 metabolism, Animals, Apoptosis drug effects, Aryl Hydrocarbon Hydroxylases genetics, Aryl Hydrocarbon Hydroxylases metabolism, Blotting, Western, Carotid Arteries metabolism, Cell Line, Tumor, Cells, Cultured, Cytochrome P-450 CYP1B1, Glutathione Transferase genetics, Glutathione Transferase metabolism, Humans, Male, Mice, Mice, Inbred C57BL, Oligonucleotide Array Sequence Analysis, Pregnane X Receptor, RNA Interference, Rats, Rats, Sprague-Dawley, Receptors, Steroid metabolism, Reverse Transcriptase Polymerase Chain Reaction, Stress, Mechanical, Xenobiotics metabolism, Xenobiotics pharmacology, Gene Expression Profiling, Human Umbilical Vein Endothelial Cells metabolism, Inactivation, Metabolic genetics, Receptors, Steroid genetics
- Abstract
Endothelial cells (ECs) are constantly exposed to xenobiotics and endobiotics or their metabolites, which perturb EC function, as well as to shear stress, which plays a crucial role in vascular homeostasis. Pregnane X receptor (PXR) is a nuclear receptor and a key regulator of the detoxification of xeno- and endobiotics. Here we show that laminar shear stress (LSS), the atheroprotective flow, activates PXR in ECs, whereas oscillatory shear stress, the atheroprone flow, suppresses PXR. LSS activation of PXR in cultured ECs led to the increased expression of a PXR target gene, multidrug resistance 1 (MDR1). An in vivo study using rats showed that the expression of MDR1 was significantly higher in the endothelium from the descending thoracic aorta, where flow is mostly laminar, than from the inner curvature of aortic arch, where flow is disturbed. Functionally, LSS-activated PXR protects ECs from apoptosis triggered by doxorubicin via the induction of MDR1 and other detoxification genes. PXR also suppressed the expression of proinflammatory adhesion molecules and monocyte adhesion in response to TNF-α and lipopolysaccharide. Overexpression of a constitutively active PXR in rat carotid arteries potently attenuated proinflammatory responses. In addition, cDNA microarray revealed a large number of the PXR-activated endothelial genes whose products are responsible for major steps of detoxification, including phase I and II metabolizing enzymes and transporters. These detoxification genes in ECs are induced by LSS in ECs in a PXR-dependent manner. In conclusion, our results indicate that PXR represents a flow-activated detoxification system to protect ECs against damage by xeno- and endobiotics.
- Published
- 2013
- Full Text
- View/download PDF
41. Single-particle analysis reveals shutoff control of the Arabidopsis ammonium transporter AMT1;3 by clustering and internalization.
- Author
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Wang Q, Zhao Y, Luo W, Li R, He Q, Fang X, Michele RD, Ast C, von Wirén N, and Lin J
- Subjects
- Arabidopsis genetics, Arabidopsis metabolism, Arabidopsis Proteins chemistry, Arabidopsis Proteins genetics, Blotting, Western, Cation Transport Proteins chemistry, Cation Transport Proteins genetics, Cell Membrane drug effects, Cell Membrane metabolism, Clathrin Heavy Chains genetics, Clathrin Heavy Chains metabolism, Cytoplasm drug effects, Cytoplasm metabolism, Green Fluorescent Proteins genetics, Green Fluorescent Proteins metabolism, Microscopy, Confocal, Microscopy, Fluorescence, Microscopy, Video methods, Mutation, Plants, Genetically Modified, Protein Multimerization, Quaternary Ammonium Compounds pharmacology, Recombinant Fusion Proteins chemistry, Recombinant Fusion Proteins genetics, Recombinant Fusion Proteins metabolism, Arabidopsis Proteins metabolism, Cation Transport Proteins metabolism, Endocytosis, Quaternary Ammonium Compounds metabolism
- Abstract
Ammonium is a preferred source of nitrogen for plants but is toxic at high levels. Plant ammonium transporters (AMTs) play an essential role in NH4(+) uptake, but the mechanism by which AMTs are regulated remains unclear. To study how AMTs are regulated in the presence of ammonium, we used variable-angle total internal reflection fluorescence microscopy and fluorescence cross-correlation spectroscopy for single-particle fluorescence imaging of EGFP-tagged AMT1;3 on the plasma membrane of Arabidopsis root cells at various ammonium levels. We demonstrated that AMT1;3-EGFP dynamically appeared and disappeared on the plasma membrane as moving fluorescent spots in low oligomeric states under N-deprived and N-sufficient conditions. Under external high-ammonium stress, however, AMT1;3-EGFPs were found to amass into clusters, which were then internalized into the cytoplasm. A similar phenomenon also occurred in the glutamine synthetase mutant gln1;2 background. Single-particle analysis of AMT1;3-EGFPs in the clathrin heavy chain 2 mutant (chc2 mutant) and Flotllin1 artificial microRNA (Flot1 amiRNA) backgrounds, together with chemical inhibitor treatments, demonstrated that the endocytosis of AMT1;3 clusters induced by high-ammonium stress could occur mainly through clathrin-mediated endocytic pathways, but the contribution of microdomain-associated endocytic pathway cannot be excluded in the internalization. Our results revealed that the clustering and endocytosis of AMT1;3 provides an effective mechanism by which plant cells can avoid accumulation of toxic levels of ammonium by eliminating active AMT1;3 from the plasma membrane.
- Published
- 2013
- Full Text
- View/download PDF
42. Identification of Chinese plague foci from long-term epidemiological data.
- Author
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Ben-Ari T, Neerinckx S, Agier L, Cazelles B, Xu L, Zhang Z, Fang X, Wang S, Liu Q, and Stenseth NC
- Subjects
- China epidemiology, Cluster Analysis, Ecosystem, History, 18th Century, History, 19th Century, History, 20th Century, Humans, Wavelet Analysis, Disease Reservoirs statistics & numerical data, Epidemics history, Plague epidemiology, Plague history, Yersinia pestis isolation & purification
- Abstract
Carrying out statistical analysis over an extensive dataset of human plague reports in Chinese villages from 1772 to 1964, we identified plague endemic territories in China (i.e., plague foci). Analyses rely on (i) a clustering method that groups time series based on their time-frequency resemblances and (ii) an ecological niche model that helps identify plague suitable territories characterized by value ranges for a set of predefined environmental variables. Results from both statistical tools indicate the existence of two disconnected plague territories corresponding to Northern and Southern China. Altogether, at least four well defined independent foci are identified. Their contours compare favorably with field observations. Potential and limitations of inferring plague foci and dynamics using epidemiological data is discussed.
- Published
- 2012
- Full Text
- View/download PDF
43. Nonlinear effect of climate on plague during the third pandemic in China.
- Author
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Xu L, Liu Q, Stige LC, Ben Ari T, Fang X, Chan KS, Wang S, Stenseth NC, and Zhang Z
- Subjects
- Animals, China epidemiology, History, 18th Century, History, 19th Century, History, 20th Century, Humans, Models, Theoretical, Plague history, Climate, Nonlinear Dynamics, Plague epidemiology
- Abstract
Over the years, plague has caused a large number of deaths worldwide and subsequently changed history, not the least during the period of the Black Death. Of the three plague pandemics, the third is believed to have originated in China. Using the spatial and temporal human plague records in China from 1850 to 1964, we investigated the association of human plague intensity (plague cases per year) with proxy data on climate condition (specifically an index for dryness/wetness). Our modeling analysis demonstrates that the responses of plague intensity to dry/wet conditions were different in northern and southern China. In northern China, plague intensity generally increased when wetness increased, for both the current and the previous year, except for low intensity during extremely wet conditions in the current year (reflecting a dome-shaped response to current-year dryness/wetness). In southern China, plague intensity generally decreased when wetness increased, except for high intensity during extremely wet conditions of the current year. These opposite effects are likely related to the different climates and rodent communities in the two parts of China: In northern China (arid climate), rodents are expected to respond positively to high precipitation, whereas in southern China (humid climate), high precipitation is likely to have a negative effect. Our results suggest that associations between human plague intensity and precipitation are nonlinear: positive in dry conditions, but negative in wet conditions.
- Published
- 2011
- Full Text
- View/download PDF
44. De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks.
- Author
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Mahfouz MM, Li L, Shamimuzzaman M, Wibowo A, Fang X, and Zhu JK
- Subjects
- Deoxyribonucleases genetics, Protein Engineering methods, Recombinant Fusion Proteins genetics, Substrate Specificity, Trans-Activators genetics, DNA chemistry, DNA Breaks, Double-Stranded, Deoxyribonucleases chemistry, Recombinant Fusion Proteins chemistry, Trans-Activators chemistry
- Abstract
Site-specific and rare cutting nucleases are valuable tools for genome engineering. The generation of double-strand DNA breaks (DSBs) promotes homologous recombination in eukaryotes and can facilitate gene targeting, additions, deletions, and inactivation. Zinc finger nucleases have been used to generate DSBs and subsequently, for genome editing but with low efficiency and reproducibility. The transcription activator-like family of type III effectors (TALEs) contains a central domain of tandem repeats that could be engineered to bind specific DNA targets. Here, we report the generation of a Hax3-based hybrid TALE nuclease with a user-selected DNA binding specificity. We show that the engineered TALE nuclease can bind to its target sequence in vitro and that the homodimeric TALE nuclease can cleave double-stranded DNA in vitro if the DNA binding sites have the proper spacing and orientation. Transient expression assays in tobacco leaves suggest that the hybrid nuclease creates DSB in its target sequence, which is subsequently repaired by nonhomologous end-joining repair. Taken together, our data show the feasibility of engineering TALE-based hybrid nucleases capable of generating site-specific DSBs and the great potential for site-specific genome modification in plants and eukaryotes in general.
- Published
- 2011
- Full Text
- View/download PDF
45. The ATM-p53 pathway suppresses aneuploidy-induced tumorigenesis.
- Author
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Li M, Fang X, Baker DJ, Guo L, Gao X, Wei Z, Han S, van Deursen JM, and Zhang P
- Subjects
- Animals, Ataxia Telangiectasia Mutated Proteins, DNA Damage, Mice, Mice, Transgenic, Reactive Oxygen Species, Aneuploidy, Cell Cycle Proteins metabolism, DNA-Binding Proteins metabolism, Neoplasms etiology, Protein Serine-Threonine Kinases metabolism, Tumor Suppressor Protein p53 metabolism, Tumor Suppressor Proteins metabolism
- Abstract
The spindle assembly checkpoint (SAC) is essential for proper sister chromatid segregation. Defects in this checkpoint can lead to chromosome missegregation and aneuploidy. An increasing body of evidence suggests that aneuploidy can play a causal role in tumorigenesis. However, mutant mice that are prone to aneuploidy have only mild tumor phenotypes, suggesting that there are limiting factors in the aneuploidy-induced tumorigenesis. Here we provide evidence that p53 is such a limiting factor. We show that aneuploidy activates p53 and that loss of p53 drastically accelerates tumor development in two independent aneuploidy models. The p53 activation depends on the ataxia-telangiectasia mutated (ATM) gene product and increased levels of reactive oxygen species. Thus, the ATM-p53 pathway safeguards not only DNA damage but also aneuploidy.
- Published
- 2010
- Full Text
- View/download PDF
46. Unipolar assembly of zinc oxide rods manifesting polarity-driven collective luminescence.
- Author
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Gautam UK, Imura M, Rout CS, Bando Y, Fang X, Dierre B, Sakharov L, Govindaraj A, Sekiguchi T, Golberg D, and Rao CN
- Abstract
Oriented assemblies of small crystals forming larger structures are common in nature and crucial for forthcoming technologies as they circumvent the difficulties of structural manipulation at microscopic scale. We have discovered two distinctive concentric assemblies of zinc oxide rods, wherein each rod has an intrinsically positive and a negative polar end induced by the noncentrosymmetric arrangement of Zn and O atoms. All the rods in a single assembly emanate out of a central core maintaining a single polar direction. Due to growth along the two polar surfaces with different atomic arrangements, these assemblies are distinct in their intrinsic properties and exhibit strong UV luminescence in the exterior of Zn-polar assemblies, unlike the O-polar assemblies. Although novel applications can be envisioned, these observations suggest that hierarchical organization with respect to internal asymmetry might be widespread in natural crystal assemblies.
- Published
- 2010
- Full Text
- View/download PDF
47. Targeting lymphotoxin-mediated negative selection to prevent prostate cancer in mice with genetic predisposition.
- Author
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Zhou P, Fang X, McNally BA, Yu P, Zhu M, Fu YX, Wang L, Liu Y, and Zheng P
- Subjects
- Adenocarcinoma genetics, Adenocarcinoma immunology, Adenocarcinoma pathology, Animals, CD4-Positive T-Lymphocytes cytology, CD4-Positive T-Lymphocytes immunology, CD4-Positive T-Lymphocytes metabolism, CD8-Positive T-Lymphocytes cytology, CD8-Positive T-Lymphocytes immunology, CD8-Positive T-Lymphocytes metabolism, Cell Lineage immunology, Female, Flow Cytometry, Genetic Predisposition to Disease, Humans, Immunoglobulin Fc Fragments genetics, Immunoglobulin Fc Fragments immunology, Lymphotoxin beta Receptor genetics, Lymphotoxin beta Receptor immunology, Lymphotoxin-alpha genetics, Lymphotoxin-alpha metabolism, Male, Mice, Mice, Inbred C57BL, Mice, Knockout, Mice, Transgenic, Prostatic Neoplasms genetics, Prostatic Neoplasms pathology, Receptors, Tumor Necrosis Factor, Member 25 genetics, Receptors, Tumor Necrosis Factor, Member 25 immunology, Receptors, Tumor Necrosis Factor, Member 25 metabolism, Recombinant Fusion Proteins administration & dosage, Recombinant Fusion Proteins genetics, Spleen cytology, Spleen immunology, Spleen metabolism, Thymus Gland cytology, Thymus Gland metabolism, Lymphotoxin-alpha immunology, Prostatic Neoplasms immunology, Recombinant Fusion Proteins immunology, Thymus Gland immunology
- Abstract
The identification of individuals genetically susceptible to cancer calls for preventive measures to minimize the cancer risk in these high-risk populations. Immune prevention is made necessary by the anticipated health threat, but lack of enough high-affinity T cells against tumor-associated antigens and the unpredictability of tumor antigens make antigen-based immune prevention untenable for cancer. To address this issue, we explored a non-antigen-based cancer immune prevention strategy using the transgenic adenocarcinoma of mouse prostate model that spontaneously develops prostate cancer with 100% penetrance. We show that targeted mutation of the lymphotoxin alpha (LTalpha) gene efficiently rescued tumor-reactive T cells, drastically reduced cancer incidence, and almost completely ablated metastasis. Remarkably, short-term treatments with the fusion protein consisting of constant region of IgG and extracellular domain of lymphotoxin beta receptor (LTbetaRIg) interrupted clonal deletion, reduced the size of the primary cancer, and completely prevented metastasis later in life. Our data demonstrated the value of non-antigen-based immune prevention for those with a genetic predisposition to cancer.
- Published
- 2009
- Full Text
- View/download PDF
48. Allogeneic human mesenchymal stem cells for treatment of E. coli endotoxin-induced acute lung injury in the ex vivo perfused human lung.
- Author
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Lee JW, Fang X, Gupta N, Serikov V, and Matthay MA
- Subjects
- Acute Disease, Adult, Amiloride pharmacology, Body Fluids metabolism, Cells, Cultured, Culture Media, Conditioned pharmacology, Endotoxins, Escherichia coli chemistry, Female, Fibroblast Growth Factor 7 genetics, Fibroblast Growth Factor 7 pharmacology, Humans, In Vitro Techniques, Leukocyte Count, Lung metabolism, Lung pathology, Lung Injury chemically induced, Male, Mesenchymal Stem Cells cytology, Middle Aged, Neutrophils pathology, Perfusion, Pulmonary Alveoli drug effects, Pulmonary Alveoli metabolism, Pulmonary Edema metabolism, Pulmonary Edema pathology, Pulmonary Edema prevention & control, Recombinant Proteins pharmacology, Sodium Channel Blockers pharmacology, Transplantation, Homologous, Lung surgery, Lung Injury surgery, Mesenchymal Stem Cell Transplantation methods, Mesenchymal Stem Cells metabolism
- Abstract
Recent studies have suggested that bone marrow-derived multipotent mesenchymal stem cells (MSCs) may have therapeutic applications in multiple clinical disorders including myocardial infarction, diabetes, sepsis, and hepatic and acute renal failure. Here, we tested the therapeutic capacity of human MSCs to restore alveolar epithelial fluid transport and lung fluid balance from acute lung injury (ALI) in an ex vivo perfused human lung preparation injured by E. coli endotoxin. Intra-bronchial instillation of endotoxin into the distal airspaces resulted in pulmonary edema with the loss of alveolar epithelial fluid transport measured as alveolar fluid clearance. Treatment with allogeneic human MSCs or its conditioned medium given 1 h following endotoxin-induced lung injury reduced extravascular lung water, improved lung endothelial barrier permeability and restored alveolar fluid clearance. Using siRNA knockdown of potential paracrine soluble factors, secretion of keratinocyte growth factor was essential for the beneficial effect of MSCs on alveolar epithelial fluid transport, in part by restoring amiloride-dependent sodium transport. In summary, treatment with allogeneic human MSCs or the conditioned medium restores normal fluid balance in an ex vivo perfused human lung injured by E. coli endotoxin.
- Published
- 2009
- Full Text
- View/download PDF
49. Single-molecule imaging reveals transforming growth factor-beta-induced type II receptor dimerization.
- Author
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Zhang W, Jiang Y, Wang Q, Ma X, Xiao Z, Zuo W, Fang X, and Chen YG
- Subjects
- Biophysical Phenomena, Cell Line, Cell Membrane chemistry, Cell Membrane drug effects, Cell Membrane metabolism, Dimerization, ErbB Receptors chemistry, ErbB Receptors genetics, ErbB Receptors metabolism, Green Fluorescent Proteins chemistry, Green Fluorescent Proteins genetics, Green Fluorescent Proteins metabolism, HeLa Cells, Humans, Ligands, Microscopy, Fluorescence, Protein Serine-Threonine Kinases genetics, Protein Serine-Threonine Kinases metabolism, Protein Structure, Quaternary, Receptor, Transforming Growth Factor-beta Type II, Receptors, Transforming Growth Factor beta genetics, Receptors, Transforming Growth Factor beta metabolism, Recombinant Fusion Proteins chemistry, Recombinant Fusion Proteins genetics, Recombinant Fusion Proteins metabolism, Signal Transduction, Transforming Growth Factor beta1 pharmacology, Protein Serine-Threonine Kinases chemistry, Receptors, Transforming Growth Factor beta chemistry
- Abstract
Transforming growth factor-beta (TGF-beta) elicits its signals through two transmembrane serine/threonine kinase receptors, type II (TbetaRII) and type I receptors. It is generally believed that the initial receptor dimerization is an essential event for receptor activation. However, previous studies suggested that TGF-beta signals by binding to the preexisting TbetaRII homodimer. Here, using single molecule microscopy to image green fluorescent protein (GFP)-labeled TbetaRII on the living cell surface, we demonstrated that the receptor could exist as monomers at the low expression level in resting cells and dimerize upon TGF-beta stimulation. This work reveals a model in which the activation of serine-threonine kinase receptors is also accomplished via dimerization of monomers, suggesting that receptor dimerization is a general mechanism for ligand-induced receptor activation.
- Published
- 2009
- Full Text
- View/download PDF
50. Homozygous deletion of glycogen synthase kinase 3beta bypasses senescence allowing Ras transformation of primary murine fibroblasts.
- Author
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Liu S, Fang X, Hall H, Yu S, Smith D, Lu Z, Fang D, Liu J, Stephens LC, Woodgett JR, and Mills GB
- Subjects
- Active Transport, Cell Nucleus, Animals, Catalysis, Cells, Cultured, Cyclin D1 metabolism, Fibroblasts, Gene Expression Regulation, Glycogen Synthase Kinase 3 genetics, Glycogen Synthase Kinase 3 beta, Mice, Mice, Knockout, beta Catenin metabolism, ras Proteins genetics, Cellular Senescence physiology, Gene Deletion, Glycogen Synthase Kinase 3 deficiency, Glycogen Synthase Kinase 3 metabolism, Homozygote, Transgenes genetics, ras Proteins metabolism
- Abstract
In primary mammalian cells, expression of oncogenes such as activated Ras induces premature senescence rather than transformation. We show that homozygous deletion of glycogen synthase kinase (GSK) 3beta (GSK3beta-/-) bypasses senescence induced by mutant Ras(V12) allowing primary mouse embryo fibroblasts (MEFs) as well as immortalized MEFs to exhibit a transformed phenotype in vitro and in vivo. Both catalytic activity and Axin-binding of GSK3beta are required to optimally suppress Ras transformation. The expression of Ras(V12) in GSK3beta-/-, but not in GSK3beta+/+ MEFs results in translocation of beta-catenin to the nucleus with concomitant up-regulation of cyclin D1. siRNA-mediated knockdown of beta-catenin decreases both cyclin D1 expression and anchorage-independent growth of transformed cells indicating a causal role for beta-catenin. Thus Ras(V12) and the lack of GSK3beta act in concert to activate the beta-catenin pathway, which may underlie the bypass of senescence and tumorigenic transformation by Ras.
- Published
- 2008
- Full Text
- View/download PDF
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