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She K, Yuan N, Huang M, Zhu W, Tang M, Ma Q, Chen J. Emerging role of microglia in the developing dopaminergic system: Perturbation by early life stress. Neural Regen Res 2026; 21:126-140. [PMID: 39589170 PMCID: PMC12094535 DOI: 10.4103/nrr.nrr-d-24-00742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 09/13/2024] [Accepted: 10/15/2024] [Indexed: 11/27/2024] Open
Abstract
Early life stress correlates with a higher prevalence of neurological disorders, including autism, attention-deficit/hyperactivity disorder, schizophrenia, depression, and Parkinson's disease. These conditions, primarily involving abnormal development and damage of the dopaminergic system, pose significant public health challenges. Microglia, as the primary immune cells in the brain, are crucial in regulating neuronal circuit development and survival. From the embryonic stage to adulthood, microglia exhibit stage-specific gene expression profiles, transcriptome characteristics, and functional phenotypes, enhancing the susceptibility to early life stress. However, the role of microglia in mediating dopaminergic system disorders under early life stress conditions remains poorly understood. This review presents an up-to-date overview of preclinical studies elucidating the impact of early life stress on microglia, leading to dopaminergic system disorders, along with the underlying mechanisms and therapeutic potential for neurodegenerative and neurodevelopmental conditions. Impaired microglial activity damages dopaminergic neurons by diminishing neurotrophic support (e.g., insulin-like growth factor-1) and hinders dopaminergic axon growth through defective phagocytosis and synaptic pruning. Furthermore, blunted microglial immunoreactivity suppresses striatal dopaminergic circuit development and reduces neuronal transmission. Furthermore, inflammation and oxidative stress induced by activated microglia can directly damage dopaminergic neurons, inhibiting dopamine synthesis, reuptake, and receptor activity. Enhanced microglial phagocytosis inhibits dopamine axon extension. These long-lasting effects of microglial perturbations may be driven by early life stress-induced epigenetic reprogramming of microglia. Indirectly, early life stress may influence microglial function through various pathways, such as astrocytic activation, the hypothalamic-pituitary-adrenal axis, the gut-brain axis, and maternal immune signaling. Finally, various therapeutic strategies and molecular mechanisms for targeting microglia to restore the dopaminergic system were summarized and discussed. These strategies include classical antidepressants and antipsychotics, antibiotics and anti-inflammatory agents, and herbal-derived medicine. Further investigations combining pharmacological interventions and genetic strategies are essential to elucidate the causal role of microglial phenotypic and functional perturbations in the dopaminergic system disrupted by early life stress.
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Affiliation(s)
- Kaijie She
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong Province, China
| | - Naijun Yuan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong Province, China
- Shenzhen People’s Hospital, The 2 Clinical Medical College, Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Shenzhen, Guangdong Province, China
| | - Minyi Huang
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong Province, China
| | - Wenjun Zhu
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong Province, China
| | - Manshi Tang
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong Province, China
| | - Qingyu Ma
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong Province, China
| | - Jiaxu Chen
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong Province, China
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
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Río P, Zubicaray J, Navarro S, Gálvez E, Sánchez-Domínguez R, Nicoletti E, Sebastián E, Rothe M, Pujol R, Bogliolo M, John-Neek P, Bastone AL, Schambach A, Wang W, Schmidt M, Larcher L, Segovia JC, Yáñez RM, Alberquilla O, Díez B, Fernández-García M, García-García L, Ramírez M, Galy A, Lefrere F, Cavazzana M, Leblanc T, García de Andoin N, López-Almaraz R, Catalá A, Barquinero J, Rodríguez-Perales S, Rao G, Surrallés J, Soulier J, Díaz-de-Heredia C, Schwartz JD, Sevilla J, Bueren JA. Haematopoietic gene therapy of non-conditioned patients with Fanconi anaemia-A: results from open-label phase 1/2 (FANCOLEN-1) and long-term clinical trials. Lancet 2025; 404:2584-2592. [PMID: 39642902 DOI: 10.1016/s0140-6736(24)01880-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 09/01/2024] [Accepted: 09/04/2024] [Indexed: 12/09/2024]
Abstract
BACKGROUND Allogeneic haematopoietic stem-cell transplantation is the standard treatment for bone marrow failure (BMF) in patients with Fanconi anaemia, but transplantation-associated complications such as an increased incidence of subsequent cancer are frequent. The aim of this study was to evaluate the safety and efficacy of the infusion of autologous gene-corrected haematopoietic stem cells as an alternative therapy for these patients. METHODS This was an open-label, investigator-initiated phase 1/2 clinical trial (FANCOLEN-1) and long-term follow-up trial (up to 7 years post-treatment) in Spain. Mobilised peripheral blood (PB) CD34+ cells from nine patients with Fanconi anaemia-A in the early stages of BMF were transduced with a therapeutic FANCA-encoding lentiviral vector and re-infused without any cytotoxic conditioning treatment. The primary efficacy endpoint of FANCOLEN-1 was the engraftment of transduced cells, as defined by the detection of at least 0·1 therapeutic vector copies per nucleated cell of patient bone marrow (BM) or PB at the second year post-infusion, without this percentage having declined substantially over the previous year. The safety coprimary endpoint was adverse events during the 3 years after infusion. The completed open-label phase 1/2 and the ongoing long-term clinical trials are registered with ClinicalTrials.gov, NCT03157804; EudraCT, 2011-006100-12; and NCT04437771, respectively. FINDINGS There were eight evaluable treated patients with Fanconi anaemia-A. Patients were recruited between Jan 7, 2016 and April 3, 2019. The primary endpoint was met in five of the eight evaluable patients (62·50%). The median number of therapeutic vector copies per nucleated cell of patient BM and PB at the second year post-infusion was 0·18 (IQR 0·01-0·20) and 0·06 (0·01-0·19), respectively. No genotoxic events related to the gene therapy were observed. Most treatment-emergent adverse events (TEAEs) were non-serious and assessed as not related to therapeutic FANCA-encoding lentiviral vector. Nine serious adverse events (grade 3-4) were reported in six patients, one was considered related to medicinal product infusion, and all resolved without sequelae. Cytopenias and viral infections (common childhood illnesses) were the most frequently reported TEAEs. INTERPRETATION These results show for the first time that haematopoietic gene therapy without genotoxic conditioning enables sustained engraftment and reversal of BMF progression in patients with Fanconi anaemia. FUNDING European Commission, Instituto de Salud Carlos III, and Rocket Pharmaceuticals.
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Affiliation(s)
- Paula Río
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Josune Zubicaray
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Pediatric Hematology and Oncology Department, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Foundation for the Biomedical Research, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Susana Navarro
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Eva Gálvez
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Pediatric Hematology and Oncology Department, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Foundation for the Biomedical Research, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Rebeca Sánchez-Domínguez
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | | | - Elena Sebastián
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Pediatric Hematology and Oncology Department, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Foundation for the Biomedical Research, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Michael Rothe
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Roser Pujol
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Institut de Recerca Sant Pau, Universitat Autónoma de Barcelona, Barcelona, Spain; Unit of Genomic Medicine, Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Massimo Bogliolo
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Institut de Recerca Sant Pau, Universitat Autónoma de Barcelona, Barcelona, Spain; Serra Hunter Fellow, Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Barcelona, Spain; Unit of Genomic Medicine, Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Philipp John-Neek
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | | | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Lise Larcher
- Université Paris Cité, Inserm, CNRS, Hôpital Saint-Louis, APHP, Paris, France
| | - José C Segovia
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Rosa M Yáñez
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Omaira Alberquilla
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Begoña Díez
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - María Fernández-García
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Laura García-García
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain
| | - Manuel Ramírez
- Pediatric Hematology and Oncology Department, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Sanitary Research Institute Fundación La Princesa, Madrid, Spain
| | - Anne Galy
- Genethon, UMR_S951, Université Paris-Saclay, Univ Evry, Inserm, Evry-Courcouronnes, France
| | - Francois Lefrere
- Hôpital Universitaire Necker Enfants-Malades, Assistance Publique Hôpitaux de Paris GHU Paris Centre, Université Paris Cité, Paris, France; Centre D'Investigation Clinique en Biotherapie INSERM, Institut Imagine, Paris, France
| | - Marina Cavazzana
- Hôpital Universitaire Necker Enfants-Malades, Assistance Publique Hôpitaux de Paris GHU Paris Centre, Université Paris Cité, Paris, France; Centre D'Investigation Clinique en Biotherapie INSERM, Institut Imagine, Paris, France
| | - Thierry Leblanc
- Robert-Debré University Hospital (APHP and Université Paris Cité), Paris, France
| | - Nagore García de Andoin
- Donostia Universitary Hospital, San Sebastián, Spain; Biogipuzkoa Health Research Institute, San Sebastián, Spain
| | - Ricardo López-Almaraz
- Cruces Universitary Hospital, Barakaldo, Spain; Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Albert Catalá
- Hospital Sant Joan de Déu, Barcelona, Spain; Research Institute Sant Joan de Déu, Barcelona, Spain
| | | | | | | | - Jordi Surrallés
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Institut de Recerca Sant Pau, Universitat Autónoma de Barcelona, Barcelona, Spain; Unit of Genomic Medicine, Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Jean Soulier
- Université Paris Cité, Inserm, CNRS, Hôpital Saint-Louis, APHP, Paris, France
| | - Cristina Díaz-de-Heredia
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Vall d'Hebron Institut de Recerca, Barcelona, Spain; Pediatric Haematology and Oncology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | | | - Julián Sevilla
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Pediatric Hematology and Oncology Department, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Foundation for the Biomedical Research, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Juan A Bueren
- Biomedical Innovation Unit, Center for Research on Energy, Environment and Technology (CIEMAT), Madrid, Spain; Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain; Sanitary Research Institute Fundación Jiménez Díaz (U.A.M), Madrid, Spain.
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Wang X, Li J, Zhou Y, Zhang J, Wang L, Liu Y, Yang X, Han H, Wang Q, Wang Y. Functional analysis of type II chalcone isomerase ( CHI) genes in regulating soybean ( Glycine max L.) nodule formation. GM CROPS & FOOD 2025; 16:305-317. [PMID: 40165359 PMCID: PMC11970754 DOI: 10.1080/21645698.2025.2486280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 03/26/2025] [Accepted: 03/26/2025] [Indexed: 04/02/2025]
Abstract
Biological nitrogen fixation (BNF) is the most cost-effective and environmentally benign method for nitrogen fertilization. Isoflavones are important signaling factors for BNF in leguminous plants. Whether chalcone isomerase (CHI), the key enzyme gene in the flavonoid synthesis pathway, contributes to soybean (Glycine max) nodulation has not yet been fully clarified. In the present study, we identified the functions of three types of GmCHI for BNF using a hairy root system. The results showed that GmCHI1A and GmCHI1B1 positively increased nodulation while GmCHI1B2 did not, with the GmCHI1A gene having a greater effect than GmCHI1B1. Meanwhile, the daidzein and genistein contents were significantly increased in composite plants overexpressing GmCHI1A and reduced in composite plants, thus interfering with GmCHI1A. However, overexpression of GmCHI1B1 significantly increased the content of glycitein but not daidzein, genistein content implied that homologous genes exhibit functional differentiation. These results provide a reference for subsequent studies on improving nitrogen fixation in soybeans and providing functional genes for the improvement of new varieties.
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Affiliation(s)
| | | | - Yuxue Zhou
- College of Plant Science, Jilin University, Changchun, China
| | - Jinhao Zhang
- College of Plant Science, Jilin University, Changchun, China
| | - Le Wang
- College of Plant Science, Jilin University, Changchun, China
| | - Yajing Liu
- College of Plant Science, Jilin University, Changchun, China
| | - Xuguang Yang
- College of Plant Science, Jilin University, Changchun, China
| | - Hongshuang Han
- College of Plant Science, Jilin University, Changchun, China
| | - Qingyu Wang
- College of Plant Science, Jilin University, Changchun, China
| | - Ying Wang
- College of Plant Science, Jilin University, Changchun, China
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Carasso S, Keshet-David R, Zhang J, Hajjo H, Kadosh-Kariti D, Gefen T, Geva-Zatorsky N. Bacteriophage-driven DNA inversions shape bacterial functionality and long-term co-existence in Bacteroides fragilis. Gut Microbes 2025; 17:2501492. [PMID: 40350564 PMCID: PMC12068327 DOI: 10.1080/19490976.2025.2501492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2025] [Revised: 04/21/2025] [Accepted: 04/28/2025] [Indexed: 05/14/2025] Open
Abstract
Bacterial genomic DNA inversions, which govern molecular phase-variations, provide the bacteria with functional plasticity and phenotypic diversity. These targeted rearrangements enable bacteria to respond to environmental challenges, such as bacteriophage predation, evading immune detection or gut colonization. This study investigated the short- and long-term effects of the lytic phage Barc2635 on the functional plasticity of Bacteroides fragilis, a gut commensal. Germ-free mice were colonized with B. fragilis and exposed to Barc2635 to identify genomic alterations driving phenotypic changes. Phage exposure triggered dynamic and prolonged bacterial responses, including significant shifts in phase-variable regions (PVRs), particularly in promoter orientations of polysaccharide biosynthesis loci. These shifts coincided with increased entropy in PVR inversion ratios, reflecting heightened genomic variability. In contrast, B. fragilis in control mice exhibited stable genomic configurations after gut adaptation. The phase-variable Type 1 restriction-modification system, which affects broad gene expression patterns, showed variability in both groups. However, phage-exposed bacteria displayed more restrained variability, suggesting phage-derived selection pressures. Our findings reveal that B. fragilis employs DNA inversions to adapt rapidly to phage exposure and colonization, highlighting a potential mechanism by which genomic variability contributes to its response to phage. This study demonstrates gut bacterial genomic and phenotypic plasticity upon exposure to the mammalian host and to bacteriophages.
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Affiliation(s)
- Shaqed Carasso
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa, Israel
| | - Roni Keshet-David
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa, Israel
| | - Jia Zhang
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa, Israel
| | - Haitham Hajjo
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa, Israel
| | - Dana Kadosh-Kariti
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa, Israel
| | - Tal Gefen
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa, Israel
| | - Naama Geva-Zatorsky
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa, Israel
- CIFAR Humans & the Microbiome Program, CIFAR, Toronto, ON, Canada
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Deshpande G, Das S, Roy AE, Ratnaparkhi GS. A face-off between Smaug and Caspar modulates primordial germ cell count and identity in Drosophila embryos. Fly (Austin) 2025; 19:2438473. [PMID: 39718186 DOI: 10.1080/19336934.2024.2438473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 11/26/2024] [Accepted: 12/01/2024] [Indexed: 12/25/2024] Open
Abstract
Proper formation and specification of Primordial Germ Cells (PGCs) is of special significance as they gradually transform into Germline Stem Cells (GSCs) that are ultimately responsible for generating the gametes. Intriguingly, not only the PGCs constitute the only immortal cell type but several specific determinants also underlying PGC specification such as Vasa, Nanos and Germ-cell-less are conserved through evolution. In Drosophila melanogaster, PGC formation and specification depends on two independent factors, the maternally deposited specialized cytoplasm (or germ plasm) enriched in germline determinants, and the mechanisms that execute the even partitioning of these determinants between the daughter cells. Prior work has shown that Oskar protein is necessary and sufficient to assemble the functional germ plasm, whereas centrosomes associated with the nuclei that invade the germ plasm are responsible for its equitable distribution. Our recent data suggests that Caspar, the Drosophila orthologue of human Fas-associated factor-1 (FAF1) is a novel regulator that modulates both mechanisms that underlie the determination of PGC fate. Consistently, early blastoderm embryos derived from females compromised for caspar display reduced levels of Oskar and defective centrosomes.
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Affiliation(s)
- Girish Deshpande
- Department of Biology, Indian Institute of Science Education & Research, Pune, India
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Subhradip Das
- Department of Biology, Indian Institute of Science Education & Research, Pune, India
| | - Adheena Elsa Roy
- Department of Biology, Indian Institute of Science Education & Research, Pune, India
| | - Girish S Ratnaparkhi
- Department of Biology, Indian Institute of Science Education & Research, Pune, India
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Forte G, Boteva L, Gilbert N, Cook PR, Marenduzzo D. Bridging-mediated compaction of mitotic chromosomes. Nucleus 2025; 16:2497765. [PMID: 40340634 PMCID: PMC12068332 DOI: 10.1080/19491034.2025.2497765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 03/27/2025] [Accepted: 04/21/2025] [Indexed: 05/10/2025] Open
Abstract
Within living cells, chromosome shapes undergo a striking morphological transition, from loose and uncondensed fibers during interphase to compacted and cylindrical structures during mitosis. ATP driven loop extrusion performed by a specialized protein complex, condensin, has recently emerged as a key driver of this transition. However, while this mechanism can successfully recapitulate the compaction of chromatids during the early stages of mitosis, it cannot capture structures observed after prophase. Here we hypothesize that a condensin bridging activity plays an additional important role, and review evidence - obtained largely through molecular dynamics simulations - that, in combination with loop extrusion, it can generate compact metaphase cylinders. Additionally, the resulting model qualitatively explains the unusual elastic properties of mitotic chromosomes observed in micromanipulation experiments and provides insights into the role of condensins in the formation of abnormal chromosome structures associated with common fragile sites.
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Affiliation(s)
- Giada Forte
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Lora Boteva
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Nick Gilbert
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Peter R. Cook
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
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7
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Zhang M, Lu Z. tRNA modifications: greasing the wheels of translation and beyond. RNA Biol 2025; 22:1-25. [PMID: 39723662 DOI: 10.1080/15476286.2024.2442856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/29/2024] [Accepted: 12/11/2024] [Indexed: 12/28/2024] Open
Abstract
Transfer RNA (tRNA) is one of the most abundant RNA types in cells, acting as an adaptor to bridge the genetic information in mRNAs with the amino acid sequence in proteins. Both tRNAs and small fragments processed from them play many nonconventional roles in addition to translation. tRNA molecules undergo various types of chemical modifications to ensure the accuracy and efficiency of translation and regulate their diverse functions beyond translation. In this review, we discuss the biogenesis and molecular mechanisms of tRNA modifications, including major tRNA modifications, writer enzymes, and their dynamic regulation. We also summarize the state-of-the-art technologies for measuring tRNA modification, with a particular focus on 2'-O-methylation (Nm), and discuss their limitations and remaining challenges. Finally, we highlight recent discoveries linking dysregulation of tRNA modifications with genetic diseases.
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Affiliation(s)
- Minjie Zhang
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Medical Epigenetics, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhipeng Lu
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
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8
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Wencker FDR, Lyon SE, Breaker RR. Evidence that ribosomal protein bS21 is a component of the OLE ribonucleoprotein complex. RNA Biol 2025; 22:1-14. [PMID: 40322971 PMCID: PMC12054373 DOI: 10.1080/15476286.2025.2491842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/25/2025] [Accepted: 04/03/2025] [Indexed: 05/08/2025] Open
Abstract
OLE RNAs represent a large and highly structured noncoding RNA (ncRNA) class that is mostly found in Gram-positive extremophiles and/or anaerobes of the Bacillota phylum. These ~600-nucleotide RNAs are among the most structurally complex and well-conserved large ncRNAs whose precise biochemical functions remain to be established. In Halalkalibacterium halodurans, OLE RNA is involved in the adaptation to various unfavourable growth conditions, including exposure to cold (≤20°C), ethanol (≥3% [v/v]), excess Mg2+ (≥4 mM), and non-glucose carbon/energy sources. OLE forms a ribonucleoprotein (RNP) complex with the OLE-associated proteins A, B and C, which are known to be essential for OLE RNP complex function in this species. Bacteria lacking OLE RNA (Δole) or a functional OLE RNP complex exhibit growth defects under the stresses listed above. Here, we demonstrate that ribosomal protein bS21 is a natural component of the OLE RNP complex and we map its precise RNA binding site. The presence of bS21 results in a conformational change in OLE RNA resembling a k-turn substructure previously reported to be relevant to the function of the OLE RNP complex. Mutational disruption of the bS21 protein or its OLE RNA binding site results in growth inhibition under cold and ethanol stress to the same extent as the deletion of the gene for OLE RNA. These findings are consistent with the hypothesis that bS21 is a biologically relevant component of the OLE RNP complex under a subset of stresses managed by the OLE RNP complex.
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Affiliation(s)
- Freya D. R. Wencker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Seth E. Lyon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Jin T, Li SY, Zheng HL, Liu XD, Huang Y, Ma G, Zhao YX, Zhao XT, Yang L, Wang QH, Wang HJ, Gu C, Pan Z, Lin F. Gut microbes-spinal connection is required for itch sensation. Gut Microbes 2025; 17:2495859. [PMID: 40289281 PMCID: PMC12036491 DOI: 10.1080/19490976.2025.2495859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 03/23/2025] [Accepted: 04/10/2025] [Indexed: 04/30/2025] Open
Abstract
The gut microbiota has been linked to a number of neurological disorders. However, it is unclear whether the gut microbiota is involved in the genesis of chronic itch, a refractory condition that afflicts patients both physically and mentally. Here, we report that depletion of gut microbiota enhances tolerance to itch in mice orally administered with antibiotics (ABX) and mice free of germ. Of note, oral gavage with Bacteroides fragilis (B. fragilis), a prominent species of the genus Bacteroides with most differential change, corrected the ABX-induced itch dysfunction through its driven metabolite acetyl-l-carnitine (ALC). Mechanistically, gut microbiota or B. fragilis depletion caused a decrease in RNA N6-methyladenosine (m6A) demethylase FTO expression in the dorsal horn and a consequent increase in RNA m6A sites in Mas-related G protein-coupled receptor F (MrgprF) mRNA, leading to decreased MRGPRF protein. The downregulation of FTO was triggered by inactivation of ETS proto-oncogene 1 (ETS1), a transcription factor that binds to the Fto promoter. These findings support a gut microbe - spinal connection in modulation of itch sensation in RNA m6A epigenetic-dependent manner and highlight a critical role of ALC in linking the altered B. fragilis and itch dysfunction.
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Affiliation(s)
- Tong Jin
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
- Department of Pain, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Si-Yuan Li
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Hong-Li Zheng
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
- Department of Pain, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Anesthesiology Department, Suzhou Municipal Hospital, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, China
| | - Xiao-Dan Liu
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
- Department of Anesthesiology, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Yue Huang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Gan Ma
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Ya-Xuan Zhao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Xiao-Tian Zhao
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Li Yang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Qi-Hui Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Hong-Jun Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Chengyong Gu
- Anesthesiology Department, Suzhou Municipal Hospital, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, China
| | - Zhiqiang Pan
- Jiangsu Province Key Laboratory of Anesthesiology, Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, China
| | - Fuqing Lin
- Department of Pain, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
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10
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Victor Atoki A, Aja PM, Shinkafi TS, Ondari EN, Adeniyi AI, Fasogbon IV, Dangana RS, Shehu UU, Akin-Adewumi A. Exploring the versatility of Drosophila melanogaster as a model organism in biomedical research: a comprehensive review. Fly (Austin) 2025; 19:2420453. [PMID: 39722550 DOI: 10.1080/19336934.2024.2420453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 10/16/2024] [Accepted: 10/16/2024] [Indexed: 12/28/2024] Open
Abstract
Drosophila melanogaster is a highly versatile model organism that has profoundly advanced our understanding of human diseases. With more than 60% of its genes having human homologs, Drosophila provides an invaluable system for modelling a wide range of pathologies, including neurodegenerative disorders, cancer, metabolic diseases, as well as cardiac and muscular conditions. This review highlights key developments in utilizing Drosophila for disease modelling, emphasizing the genetic tools that have transformed research in this field. Technologies such as the GAL4/UAS system, RNA interference (RNAi) and CRISPR-Cas9 have enabled precise genetic manipulation, with CRISPR-Cas9 allowing for the introduction of human disease mutations into orthologous Drosophila genes. These approaches have yielded critical insights into disease mechanisms, identified novel therapeutic targets and facilitated both drug screening and toxicological studies. Articles were selected based on their relevance, impact and contribution to the field, with a particular focus on studies offering innovative perspectives on disease mechanisms or therapeutic strategies. Our findings emphasize the central role of Drosophila in studying complex human diseases, underscoring its genetic similarities to humans and its effectiveness in modelling conditions such as Alzheimer's disease, Parkinson's disease and cancer. This review reaffirms Drosophila's critical role as a model organism, highlighting its potential to drive future research and therapeutic advancements.
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Affiliation(s)
| | - Patrick Maduabuchi Aja
- Department of Biochemistry, Kampala International University, Ishaka, Uganda
- Department of Biochemistry, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | | | - Erick Nyakundi Ondari
- Department of Biochemistry, Kampala International University, Ishaka, Uganda
- School of Pure and Applied Sciences, Department of Biological Sciences, Kisii University, Kisii, Kenya
| | | | | | | | - Umar Uthman Shehu
- Department of Physiology, Kampala International University, Ishaka, Uganda
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11
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Funikov S, Rezvykh A, Akulenko N, Liang J, Sharakhov IV, Kalmykova A. Analysis of somatic piRNAs in the malaria mosquito Anopheles coluzzii reveals atypical classes of genic small RNAs. RNA Biol 2025; 22:1-16. [PMID: 39916410 PMCID: PMC11834523 DOI: 10.1080/15476286.2025.2463812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 01/28/2025] [Accepted: 02/03/2025] [Indexed: 02/18/2025] Open
Abstract
Piwi-interacting small RNAs (piRNA) play a key role in controlling the activity of transposable elements (TEs) in the animal germline. In diverse arthropod species, including the pathogen vectors mosquitoes, the piRNA pathway is also active in nongonadal somatic tissues, where its targets and functions are less clear. Here, we studied the features of small RNA production in head and thorax tissues of an uninfected laboratory strain of Anopheles coluzzii focusing on the 24-32-nt-long RNAs. Small RNAs derived from repetitive elements constitute a minor fraction while most small RNAs process from long noncoding RNAs (lncRNAs) and protein-coding gene mRNAs. The majority of small RNAs derived from repetitive elements and lncRNAs exhibited typical piRNAs features. By contrast, majority of protein-coding gene-derived 24-32 nt small RNAs lack the hallmarks of piRNAs and have signatures of nontemplated 3' end tailing. Most of the atypical small RNAs exhibit female-biased expression and originate from mitochondrial and nuclear genes involved in energy metabolism. We also identified atypical genic small RNAs in Anopheles gambiae somatic tissues, which further validates the noncanonical mechanism of their production. We discuss a novel mechanism of small RNA production in mosquito somatic tissues and the possible functional significance of genic small RNAs.
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Affiliation(s)
- Sergei Funikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Rezvykh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Natalia Akulenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Jiangtao Liang
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Igor V. Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- The Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- Department of Genetics and Cell Biology, Tomsk State University, Tomsk, Russia
| | - Alla Kalmykova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
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12
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Zhao Z, Geisbrecht ER. Stage-specific modulation of Drosophila gene expression with muscle GAL4 promoters. Fly (Austin) 2025; 19:2447617. [PMID: 39772988 PMCID: PMC11730430 DOI: 10.1080/19336934.2024.2447617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 12/19/2024] [Accepted: 12/20/2024] [Indexed: 01/11/2025] Open
Abstract
The bipartite GAL4/UAS system is the most widely used method for targeted gene expression in Drosophila melanogaster and facilitates rapid in vivo genetic experimentation. Defining precise gene expression patterns for tissues and/or cell types under GAL4 control will continue to evolve to suit experimental needs. However, the precise spatial and temporal expression patterns for some commonly used muscle tissue promoters are still unclear. This missing information limits the precise timing of experiments during development. Here, we focus on three muscle-enriched GAL4 drivers (Mef2-GAL4, C57-GAL4 and G7-GAL4) to better inform selection of the most appropriate muscle promoter for experimental needs. Specifically, C57-GAL4 and G7-GAL4 turn on in the first or second instar larval stages, respectively, and can be used to bypass myogenesis for studies of muscle function after development.
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Affiliation(s)
- Ziwei Zhao
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, USA
| | - Erika R Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, USA
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13
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Wang X, Chen W, Liu S, Xu Y, Xiong Z, Li Y, Huang L, Jiang L, Zhang J, Sun L, Zhang Y, Liu M. Detection of mitophagy in live cells with indole derived near-infrared fluorogenic probes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2025; 340:126368. [PMID: 40367757 DOI: 10.1016/j.saa.2025.126368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2025] [Revised: 04/29/2025] [Accepted: 05/08/2025] [Indexed: 05/16/2025]
Abstract
Mitophagy is an indispensable cellular process that plays a crucial role in regulating mitochondrial quality control and cellular metabolism. Therefore, monitoring the changes in the mitochondrial and lysosomal microenvironment during the mitophagy process is extremely important. However, existing mitophagy probes only target changes in a single indicator (viscosity, pH value, or polarity) within the microenvironment, which may reduce the selectivity and accuracy of assessing mitophagy in complex biological settings. To address this, we have developed a dual-channel detection near-infrared (NIR) fluorescent probe (ADMI). In vitro analysis experiments have shown that ADMI not only responds to pH and activates the NIR fluorescence channel but also that the green fluorescence channel exhibits high sensitivity to changes in polarity. This dual-response mechanism probe enables dual fluorescent detection of pH and polarity, providing a highly promising tool for monitoring the microenvironment of mitophagy in living cells. Ultimately, we applied ADMI to real-time monitoring of mitophagy induced by starvation or rapamycin, during which the decrease in pH and polarity resulted in a red shift in wavelength and increased fluorescence. Additionally, ADMI was able to observe changes in mitochondria during ferroptosis. This probe may serve as a useful tool for imaging mitophagy in living cells.
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Affiliation(s)
- Xuanyuan Wang
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China
| | - Wen Chen
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China.
| | - Shuangling Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 Hunan, PR China
| | - Yihong Xu
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China
| | - Zhimei Xiong
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China
| | - Yingzi Li
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China
| | - Leyuan Huang
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China
| | - Lu Jiang
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China
| | - Jingting Zhang
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China
| | - Leying Sun
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China
| | - Yuan Zhang
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China.
| | - Mengqin Liu
- College of Chemistry and Material Science, Hengyang Normal University, Hengyang 421001, PR China
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14
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Moyo B, Brown LBC, Khondaker II, Bao G. Engineering adeno-associated viral vectors for CRISPR/Cas based in vivo therapeutic genome editing. Biomaterials 2025; 321:123314. [PMID: 40203649 DOI: 10.1016/j.biomaterials.2025.123314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Revised: 03/30/2025] [Accepted: 04/01/2025] [Indexed: 04/11/2025]
Abstract
The recent approval of the first gene editing therapy for sickle cell disease and transfusion-dependent beta-thalassemia by the U.S. Food and Drug Administration (FDA) demonstrates the immense potential of CRISPR (clustered regularly interspaced short palindromic repeats) technologies to treat patients with genetic disorders that were previously considered incurable. While significant advancements have been made with ex vivo gene editing approaches, the development of in vivo CRISPR/Cas gene editing therapies has not progressed as rapidly due to significant challenges in achieving highly efficient and specific in vivo delivery. Adeno-associated viral (AAV) vectors have shown great promise in clinical trials as vehicles for delivering therapeutic transgenes and other cargos but currently face multiple limitations for effective delivery of gene editing machineries. This review elucidates these challenges and highlights the latest engineering strategies aimed at improving the efficiency, specificity, and safety profiles of AAV-packaged CRISPR/Cas systems (AAV-CRISPR) to enhance their clinical utility.
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Affiliation(s)
- Buhle Moyo
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Lucas B C Brown
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA; Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, 77030, USA
| | - Ishika I Khondaker
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA.
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15
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Wang C, Tian Z, Luan X, Zhang H, Zhang Y, Yang M. Distribution of antibiotic resistance genes on chromosomes, plasmids and phages in aerobic biofilm microbiota under antibiotic pressure. J Environ Sci (China) 2025; 156:647-659. [PMID: 40412963 DOI: 10.1016/j.jes.2024.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 10/05/2024] [Accepted: 10/10/2024] [Indexed: 05/27/2025]
Abstract
The objective of this study is to quantitatively reveal the main genetic carrier of antibiotic resistance genes (ARGs) for blocking their environmental dissemination. The distribution of ARGs in chromosomes, plasmids, and phages for understanding their respective contributions to the development of antimicrobial resistance in aerobic biofilm consortium under increasing stresses of oxytetracycline, streptomycin, and tigecycline were revealed based on metagenomics analysis. Results showed that the plasmids harbored 49.2 %-83.9 % of resistomes, which was higher (p < 0.001) than chromosomes (2.0 %-35.6 %), and no ARGs were detected in phage contigs under the strict alignment standard of over 80 % identity used in this study. Plasmids and chromosomes tended to encode different types of ARGs, whose abundances all increased with the hike of antibiotic concentrations, and the variety of ARGs encoded by plasmids (14 types and 64 subtypes) was higher than that (11 types and 27 subtypes) of chromosomes. The dosing of the three antibiotics facilitated the transposition and recombination of ARGs on plasmids, mediated by transposable and integrable transfer elements, which increased the co-occurrence of associated and unassociated ARGs. The results quantitatively proved that plasmids dominate the proliferation of ARGs in aerobic biofilm driven by antibiotic selection, which should be a key target for blocking ARG dissemination.
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Affiliation(s)
- Chen Wang
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhe Tian
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiao Luan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100048, China
| | - Hong Zhang
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yu Zhang
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Yang
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Nishigaya Y, Takase S, Sumiya T, Kikuzato K, Hiroyama T, Maemoto Y, Aoki K, Sato T, Niwa H, Sato S, Ihara K, Nakata A, Matsuoka S, Hashimoto N, Namie R, Honma T, Umehara T, Shirouzu M, Koyama H, Nakamura Y, Yoshida M, Ito A, Shirai F. Discovery of potent substrate-type lysine methyltransferase G9a inhibitors for the treatment of sickle cell disease. Eur J Med Chem 2025; 293:117721. [PMID: 40367677 DOI: 10.1016/j.ejmech.2025.117721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Revised: 04/22/2025] [Accepted: 05/02/2025] [Indexed: 05/16/2025]
Abstract
Structurally novel inhibitors of the lysine methyltransferase G9a have attracted considerable interest as potential drug candidates for cancer and genetic diseases. Here, a detailed account of potency optimization from early leads 8 and 9 to compound 16g is presented. Our search for an alternative scaffold for the 4-oxo-4,5,6,7-tetrahydro-1H-indole moiety of compounds 8 and 9 via parallel synthesis led to the identification of the 4-pyridin-4-ylamino phenyl substructure in compound 16g. This substructure was found to bind to the enzyme in a horizontally flipped manner compared with compound 8 in X-ray crystallographic analysis. Compound 16g is a highly potent G9a inhibitor (IC50 = 0.0020 μM) and structurally distinct from other G9a inhibitors reported in the literature. Importantly, compound 16g exhibited dose-dependent induction of γ-globin mRNA in HUDEP-2, leading to elevated γ-globin protein levels and F cell numbers in CD34+ bone marrow (BM)‒derived hematopoietic cells. Kinetic studies using surface plasmon resonance (SPR) analysis suggested that compound 16g interacts with G9a via a unique binding mode, as indicated by the markedly higher dissociation constant (KD) compared to those of compounds 8 and 9. Interestingly, X-ray crystallographic studies revealed that the binding motif of compound 16g was quite different from our previous series, including RK-701, and somewhat resembles that of endogenous substrates. Insights obtained in this lead optimization exercise on the association/dissociation constants as well as the binding motifs are expected to help in designing future G9a inhibitors for the treatment of sickle cell disease.
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Affiliation(s)
- Yosuke Nishigaya
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi, 329-0114, Japan.
| | - Shohei Takase
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Tatsunobu Sumiya
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi, 329-0114, Japan
| | - Ko Kikuzato
- Drug Discovery Chemistry Platform Unit, Japan
| | - Takashi Hiroyama
- Cell Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yuki Maemoto
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Komei Aoki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Tomohiro Sato
- Drug Discovery Computational Chemistry Platform Unit, Japan
| | - Hideaki Niwa
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Shin Sato
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kentaro Ihara
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Akiko Nakata
- Drug Discovery Seed Compounds Exploratory Unit, Japan
| | | | - Noriaki Hashimoto
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi, 329-0114, Japan
| | - Ryosuke Namie
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi, 329-0114, Japan
| | - Teruki Honma
- Drug Discovery Computational Chemistry Platform Unit, Japan
| | - Takashi Umehara
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Mikako Shirouzu
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Minoru Yoshida
- Drug Discovery Seed Compounds Exploratory Unit, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan; the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Akihiro Ito
- Drug Discovery Seed Compounds Exploratory Unit, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan; School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Fumiyuki Shirai
- Drug Discovery Chemistry Platform Unit, Japan; Center for One Medicine Innovative Translational Research (COMIT), Institute for Advanced Study, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
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17
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Oryani MA, Mohammad Al-Mosawi AK, Javid H, Tajaldini M, Karimi-Shahri M. A Bioligical Perspective on the role of miR-206 in Colorectal cancer. Gene 2025; 961:149552. [PMID: 40339768 DOI: 10.1016/j.gene.2025.149552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Revised: 04/30/2025] [Accepted: 05/05/2025] [Indexed: 05/10/2025]
Abstract
MicroRNAs (miRs) have emerged as pivotal regulators in the development and progression of colorectal cancer (CRC), and MicroRNA-206 (miR-206) has garnered attention as a potentially influential factor. However, the specific biological functions and complete mechanistic understanding of miR-206 in CRC remain largely uncharacterized. This study aims to bridge this research gap by providing a comprehensive analysis of miR-206's role in CRC. An exploration of the molecular mechanisms regulated by miR-206, its intricate interplay with target genes, and its significant impact on cellular processes highlights its potential utility as both a diagnostic marker and a therapeutic target. The significance of this research lies in potentially enabling the development of innovative therapeutic approaches, ultimately aiming to improve prognosis and survival rates in CRC patients by elucidating the functions of miR-206. Critical pathways, such as c-Met and PTEN/AKT, play crucial roles within the regulatory network of miR-206 in CRC and impact various cellular processes involved in CRC pathogenesis, metastasis, and treatment response. Understanding the complex interactions between miR-206 and key signaling pathways like c-Met and PTEN/AKT is crucial for understanding the underlying mechanisms driving CRC initiation and progression. This knowledge can inform the development of targeted therapeutic interventions, potentially leading to improved patient outcomes and advances in CRC management.
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Affiliation(s)
- Mahsa Akbari Oryani
- Department of Pathology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Hossein Javid
- Department of Medical Laboratory Sciences, Varastegan Institute for Medical Sciences, Mashhad, Iran; Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahboubeh Tajaldini
- Ischemic Disorder Research Center, Golestan University of Medical Sciences. Gorgan, Iran
| | - Mehdi Karimi-Shahri
- Department of Pathology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pathology, School of Medicine, Gonabad University of Medical Sciences, Gonabad, Iran.
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18
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Pachinger C, Dobbelaere J, Rumpf-Kienzl C, Raina S, Garcia-Baucells J, Sarantseva M, Brauneis A, Dammermann A. A conserved role for centriolar satellites in translation of centrosomal and ciliary proteins. J Cell Biol 2025; 224:e202408042. [PMID: 40396915 DOI: 10.1083/jcb.202408042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 01/30/2025] [Accepted: 03/18/2025] [Indexed: 05/22/2025] Open
Abstract
Centriolar satellites are cytoplasmic particles found in the vicinity of centrosomes and cilia whose specific functional contribution has long been unclear. Here, we identify Combover as the Drosophila ortholog of the main scaffolding component of satellites, PCM1. Like PCM1, Combover localizes to cytoplasmic foci containing centrosomal proteins and its depletion or mutation results in centrosomal and ciliary phenotypes. Strikingly, however, the concentration of satellites near centrosomes and cilia is not a conserved feature, nor do Combover foci display directed movement. Proximity interaction analysis revealed not only centrosomal and ciliary proteins, but also RNA-binding proteins and proteins involved in quality control. Further work in Drosophila and vertebrate cells found satellites to be associated with centrosomal and ciliary mRNAs, as well as evidence for protein synthesis occurring directly at satellites. Given that PCM1 depletion does not affect overall protein levels, we propose that satellites instead promote the coordinate synthesis of centrosomal and ciliary proteins, thereby facilitating the formation of protein complexes.
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Affiliation(s)
- Claudia Pachinger
- Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna , Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna , Vienna, Austria
| | - Jeroen Dobbelaere
- Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna , Vienna, Austria
| | | | - Shiviya Raina
- Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna , Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna , Vienna, Austria
| | - Júlia Garcia-Baucells
- Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna , Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna , Vienna, Austria
| | - Marina Sarantseva
- Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna , Vienna, Austria
| | - Andrea Brauneis
- Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna , Vienna, Austria
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19
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Kothe CI, Renault P. Metagenomic driven isolation of poorly culturable species in food. Food Microbiol 2025; 129:104722. [PMID: 40086981 DOI: 10.1016/j.fm.2025.104722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 01/02/2025] [Accepted: 01/02/2025] [Indexed: 03/16/2025]
Abstract
Although isolating microorganisms from food microbiota may appear less challenging than from the gut or environmental sources, recovering all representative species from food remains a difficult task. Here, we showed by metagenomic analysis that several abundant species had escaped isolation in a previous study of ten cheeses, including several previously uncharacterized species. This highlights the ongoing challenge of achieving a comprehensive recovery of microbes from food. To address this gap, we designed a novel strategy integrating metagenomics-based probes targeting the species of interest, coupled with an incremental culturing approach using pooled samples. As proof of concept, we applied this strategy to two cheeses containing species that were not isolated in our previous study, with the objective of isolating all species present at levels above 2% and, in particular, potential novel food species. Through this approach, we successfully performed the targeted isolation of two Psychrobacter and two Vibrio species from the first cheese, and four Halomonas and two Pseudoalteromonas species from the second one. Notably, P. undina and V. litoralis represented, as far as we know, the first cheese isolates characterized for these species. However, we were unable to isolate a novel species of Pseudoalteromonas, with no characterized representative to date, and Marinomonas foliarum, previously isolated from marine environment. Using metagenome-assembled genomes (MAGs) and metagenomic analysis, we discussed the possible reasons for their non-recovery. Finally, this strategy offers a promising approach for isolating a set of strains representative of the microbial diversity present in food ecosystems. These isolates can serve as a basis for investigating their roles in the communities, their impact on product development, safety implications and their potential in the development of starter cultures.
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Affiliation(s)
- Caroline Isabel Kothe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Pierre Renault
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
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20
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Shen J, Yasir M, Willcox M. Whole genome sequencing-based prediction of antibiotic-resistance of ocular Staphylococcus aureus across six continents. Exp Eye Res 2025; 257:110425. [PMID: 40409356 DOI: 10.1016/j.exer.2025.110425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2025] [Revised: 05/05/2025] [Accepted: 05/15/2025] [Indexed: 05/25/2025]
Abstract
Staphylococcus aureus is a leading cause of ocular infections, resulting in vision loss in severe cases. Understanding the antibiotic resistance profiles of ocular S. aureus can help customize treatments. However, there is a lack of global data on the resistance patterns of ocular isolates and comparative regional analyses. Hence, WGS data from 195 ocular S. aureus isolates across six continents were analysed to identify antibiotic resistance genes (ARGs) and predict antibiotic resistance phenotypes in this study. A total of 40 ARGs were detected, involving resistance mechanisms against aminoglycosides, beta-lactams, macrolide-lacosamide-streptogramin B (MLSB), glycopeptides, tetracyclines, other antibiotic classes, and efflux pump regulators. Notably, the prevalences of ARGs associated with efflux pump regulators and beta-lactams were particularly high (>80 %). Resistance to 45 antibiotics was predicted across the isolates, with 51 % identified as multidrug-resistant (MDR), while only 8 % were predicted to be fully susceptible to all predicted antibiotics. Regional data varied, with isolates from North America and Asia exhibiting the most extensive resistance patterns, showing predicted resistance to 45 and 41 antibiotics, respectively. In contrast, Oceanian isolates were predicted to be resistant to only 14 antibiotics. Beta-lactams showed the highest predicted resistance prevalence among all antibiotic classes. Notably, North American isolates showed markedly higher resistance to MLSB antibiotics. A high proportion of cloud genes highlights the need for monitoring regional resistance. This study provides antibiotic resistance profiles among ocular S. aureus using WGS prediction, emphasizing the importance of regional surveillance and antimicrobial stewardship to suggest effective treatment strategies. It is recommended that WGS of more strains be deposited to overcome limited data, and laboratory tests be performed to analyse the consistency between genetic predicted and phenotypic resistance.
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Affiliation(s)
- Jiawei Shen
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Muhammad Yasir
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Mark Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW, 2052, Australia.
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21
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Wong DPH, Wong KH, Park S, Boël G, Hunt JF, Aalberts DP. OPT: Codon optimize gene sequences for E. coli protein overexpression. J Mol Biol 2025; 437:168965. [PMID: 40133777 PMCID: PMC12145263 DOI: 10.1016/j.jmb.2025.168965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2024] [Revised: 01/23/2025] [Accepted: 01/23/2025] [Indexed: 03/27/2025]
Abstract
The ability to overexpress proteins is valuable for biotechnology, but not all sequences are compatible with high yield. We previously analyzed the sequence features and mRNA folding stability of a large data set of 6,384 distinct gene constructs, and developed a model for protein yield. Our OPT.williams.edu server (1) predicts the probability an input sequence will produce protein at a high level when overexpressed in E. coli, and (2) returns optimized synonymous sequences designed to boost protein expression. Here we also present experimental evidence of the high yields of our OPT constructs for eight commercially produced proteins.
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Affiliation(s)
- Daniel P H Wong
- Physics Department, Williams College, Williamstown, MA 01267, USA
| | - Kam-Ho Wong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Sunjae Park
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Grégory Boël
- Expression Génétique Microbienne, CNRS, Universite Paris Cite, Institut de Biologie Physio-Chimique, F-75005 Paris, France.
| | - John F Hunt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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22
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Pattano J, Jintasakul V, Jantapaso H, Mittraparp-Arthorn P. Inhibition of quorum sensing, biofilm formation, and virulence-related characteristics in shrimp pathogenic Vibrio campbellii by rambutan (Nephelium lappaceum L. cv. Rong Rian) peel extract. Microb Pathog 2025; 205:107702. [PMID: 40373944 DOI: 10.1016/j.micpath.2025.107702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 05/08/2025] [Accepted: 05/12/2025] [Indexed: 05/17/2025]
Abstract
Vibrio campbellii is a significant pathogen in shrimp aquaculture, causing luminous vibriosis and leading to considerable declines in productivity and quality. The rapid emergence of multi-drug and detergent-resistant strains presents a major challenge in controlling this pathogen. This study investigates the inhibitory effects of rambutan peel extract (RPE) on quorum sensing (QS) systems, biofilm formation, and virulence-related traits in V. campbellii. The minimum inhibitory concentration (MIC) of RPE was found to be 2048 μg/ml for the pathogenic strain V. campbellii HY01 and 1024 μg/ml for the non-pathogenic QS reporter strains. Sub-inhibitory concentrations significantly reduced bioluminescence in V. campbellii, indicating interference with QS systems, particularly harveyi autoinducer-1 (HAI-1) and autoinducer-2 (AI-2). RPE disrupted autoinducer detection, down-regulated the expression of QS sensor genes, inhibited phosphorylation, and affected the transcription of QS regulator AphA. Additionally, RPE reduced biofilm formation, swimming motility, caseinase production, and virulence gene expression in the shrimp pathogenic strain HY01. These findings demonstrate the strong anti-QS activity of RPE against V. campbellii by targeting QS systems, phosphorylation pathways, and the master QS regulator. The study highlights the potential of RPE as a sustainable approach to control luminous vibriosis, offering a promising strategy for managing disease outbreaks and improving shrimp health in aquaculture.
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Affiliation(s)
- Jiranan Pattano
- Division of Biological Science, Faculty of Science, Prince of Songkla University, 90110, Hat Yai, Songkhla, Thailand; Center of Research and Innovation Development of Microbiology for Sustainability (RIMS), Faculty of Science, Prince of Songkla University, 90110, Hat Yai, Songkhla, Thailand
| | - Valalak Jintasakul
- Division of Biological Science, Faculty of Science, Prince of Songkla University, 90110, Hat Yai, Songkhla, Thailand; Center of Research and Innovation Development of Microbiology for Sustainability (RIMS), Faculty of Science, Prince of Songkla University, 90110, Hat Yai, Songkhla, Thailand
| | - Husanai Jantapaso
- Division of Biological Science, Faculty of Science, Prince of Songkla University, 90110, Hat Yai, Songkhla, Thailand; Center of Research and Innovation Development of Microbiology for Sustainability (RIMS), Faculty of Science, Prince of Songkla University, 90110, Hat Yai, Songkhla, Thailand
| | - Pimonsri Mittraparp-Arthorn
- Division of Biological Science, Faculty of Science, Prince of Songkla University, 90110, Hat Yai, Songkhla, Thailand; Center of Research and Innovation Development of Microbiology for Sustainability (RIMS), Faculty of Science, Prince of Songkla University, 90110, Hat Yai, Songkhla, Thailand.
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23
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Jiang S, Matuszewska M, Chen M, Hong Y, Chen Y, Wang Z, Zhuang H, Sun L, Zhu F, Wang H, Wu X, Ji S, Holmes MA, Ba X, Chen Y, Yu Y. Emergence and spread of ST5 methicillin-resistant Staphylococcus aureus with accessory gene regulator dysfunction: genomic insights and antibiotic resistance. Microbiol Res 2025; 297:128196. [PMID: 40311457 DOI: 10.1016/j.micres.2025.128196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Revised: 04/23/2025] [Accepted: 04/24/2025] [Indexed: 05/03/2025]
Abstract
The globally disseminated Staphylococcus aureus ST5 clone poses a major public health threat due to its multidrug resistance and virulence. Here, we identified an agr-dysfunctional (agrA-I238K) ST5 MRSA clone that has spread across East and Southeast Asia, with recent increases in China since its emergence in the 1970s. Comparative genomic analyses identified distinct single-nucleotide polymorphisms and mobile genetic elements linked to enhanced resistance and virulence. This clone exhibits resistance to seven antimicrobial classes, including third-generation tetracyclines and fusidic acid, and shares phenotypic and genetic similarities with the vancomycin-intermediate S. aureus Mu50 strain, including reduced susceptibility to vancomycin, teicoplanin, and daptomycin. The agrA-I238K mutation attenuates hemolytic activity, increases biofilm formation, and reduces daptomycin susceptibility, suggesting a key role in the clone's success. Our results demonstrate the important role of agrA-I238K mutation in the widespread distribution of agr-dysfunctional MRSA and highlight the importance of genomic surveillance in tracking the spread of agr-dysfunctional ST5 MRSA.
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Affiliation(s)
- Shengnan Jiang
- Centre of Laboratory Medicine, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China; Zhejiang University School of Medicine, Hangzhou, Hangzhou, Zhejiang, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, University of Cambridge, Cambridge, UK
| | - Mengzhen Chen
- Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Yueqin Hong
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yiyi Chen
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhengan Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hemu Zhuang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lu Sun
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Feiteng Zhu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Haiping Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xueqing Wu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shujuan Ji
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| | - Yan Chen
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Yunsong Yu
- Centre of Laboratory Medicine, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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24
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Caigoy JC, Nariya H, Shimamoto T, Yan Z, Shimamoto T. ArcAB system promotes biofilm formation through direct repression of hapR transcription in Vibrio cholerae. Microbiol Res 2025; 297:128155. [PMID: 40185028 DOI: 10.1016/j.micres.2025.128155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Revised: 03/10/2025] [Accepted: 03/25/2025] [Indexed: 04/07/2025]
Abstract
Vibrio cholerae, the causative agent of cholera, can efficiently adapt its metabolic processes, including biofilm formation, in response to varying respiratory conditions- such as aerobic, microaerobic, and anaerobic- through the ArcAB system. In this study, we elucidate the activation mechanism of V. cholerae ArcB and ArcA and identify ArcB residues H292, D577, and H722, along with ArcA residue D54 as key phosphorylation sites. Furthermore, we demonstrate that the ArcAB system plays a crucial role in regulating biofilm formation under both aerobic and anaerobic conditions. Our findings reveal that the positive regulation of biofilm formation by the ArcAB systems involves the high cell density (HCD) quorum sensing (QS) regulator HapR. Specifically, phosphorylated ArcA represses hapR transcription, thereby promoting biofilm formation under anaerobic condition. This study also highlights an epistatic relationship between ArcA and HapR in biofilm regulation. Overall, our results underscore the critical role of the ArcAB system in the biofilm formation of pathogenic V. cholerae under oxygen-limiting conditions.
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Affiliation(s)
- Jant Cres Caigoy
- Graduate School of Integrated Sciences for Life, Hiroshima University, Japan
| | - Hirofumi Nariya
- Graduate School of Human Life Sciences, Jumonji University, Japan
| | - Toshi Shimamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Japan
| | - Zhiqun Yan
- Graduate School of Biosphere Science, Hiroshima University, Japan
| | - Tadashi Shimamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Japan.
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25
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Li HY, Granger L, Raimi-Abraham BT, Shattock RJ, Makatsoris C, Forbes B. Pulmonary delivery of LNP-mRNAs aerosolised by vibrating mesh nebulizer: An emphasis on variations and in-depth analyses of physicochemical properties. Int J Pharm 2025; 680:125796. [PMID: 40446870 DOI: 10.1016/j.ijpharm.2025.125796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2025] [Revised: 05/19/2025] [Accepted: 05/27/2025] [Indexed: 06/02/2025]
Abstract
The delivery of lipid nanoparticle (LNP)-mRNAs to the lungs attracts fast increasing interests for vaccination, as the mucosal immunity in the airway can prevent the establishment of an infection rather than only reduce the level of infection associated with systemic immunity triggered via intramuscular injection. The vibrating mesh nebuliser was well utilized to atomize inhalation solutions/suspensions for pulmonary delivery hence employed in this study for aerosolising LNP-mRNAs. In comparison with pre-aerosolised LNP-mRNAs, the post-aerosolised vectors demonstrated a significant increase (t-test, unpaired, p < 0.05) in particle size (215-363 nm vs. 116-130 nm), polydispersity index (PDI: > 0.33 vs. < 0.27), zeta potential (ZP: 11-14 mV vs. 2.6-7.7 mV), and encapsulation efficiency (EE: ∼99 % w/w vs. ∼91 % w/w), indicating a structural alteration upon high-frequency mesh vibration (HFMV). The particle sizes of LNP-mRNAs were further enlarged upon inertial impaction, and the size increments were dependent on the velocities of airflow for impaction and the N/P ratios. The aerosolised mists were fine, with >54 % w/w deposited in lower respiratory tract and >28.5 % w/w further delivered to alveolar regions. Further, a model was created to elucidate the variations of physicochemical properties for LNP-mRNAs upon HFMV and inertial impaction, and it disclosed that the fluidity and shear-induced fusion of LNPs were the fundamental reasons to cause these unfavourable changes particularly the size enlargement. These insights reveal that the effective development of inhaled LNP-mRNAs will rely on shear-less devices, formulation optimizations, inhalable dry powders, and their potential combinations.
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Affiliation(s)
- Hao-Ying Li
- Institute of Pharmaceutical Sciences, King's College London, London SE1 9NH, United Kingdom.
| | - Luke Granger
- Department of Infectious Diseases, Section of Immunology of Infection, Imperial College London, London W2 1PG, United Kingdom
| | | | - Robin J Shattock
- Department of Infectious Diseases, Section of Immunology of Infection, Imperial College London, London W2 1PG, United Kingdom
| | - Charalampos Makatsoris
- Department of Engineering, Faculty of Natural/Mathematical Sciences, King's College London, London WC2R 2LS, United Kingdom
| | - Ben Forbes
- Institute of Pharmaceutical Sciences, King's College London, London SE1 9NH, United Kingdom.
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26
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Hirano T. Mitotic genome folding. J Cell Biol 2025; 224:e202504075. [PMID: 40492990 DOI: 10.1083/jcb.202504075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2025] [Revised: 05/30/2025] [Accepted: 06/02/2025] [Indexed: 06/12/2025] Open
Abstract
Mitotic genome folding, or mitotic chromosome assembly, is essential for the faithful segregation of genetic information into daughter cells. While this process was once thought to be highly complex, requiring a myriad of protein components, recent studies have begun to revise this conventional view. An emerging view is that the core reaction of mitotic genome folding is mediated by a dynamic interplay of a limited number of structural components, namely, condensins, topoisomerase II (topo II), and histones. Condensins and topo II are two distinct classes of ATPases that cooperate to actively form and manipulate DNA loops, both accumulating at the central axial regions of the resulting chromosomes. In contrast, nucleosomes and linker histones help to compact DNA loops by cooperating and competing with the action of these ATPases. In this review, I will focus on the recent advances in the field, with an emphasis on the mechanistic aspects of mitotic genome folding.
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27
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Babzada SA, Raja V, Bhat AH, Qadir SU, Radhakrishnan A, Kumar N, Alsahli AA, Ahmad P. Alleviating lanthanum stress in tomato plants using MnO nanoparticles and triacontanol: Impacts on growth, photosynthesis, and antioxidant defense. JOURNAL OF HAZARDOUS MATERIALS 2025; 491:137746. [PMID: 40122002 DOI: 10.1016/j.jhazmat.2025.137746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Revised: 02/23/2025] [Accepted: 02/23/2025] [Indexed: 03/25/2025]
Abstract
The present study evaluated the synthesis, characterization, and ameliorative potential of manganese oxide nanoparticles (MnO NPs) against lanthanum (La)-induced stress in tomato plants. Biosynthesized MnO NPs exhibited a characteristic UV-Vis absorption peak at 276 nm and a cubic crystalline structure with an average crystallite size of 13 nm, as determined by XRD. TEM images confirmed pseudo-spherical morphology and homogenous distribution. Under La stress, tomato plants showed a significant reduction in shoot length (54.90 %), root length (62.39 %), shoot dry weight (49.71 %), and root dry weight (37.17 %). Application of MnO NPs and triacontanol (TRIA) mitigated these effects, with combined treatments enhanced shoot and root lengths by 155.81 % and 216.66 %, respectively, and dry weights by 116.58 % (shoot) and 173.06 % (root). La stressed plants demonstrated decreased accumulation of La in roots and shoots by about 36.64 % and 32.21 %, respectively, upon synergistic application of MnO NPs and TRIA. La stress decreased photosynthetic pigments, including chlorophyll a (53.56 %), chlorophyll b (51.28 %), total chlorophyll (53.10 %), and carotenoids (26.36 %). Combined MnO NPs and TRIA treatment significantly increased these pigments by 110.23 %, 263.15 %, 142.27 %, and 266.66 %, respectively. Photosynthetic efficiency parameters, such as net photosynthetic rate, stomatal conductance, and transpiration rate, also improved by up to 74.44 %, 119.00 %, and 89.44 %, respectively, under combined treatments. Relative water content (RWC) decreased by 49.83 % under La stress but increased by 84.75 % following combined treatments. Osmolytes like proline and glycine betaine were elevated by 20.13 % and 38.47 %, respectively. Reactive oxygen species (ROS)-related markers, including H₂O₂, malondialdehyde, and electrolyte leakage, were significantly reduced by 58.14 %, 28.46 %, and 39.81 %, respectively, with MnO NPs and TRIA. Antioxidant enzyme activities were enhanced, with combined treatments elevating SOD (27.02 %), CAT (15.38 %), APX (90.37 %), and GR (90.38 %). Moreover, activities of DHAR and MDHAR, previously suppressed by La, increased by 91.64 % and 81.75 %, respectively. The findings highlight the synergistic role of MnO NPs and TRIA in alleviating La toxicity by enhancing growth, photosynthetic efficiency, antioxidant defense, and reducing ROS, offering a sustainable approach for crop improvement under metal stress conditions.
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Affiliation(s)
- Shahid Ahmad Babzada
- Department of Chemistry, Chandigarh University, Gharuan, Mohali, Punjab 140413, India
| | - Vaseem Raja
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413, India.
| | - Aashaq Hussain Bhat
- Department of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, India
| | - Sami Ullah Qadir
- Department of Environmental Sciences, Govt Degree College Pampore, Pulwama, Jammu and Kashmir 192121, India
| | - Arunkumar Radhakrishnan
- Department of Pharmacology, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu 603103, India
| | - Naveen Kumar
- Galgotias Multidisplinary Research and Development Cell (G-MRDC), Galgotias University,Greater Noida, Uttar Pradesh, 203201, India
| | - Abdulaziz Abdullah Alsahli
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Parvaiz Ahmad
- Department of Botany, GDC, Pulwama, Jammu and Kashmir 192301, India; Research and Development Cell, Lovely Professional University, Phagwara, Punjab, 144411, India.
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28
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Koyama T, Saeed U, Rewitz K, Halberg KV. The Integrative Physiology of Hormone Signaling: Insights from Insect Models. Physiology (Bethesda) 2025; 40:0. [PMID: 39887191 DOI: 10.1152/physiol.00030.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 11/18/2024] [Accepted: 01/24/2025] [Indexed: 02/01/2025] Open
Abstract
Hormones orchestrate virtually all physiological processes in animals and enable them to adjust internal responses to meet diverse physiological demands. Studies in both vertebrates and insects have uncovered many novel hormones and dissected the physiological mechanisms they regulate, demonstrating a remarkable conservation in endocrine signaling across the tree of life. In this review, we focus on recent advances in insect research, which have provided a more integrative view of the conserved interorgan communication networks that control physiology. These new insights have been driven by experimental advantages inherent to insects, which over the past decades have aligned with new technologies and sophisticated genetic tools, to transform insect genetic models into a powerful testbed for posing new questions and exploring longstanding issues in endocrine research. Here, we illustrate how insect studies have addressed classic questions in three main areas, hormonal control of growth and development, neuroendocrine regulation of ion and water balance, and hormonal regulation of behavior and metabolism, and how these discoveries have illuminated our fundamental understanding of endocrine signaling in animals. The application of integrative physiology in insect systems to questions in endocrinology and physiology is expanding and is poised to be a crucible of discovery, revealing fundamental mechanisms of hormonal regulation that underlie animal adaptations to their environments.
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Affiliation(s)
- Takashi Koyama
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Usama Saeed
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kim Rewitz
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth V Halberg
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Tan SL, Vera-Vives AM, Alboresi A, Morosinotto T. Light intensity activation of alternative electron transport mechanisms in the moss Physcomitrium patens. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2025; 224:109904. [PMID: 40288259 DOI: 10.1016/j.plaphy.2025.109904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 03/17/2025] [Accepted: 04/07/2025] [Indexed: 04/29/2025]
Abstract
Photosynthetic organisms exploit sunlight to drive an electron transport chain and obtain the chemical energy supporting their metabolism. In highly dynamic environmental conditions, excitation energy and electron transport need to be continuously modulated to prevent over-reduction and the consequent damage. An essential role in the regulation of electron transport is played by alternative electron transport mechanisms such as cyclic electron transport (CET) facilitated by PGRL1/PGR5 and NDH complex and pseudo-cyclic electron transport (PCET) mediated by the flavodiiron proteins (FLV) and the Mehler reaction. In this work mutant lines of the moss Physcomitrium patens depleted in PCET (flva KO) or CET (pgrl1/ndhm KO) were compared to wild-type plants for their ability to regulate photosynthetic electron transport in response to light fluctuations of different intensities. FLV activity enables a very fast increase in electron transport capacity but its impact is transient and becomes undetectable after 3 min from a light change. The FLV electron transport capacity is saturated at 100 μmol photons m-2 s-1 and does not increase even if exposed to stronger illumination. On the other hand, CET activation after an increase in illumination has a smaller contribution on electron transport capacity, but it provides a steady contribution for several minutes after a change in illumination intensity. Overall, these results demonstrate that light adapted plants CO2 fixation capacity needs approx. 3 min to adjust to different illumination intensities. In this interval CET and PCET enable adjusting temporary unbalances in electron transport, fully responding to 2-4 time increases in illumination. In case of larger increases, these mechanisms still contribute to protection from light damage by reducing the accumulation of electrons at PSI acceptor side. While the two mechanisms play an overlapping function, their activity shows distinctive kinetics and electron transport capacity thus they are complementary in ensuring optimal photoprotection.
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Affiliation(s)
- Shun-Ling Tan
- Department of Biology, University of Padova, Padova, Italy
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30
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Syed AM, Karius AK, Ma J, Wang PY, Hwang PM. Mitochondrial Dysfunction in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Physiology (Bethesda) 2025; 40:0. [PMID: 39960432 DOI: 10.1152/physiol.00056.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 12/27/2024] [Accepted: 02/11/2025] [Indexed: 04/26/2025] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating multisystem disorder of unclear etiology that affects many individuals worldwide. One of its hallmark symptoms is prolonged fatigue following exertion, a feature also observed in long COVID, suggesting an underlying dysfunction in energy production in both conditions. Here, mitochondrial dysfunction and its potential pathogenetic role in these disorders are reviewed.
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Affiliation(s)
- Abu Mohammad Syed
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States
| | - Alexander K Karius
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States
| | - Jin Ma
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States
| | - Ping-Yuan Wang
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States
| | - Paul M Hwang
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, United States
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31
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Beltrán-Rivera A, García-Arrarás JE. Cellular dedifferentiation. Revisiting Betty Hay's legacy. Dev Biol 2025; 523:1-8. [PMID: 40164323 DOI: 10.1016/j.ydbio.2025.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2024] [Revised: 03/25/2025] [Accepted: 03/28/2025] [Indexed: 04/02/2025]
Abstract
The concept of mature specialized cells and the stability of the differentiated state was fundamentally challenged by Elizabeth Hay's groundbreaking observations on amphibian limb regeneration, published in 1959. Building on previous work by C.S. Thornton, she discovered that muscle cells could dedifferentiate and transform into progenitor cells within the regeneration blastema reshaping our understanding of cell differentiation. This pivotal finding reshaped our understanding of cell differentiation, opening new avenues of research. Though controversial, her findings significantly advanced the fields of cell plasticity and regenerative biology.
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32
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Phillips R. Diet, Mitochondrial Dysfunction, Vascular Endothelial Damage, and the Microbiome: Drivers of Ocular Degenerative and Inflammatory Diseases. Ophthalmol Ther 2025; 14:1429-1452. [PMID: 40434533 DOI: 10.1007/s40123-025-01160-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Accepted: 04/24/2025] [Indexed: 05/29/2025] Open
Abstract
There is abundant evidence in medical literature that Western diet and lifestyle drive the cellular and metabolic processes which underlie chronic non-communicable diseases. However, non-pharmaceutical interventions, which focus on nutrition, the microbiome and lifestyle, to prevent non-communicable diseases are not part of mainstream treatment, for a variety of reasons. Lack of progress in stemming the rise in chronic non-communicable diseases can be attributed to the current 'downstream' medical paradigm which is focused on treating disease and symptoms, rather than preventing disease via an 'upstream' approach, which looks at cause and process. Metabolic abnormalities and obesity have previously been noted as correlated with common chronic ophthalmic conditions such as age related macular degeneration (AMD), glaucoma, ocular inflammation, diabetic retinopathy and retinal vascular occlusive disease. These are ocular manifestations of an underlying common cause. The aim of this paper, using an ophthalmic context, is to provide an overview of the cellular pathophysiological mechanisms that underlie chronic non-communicable diseases, including ophthalmic diseases, and to draw the links between diet and lifestyle, the microbiome and chronic non-communicable diseases.
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Affiliation(s)
- Russell Phillips
- Flinders Medical Centre, Adelaide, Australia.
- Queen Elizabeth Hospital, Adelaide, Australia.
- Eyemedics, Adelaide, Australia.
- Flinders University, Adelaide, Australia.
- University of Adelaide, Adelaide, Australia.
- Vista Day Surgery, Adelaide, Australia.
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33
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Chen Y, Xu R, Meng F. Biodegradable polylactic acid plastic can aid to achieve partial nitrification/denitrification for low carbon to nitrogen ratio wastewater treatment: Performance and microbial mechanism. BIORESOURCE TECHNOLOGY 2025; 427:132411. [PMID: 40118223 DOI: 10.1016/j.biortech.2025.132411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 03/17/2025] [Accepted: 03/17/2025] [Indexed: 03/23/2025]
Abstract
The partial nitrification/denitrification (PND) process is a green biotechnology for nitrogen removal in low carbon to nitrogen ratio wastewater, however, inhibiting nitrite-oxidizing bacteria (NOB) remains a challenge. This study uncovered that polylactic acid (PLA) can eliminate NOB and regulate the structure and function of nitrogen-transforming bacteria (NTB). An anoxic/aerobic membrane bioreactor with PLA achieved a total nitrogen removal efficiency of 64.8%, much higher than the 32.4% without PLA. Nitrite accumulation during nitrification stage reached 66.7% with PLA addition. Ammonia-oxidizing bacteria were transiently inhibited by PLA but recovered quickly. NOB were maintained at low levels due to the absence of genes for protein and DNA repair, while denitrifiers lacking NarGHI/NapAB genes were enriched. OLB8, with a relative abundance of 13.7%, played a central role in regulating NTB interaction and facilitating PND. In summary, this study provided a new strategy for improving nitrogen removal from wastewater through the reuse of PLA plastics.
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Affiliation(s)
- Yanxi Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, PR China
| | - Ronghua Xu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510275, PR China.
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Naeem M, Han R, Xu A, Shan X, Zhao L. Strigolactone (GR24) regulates fruit ripening in yft3 tomatoes by altering ABA biosynthesis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2025; 356:112484. [PMID: 40164312 DOI: 10.1016/j.plantsci.2025.112484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Revised: 03/13/2025] [Accepted: 03/26/2025] [Indexed: 04/02/2025]
Abstract
Color development in tomato fruits is a key indicator of ripening, and is driven by complex hormonal and molecular interactions. The present study investigated the effects of exogenous treatment with abscisic acid (ABA), GR24 (a synthetic strigolactone analog), and water (ddH2O as control) on tomato fruit ripening, ethylene emission, carotenoid biosynthesis, ABA metabolism, and chromoplast development in yft3 and wild-type (WT cv. M82) tomato fruits at 35, 47, and 54 days post-anthesis (dpa). Results showed that GR24 significantly accelerated ripening in yft3, transitioning from green to deep orange at 54 dpa, whereas ABA had a moderate effect. In cv. M82, both treatments enhanced color development, leading to a deep red phenotype. GR24 increased ethylene emission and upregulated the expression of ethylene related genes (ACO1, ACS2/4), with yft3 showing increased sensitivity than cv. M82. Carotenoid profiling revealed higher lycopene and β-carotene contents in yft3, with GR24 enhancing β-carotene and lutein, whereas ABA increased lycopene. GR24 and ABA strongly induced the expression of carotenoid-related genes (CRTISO, PSY1, and CYCB), particularly in yft3 at 54 dpa. Moreover, ABA-content and the expression of genes involved in ABA biosynthesis (NCED, AAO), catabolism (CYP707A), conjugation (GT), and activation (BG) were significantly altered by ABA and GR24 treatments. Furthermore, ultrastructural analysis revealed that GR24 promoted plastoglobule formation and chromoplast differentiation, with yft3 exhibiting a stronger response than cv. M82. These findings highlight that GR24 plays vital roles in regulating tomato fruit ripening, ethylene biosynthesis, carotenoids accumulation, as well as ABA-metabolism, with implications for improving fruit quality in tomatoes.
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Affiliation(s)
- Muhammad Naeem
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Rong Han
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Anran Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Xuemeng Shan
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Lingxia Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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Wang H, Wang Y, Zhong Y, Yu B, Liu D, Jia C, Wu J, Zeng G, Wang Q, Liu F, Sheng C, Huang L. Pasteurized Akkermansia muciniphila ameliorates preeclampsia via inhibiting mitochondrial dysfunction-mediated placental apoptosis in vivo and in vitro. Free Radic Biol Med 2025; 234:233-247. [PMID: 40294855 DOI: 10.1016/j.freeradbiomed.2025.04.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2025] [Revised: 04/15/2025] [Accepted: 04/25/2025] [Indexed: 04/30/2025]
Abstract
Preeclampsia (PE) is a severe metabolic disorder that occurs during pregnancy and is linked to dysbiosis of the gut microbiota, characterised by a decrease in Akkermansia muciniphila (AKK). Emerging evidence suggests that pasteurized Akkermansia muciniphila (pAKK) is a promising candidate for preventing or treating obesity-related metabolic disorders. However, the modulatory function and the underlying mechanisms of pAKK supplementation in PE remain to be fully elucidated. In this study, we examined the impact of pAKK oral administration on PE and its underlying mechanisms. Our findings demonstrate that pAKK significantly improved PE-like symptoms in mice induced by nitro-L-arginine methylester (L-NAME) in a dose-dependent manner. Of note, pAKK inhibited L-NAME-induced placental apoptosis, countered apoptosis-related biochemical alterations like the increase in the Bax/Bcl-2 ratio, and the activation of cleaved-Caspase-3, alongside mitigating L-NAME-induced placental mitochondrial dysfunction. Hypoxia-reoxygenation (H/R)-induced HTR8/SVneo cells have been established as an in vitro model to mimic the condition of PE. Interestingly, similar results were also obtained in vitro; mitochondrial dysfunction-mediated apoptosis induced by H/R in HTR-8/SVneo cells was prevented by pAKK. Importantly, the PI3K inhibitor (LY-294002) significantly negated the protective effects of pAKK on mitochondrial dysfunction and apoptosis. Furthermore, we observed that pAKK treatment improved the composition of gut microbiota communities in PE mice. Our findings indicate that pAKK improved PE-like symptoms both in vivo and in vitro by activating the PI3K/Akt signalling pathway, highlighting the potential for developing a probiotic therapeutic agent based on AKK for PE.
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Affiliation(s)
- Haizhen Wang
- Department of Obstetrics and Gynecology, the Fifth Affiliated Hospital of Southern Medical University, Guangzhou, 510900, Guangdong, China
| | - Yu Wang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yawen Zhong
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Bo Yu
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Di Liu
- Department of Neurology, Xuanwu Hospital Capital Medical University, National Center for Neurological Disorders, Beijing, 100053, China
| | - Chunhong Jia
- Department of Neonatology, Guangzhou Key Laboratory of Neonatal Intestinal Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
| | - Jiaying Wu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Guanfeng Zeng
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Qiqiong Wang
- Department of Neonatology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Fang Liu
- Department of Obstetrics and Gynecology, the Fifth Affiliated Hospital of Southern Medical University, Guangzhou, 510900, Guangdong, China.
| | - Chao Sheng
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| | - Liping Huang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
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Huang WL, Huang WT, Chen XF, Wu T, Tong LY, Xia TT, Wu BS, Lu F, Lai NW, Yang LT, Chen LS. Exogenous coumarin improves cell wall and plasma membrane stability and function by maintaining copper and calcium homeostasis in citrus roots under copper excess. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2025; 224:109949. [PMID: 40319587 DOI: 10.1016/j.plaphy.2025.109949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2025] [Accepted: 04/23/2025] [Indexed: 05/07/2025]
Abstract
Most citrus trees are planted in acidic soil with high availability of copper (Cu). Little is known about the mechanisms by which coumarin (COU) reduces Cu excess in plants. 'Xuegan' (Citrus sinensis) seedlings were treated with 0.5 (Cu0.5) or 400 (Cu excess or Cu400) CuCl2 and 0 (COU0) or 100 (COU100) μM COU for 24 weeks. COU100 alleviated Cu400-induced alterations in gene expression and metabolite profiles, cell wall (CW) materials (CWMs), CW components (CWCs), and Fourier transform infrared (FTIR) spectra of CWMs in roots; increase in Cu concentration in roots, root CWMs (RCWMs), root CWCs (RCWCs), Cu and Ca fractions in RCWMs, and Cu fraction in CW pectin; and decrease in Ca concentrations in roots, RCWMs, and RCWCs. In addition, COU100 mitigated Cu400-induced increase in electrolyte leakage and concentrations of total coumarins, total phenolics, total falvonoids, and nonstructural carbohydrates (NCs) and decrease in total free amino acid concentration in roots, as well as impairment in root system architecture (RSA) and root growth. Our results corroborated the hypothesis that the alleviation of root Cu excess by COU was caused by the combination of following several aspects: (a) reduced impairment to root growth and RSA; (b) upregulated ability to maintain CW and plasma membrane stability and function by maintaining Cu and calcium homeostasis; (c) elevated adaptability of primary metabolism to Cu excess; and (d) upregulated biosynthesis and catabolism (turnover) of secondary metabolites (SMs) and less upregulation of SMs. COU0-treated roots underwent some physiological and molecular adaptations to Cu excess.
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Affiliation(s)
- Wei-Lin Huang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Wei-Tao Huang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xu-Feng Chen
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Ti Wu
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Fujian Provincial Key Laboratory of Ecology-Toxicological Effects & Control for Emerging Contaminants/Key Laboratory of Ecological Environment and Information Atlas, College of Environmental and Biological Engineering, Putian University, Putian, 351100, China.
| | - Liang-Yuan Tong
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Tian-Tian Xia
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Bi-Sha Wu
- Fujian Provincial Key Laboratory of Ecology-Toxicological Effects & Control for Emerging Contaminants/Key Laboratory of Ecological Environment and Information Atlas, College of Environmental and Biological Engineering, Putian University, Putian, 351100, China.
| | - Fei Lu
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Ning-Wei Lai
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Lin-Tong Yang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Li-Song Chen
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Wu Z, Famous M, Stoikidou T, Bowden FES, Dominic G, Huws SA, Godoy-Santos F, Oyama LB. Unravelling AMR dynamics in the rumenofaecobiome: Insights, challenges and implications for One Health. Int J Antimicrob Agents 2025; 66:107494. [PMID: 40120959 DOI: 10.1016/j.ijantimicag.2025.107494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 03/01/2025] [Accepted: 03/13/2025] [Indexed: 03/25/2025]
Abstract
Antimicrobial resistance (AMR) is a critical global threat to human, animal and environmental health, exacerbated by horizontal gene transfer (HGT) via mobile genetic elements. This poses significant challenges that have a negative impact on the sustainability of the One Health approach, hindering its long-term viability and effectiveness in addressing the interconnectedness of global health. Recent studies on livestock animals, specifically ruminants, indicate that culturable ruminal bacteria harbour AMR genes with the potential for HGT. However, these studies have focused predominantly on using the faecobiome as a proxy to the rumen microbiome or using easily isolated and culturable bacteria, overlooking the unculturable population. These unculturable microbial groups could have a profound influence on the rumen resistome and AMR dynamics within livestock ecosystems, potentially holding critical insights for advanced understanding of AMR in One Health. In order to address this gap, this review of current research on the burden of AMR in livestock was undertaken, and it is proposed that combined study of the rumen microbiome and faecobiome, termed the 'rumenofaecobiome', should be performed to enhance understanding of the risks of AMR in ruminant livestock. This review discusses the complexities of the rumen microbiome and the risks of AMR transmission in this microbiome in a One Health context. AMR transmission dynamics and methodologies for assessing the risks of AMR in livestock are summarized, and future considerations for researching the impact of AMR in the rumen microbiome and the implications within the One Health framework are discussed.
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Affiliation(s)
- Ziming Wu
- School of Biological Science, Institute for Global Food Security, Queen's University Belfast, Belfast, UK.
| | - Mustasim Famous
- School of Biological Science, Institute for Global Food Security, Queen's University Belfast, Belfast, UK; Department of Animal Science, Khulna Agricultural University, Khulna, Bangladesh
| | - Theano Stoikidou
- School of Biological Science, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Freya E S Bowden
- School of Biological Science, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Gama Dominic
- School of Biological Science, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Sharon A Huws
- School of Biological Science, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Fernanda Godoy-Santos
- School of Biological Science, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Linda B Oyama
- School of Biological Science, Institute for Global Food Security, Queen's University Belfast, Belfast, UK.
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38
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Hylton-McComas HM, Cordes A, Floros KV, Faber AC, Drapkin BJ, Miles WO. Myc family proteins: Molecular drivers of tumorigenesis and resistance in neuroendocrine tumors. Biochim Biophys Acta Rev Cancer 2025; 1880:189332. [PMID: 40280500 DOI: 10.1016/j.bbcan.2025.189332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 04/18/2025] [Accepted: 04/21/2025] [Indexed: 04/29/2025]
Abstract
Neuroendocrine cancers are a diverse and poorly understood collection of malignancies derived from neuroendocrine cells throughout the body. These cancers uniquely exhibit properties of both the nervous and endocrine systems. Only a limited number of genetic driver mutations have been identified in neuroendocrine cancers, however the mechanisms of how these genetic aberrations alter tumor biology remain elusive. Recent studies have implicated the MYC family of transcription factors as important oncogenic factors in neuroendocrine tumors. We take a systematic approach to understand the roles of the MYC family (c-MYC, n-MYC, l-MYC) in the tumorigenesis of neuroendocrine cancers of the lung, GI tract, pancreas, kidney, prostate, pediatric neuroblastoma, and adrenal glands. Reflecting the complexity of neuroendocrine cancers, we highlight the roles of the MYC family in deregulating the cell cycle and transcriptional networks, invoking cellular plasticity, affecting proliferation capacity, aiding in chromatin remodeling, angiogenesis, metabolic changes, and resistance mechanisms. Depicting the diversity of neuroendocrine cancers, we suggest new approaches in understanding the underlying tumorigenic processes of neuroendocrine cancers from the perspective of MYC.
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Affiliation(s)
- Hannah M Hylton-McComas
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12(th) Avenue, Columbus, OH 43210, USA; The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12(th) Avenue, Columbus, OH 43210, USA
| | - Alyssa Cordes
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Konstantinos V Floros
- VCU Philips Institute, Virginia Commonwealth University School of Dentistry and Massey Comprehensive Cancer Center, Richmond, VA 23298, USA; Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Anthony C Faber
- VCU Philips Institute, Virginia Commonwealth University School of Dentistry and Massey Comprehensive Cancer Center, Richmond, VA 23298, USA; Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Benjamin J Drapkin
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wayne O Miles
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12(th) Avenue, Columbus, OH 43210, USA; The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12(th) Avenue, Columbus, OH 43210, USA.
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Li YP, Su LY, Huang T, Liu H, Tan SS, Deng YJ, Wang YH, Xiong AS. The telomere-to-telomere genome of Pucai () ( Typha angustifolia L.): a distinctive semiaquatic vegetable with lignin and chlorophyll as quality characteristics. HORTICULTURE RESEARCH 2025; 12:uhaf079. [PMID: 40343350 PMCID: PMC12058305 DOI: 10.1093/hr/uhaf079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Accepted: 03/03/2025] [Indexed: 05/11/2025]
Abstract
Pucai () (Typha angustifolia L.), within the Typha spp., is a distinctive semiaquatic vegetable. Lignin and chlorophyll are two crucial traits and quality indicators for Pucai. In this study, we assembled a 207.00-Mb high-quality gapless genome of Pucai, telomere-to-telomere (T2T) level with a contig N50 length of 13.73 Mb. The most abundant type of repetitive sequence, comprising 16.98% of the genome, is the long terminal repeat retrotransposons (LTR-RT). A total of 30 telomeres and 15 centromeric regions were predicted. Gene families related to lignin, chlorophyll biosynthesis, and disease resistance were greatly expanded, which played important roles in the adaptation of Pucai to wetlands. The slow evolution of Pucai was indicated by the σ whole-genome duplication (WGD)-associated Ks peaks from different Poales and the low activity of recent LTR-RT in Pucai. Meanwhile, we found a unique WGD event in Typhaceae. A statistical analysis and annotation of genomic variations were conducted in interspecies and intraspecies of Typha. Based on the T2T genome, we constructed lignin and chlorophyll metabolic pathways of Pucai. Subsequently, the candidate structural genes and transcription factors that regulate lignin and chlorophyll biosynthesis were identified. The T2T genomic resources will provide molecular information for lignin and chlorophyll accumulation and help to understand genome evolution in Pucai.
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Affiliation(s)
- Ya-Peng Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Li-Yao Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ting Huang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Hui Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Shan-Shan Tan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuan-Jie Deng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ya-Hui Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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Duan WL, Gu LH, Guo A, Wang XJ, Ding YY, Zhang P, Zhang BG, Li Q, Yang LX. Molecular mechanisms of programmed cell death and potential targeted pharmacotherapy in ischemic stroke (Review). Int J Mol Med 2025; 56:103. [PMID: 40341937 PMCID: PMC12081036 DOI: 10.3892/ijmm.2025.5544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Accepted: 04/15/2025] [Indexed: 05/11/2025] Open
Abstract
Stroke poses a threat to the elderly, being the second leading cause of death and the third leading cause of disability worldwide. Ischemic stroke (IS), resulting from arterial occlusion, accounts for ~85% of all strokes. The pathophysiological processes involved in IS are intricate and complex. Currently, tissue plasminogen activator (tPA) is the only Food and Drug Administration‑approved drug for the treatment of IS. However, due to its limited administration window and the risk of symptomatic hemorrhage, tPA is applicable to only ~10% of patients with stroke. Additionally, the reperfusion process associated with thrombolytic therapy can further exacerbate damage to brain tissue. Therefore, a thorough understanding of the molecular mechanisms underlying IS‑induced injury and the identification of potential protective agents is critical for effective IS treatment. Over the past few decades, advances have been made in exploring potential protective drugs for IS. The present review summarizes the specific mechanisms of various forms of programmed cell death (PCD) induced by IS and highlights potential protective drugs targeting different PCD pathways investigated over the last decade. The present review provides a theoretical foundation for basic research and insights for the development of pharmacotherapy for IS.
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Affiliation(s)
- Wan-Li Duan
- Medical Research Center, Shaoxing People's Hospital, Shaoxing, Zhejiang 312000, P.R. China
- Department of Diagnostic Pathology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang, Shandong 261041, P.R. China
| | - Li-Hui Gu
- Department of Diagnostic Pathology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang, Shandong 261041, P.R. China
| | - Ai Guo
- Department of Diagnostic Pathology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang, Shandong 261041, P.R. China
| | - Xue-Jie Wang
- Department of Diagnostic Pathology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang, Shandong 261041, P.R. China
- Department of Pathology, Shaoxing People's Hospital, Shaoxing, Zhejiang 312000, P.R. China
| | - Yi-Yue Ding
- Department of Diagnostic Pathology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang, Shandong 261041, P.R. China
| | - Peng Zhang
- Department of Cardiology, Shaoxing People's Hospital, Shaoxing, Zhejiang 312000, P.R. China
| | - Bao-Gang Zhang
- Department of Diagnostic Pathology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang, Shandong 261041, P.R. China
- Department of Pathology, Shaoxing People's Hospital, Shaoxing, Zhejiang 312000, P.R. China
| | - Qin Li
- Rehabilitation Medicine and Health College, Hunan University of Medicine, Huaihua, Hunan 418000, P.R. China
| | - Li-Xia Yang
- Medical Research Center, Shaoxing People's Hospital, Shaoxing, Zhejiang 312000, P.R. China
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Van Etten JL, Agarkova IV, Dunigan DD, Shao Q, Fang Q. Emerging structure of chlorovirus PBCV-1. Virology 2025; 608:110552. [PMID: 40286469 DOI: 10.1016/j.virol.2025.110552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 04/16/2025] [Accepted: 04/17/2025] [Indexed: 04/29/2025]
Abstract
The large plaque-forming chloroviruses infect isolates of eukaryotic chlorella-like green algae. Initial cryo-electron microscopy (cryo-EM) studies revealed that PBCV-1 was icosahedral, with a multilaminate shell surrounding an electron-dense core, and that PBCV-1 particles measured about 1900 Å in diameter with a triangulation number of 169d. However, as described in this review cryo-EM procedures have improved and PBCV-1 is more complex than originally described. A five-fold symmetry reconstruction of cryo-EM images at 8.5 Å revealed that the virus contains a unique vertex with a spike-structure and an internal single lipid bi-layered membrane. Improvement to 3.5 Å resolution revealed that the capsid contains 30 virus-encoded proteins and that it contains six different types of capsomers. The outer surface of three of the six types of capsomers are attached to fiber structures.
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Affiliation(s)
- James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA, 68583-0900.
| | - Irina V Agarkova
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA, 68583-0900
| | - David D Dunigan
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA, 68583-0900
| | - Qianqian Shao
- School of Public Health (Shenzhen) Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Qianglin Fang
- School of Public Health (Shenzhen) Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
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Xiao J, Liu W, Wu B, Zhang Y, Li S, Li E. Root hair: An important guest-meeting avenue for rhizobia in legume-Rhizobium symbiosis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2025; 356:112518. [PMID: 40274194 DOI: 10.1016/j.plantsci.2025.112518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Revised: 04/14/2025] [Accepted: 04/18/2025] [Indexed: 04/26/2025]
Abstract
Root hairs anchor the plant in the soil, facilitating nutrient assimilation, water absorption, and interaction of plants with their environment. In legumes, they play a key role in the early infection of rhizobia. This review aimed to summarize the recent progress about the nodulation factor receptors on the root hair surface. It also discussed the importance of downstream signaling pathways of nodulation factor receptors and highlighted Rho of plants signaling pathway that controls infection thread polar growth and nodulation.
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Affiliation(s)
- Jingwen Xiao
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Wenxu Liu
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Bicong Wu
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Yuling Zhang
- School of Foreign Languages, Qingdao Agricultural University, Qingdao 266109, China
| | - Sha Li
- QAU-RAU Joint Institute for Advanced Agricultural Technology Institute, Qingdao Agricultural University, Qingdao 266109, China
| | - En Li
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
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Bogart AH, Brooks ER. Canonical Wnt pathway modulation is required to correctly execute multiple independent cellular dynamic programs during cranial neural tube closure. Dev Biol 2025; 523:115-131. [PMID: 40280384 DOI: 10.1016/j.ydbio.2025.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 04/21/2025] [Accepted: 04/22/2025] [Indexed: 04/29/2025]
Abstract
Defects in cranial neural tube closure are among the most common and deleterious human structural birth defects. Correct cranial closure requires the coordination of multiple cell dynamic programs including cell proliferation and cell shape change. Mutations that impact Wnt signaling, including loss of the pathway co-receptor LRP6, lead to defects in cranial neural tube closure, but the cellular dynamics under control of the Wnt pathway during this critical morphogenetic process remain unclear. Here, we use mice mutant for LRP6 to examine the consequences of conditional and global reduction in Wnt signaling and mutants with conditional inactivation of APC to examine the consequences of pathway hyperactivation. Strikingly, we find that regulated Wnt signaling is required for two independent events during cranial neural tube closure. First, global reduction of Wnt leads to a surprising hyperplasia of the cranial neural folds driven by excessive cell proliferation at early pre-elevation stages, with the increased tissue volume creating a mechanical blockade to efficient closure despite normal apical constriction and cell polarization at later stages. Conversely, conditional hyperactivation of the pathway at later elevation stages prevents correct actin organization, blocking apical constriction and neural fold elevation without impacting tissue scaling. Together these data reveal that Wnt signaling levels must be modulated to restrict proliferation at early stages and promote apical constriction at later elevation stages to drive efficient closure of the cranial neural tube.
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Affiliation(s)
- Amber Huffine Bogart
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, United States
| | - Eric R Brooks
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, United States.
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Benhassoun R, Morel AP, Jacquot V, Puisieux A, Ouzounova M. The epipliancy journey: Tumor initiation at the mercy of identity crisis and epigenetic drift. Biochim Biophys Acta Rev Cancer 2025; 1880:189307. [PMID: 40174706 DOI: 10.1016/j.bbcan.2025.189307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 03/05/2025] [Accepted: 03/27/2025] [Indexed: 04/04/2025]
Abstract
Cellular pliancy refers to the unique disposition of different stages of cellular differentiation to transform when exposed to specific oncogenic insults. This concept highlights a strong interconnection between cellular identity and tumorigenesis, and implies overcoming of epigenetic barriers defining cellular states. Emerging evidence suggests that the cell-type-specific response to intrinsic and extrinsic stresses is modulated by accessibility to certain areas of the genome. Understanding the interplay between epigenetic mechanisms, cellular differentiation, and oncogenic insults is crucial for deciphering the complex nature of tumorigenesis and developing targeted therapies. Hence, cellular pliancy relies on a dynamic cooperation between the cellular identity and the cellular context through epigenetic control, including the reactivation of cellular mechanisms, such as epithelial-to-mesenchymal transition (EMT). Such mechanisms and pathways confer plasticity to the cell allowing it to adapt to a hostile environment in a context of tumor initiation, thus changing its cellular identity. Indeed, growing evidence suggests that cancer is a disease of cell identity crisis, whereby differentiated cells lose their defined identity and gain progenitor characteristics. The loss of cell fate commitment is a central feature of tumorigenesis and appears to be a prerequisite for neoplastic transformation. In this context, EMT-inducing transcription factors (EMT-TFs) cooperate with mitogenic oncoproteins to foster malignant transformation. The aberrant activation of EMT-TFs plays an active role in tumor initiation by alleviating key oncosuppressive mechanisms and by endowing cancer cells with stem cell-like properties, including the ability to self-renew, thus changing the course of tumorigenesis. This highly dynamic phenotypic change occurs concomitantly to major epigenome reorganization, a key component of cell differentiation and cancer cell plasticity regulation. The concept of pliancy was initially proposed to address a fundamental question in cancer biology: why are some cells more likely to become cancerous in response to specific oncogenic events at particular developmental stages? We propose the concept of epipliancy, whereby a difference in epigenetic configuration leads to malignant transformation following an oncogenic insult. Here, we present recent studies furthering our understanding of how the epigenetic landscape may impact the modulation of cellular pliancy during early stages of cancer initiation.
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Affiliation(s)
- Rahma Benhassoun
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, France; LabEx DEVweCAN, Université de Lyon, France
| | - Anne-Pierre Morel
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, France; LabEx DEVweCAN, Université de Lyon, France
| | - Victoria Jacquot
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, France
| | - Alain Puisieux
- Equipe labellisée Ligue contre le cancer, U1339 Inserm - UMR3666 CNRS, Paris, France; Institut Curie, PSL Research University, Paris, France
| | - Maria Ouzounova
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, France; LabEx DEVweCAN, Université de Lyon, France.
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Liu R, Wang G, Qian Y, Jiang Z, Wang W, Cai M, Zhang S, Wang G, Wang C, Zou T, Cao H, Zhang D, Wang X, Deng S, Li T, Gu J. Hexosamine biosynthesis dysfunction-induced LIFR N-glycosylation deficiency exacerbates steatotic liver ischemia/reperfusion injury. Metabolism 2025; 168:156258. [PMID: 40185397 DOI: 10.1016/j.metabol.2025.156258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2025] [Revised: 03/25/2025] [Accepted: 04/01/2025] [Indexed: 04/07/2025]
Abstract
BACKGROUND More and more steatotic livers undergo resection or transplantation but they exhibit higher susceptibility to ischemia-reperfusion injury (IRI), which results in increased perioperative complication morbidity and mortality. IRI is driven by various cytokines and receptors, both of which are extensively modified by N-glycosylation. We aim to elucidate susceptibility of steatotic livers to IRI from the perspective of N-glycosylation. METHODS Differentially expressed genes and glycoproteins were identified with RNA-seq and N-glycoproteomics. Myeloid LIF or hepatocyte LIFR knockout mice were developed to examine the function of LIF and LIFR. Modalities including phosphoproteomics, ChIP-seq, single cell RNA-seq, metabolomics and immunoblotting were utilized to investigate underlying mechanisms. RESULTS LIF transcription in myeloid cells and LIFR N-glycosylation in hepatocytes were substantially induced by IRI of normal livers. LIF and LIFR protected normal livers from IRI through activating STAT3 and promoting downstream TNFAIP3 expression, which was facilitated by LIFR N-glycosylation. Mechanistically, N-glycosylation at N238 stabilized LIFR protein by disrupting TRIM28-mediated K48 ubiquitination at LIFR K254. Furthermore, N-glycosylation at N358/N658/N675 of LIFR facilitated LIF/LIFR/gp130 complex formation and subsequent signal transduction. However, in steatotic livers, myeloid cell LIF transcription was partially inhibited due to hepatic microenvironment L-arginine insufficiency, while hepatocyte LIFR N-glycosylation was defective due to intracellular UDP-GlcNAc exhaustion. Importantly, combined L-arginine and GlcNAc treatment reversed LIF expression and LIFR N-glycosylation insufficiency, which represents potential therapeutic strategy to protect steatotic livers. CONCLUSIONS LIF expression and LIFR N-glycosylation insufficiency aggravates steatotic liver IRI, which can be reversed by combined L-arginine and GlcNAc treatment.
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Affiliation(s)
- Ran Liu
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Gengqiao Wang
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Yongbing Qian
- Department of Liver Surgery, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhengting Jiang
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Weimin Wang
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Mao Cai
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Shuhua Zhang
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Guoliang Wang
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Chuanzheng Wang
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Tianhao Zou
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Huan Cao
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Di Zhang
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Xueling Wang
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Shenghe Deng
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Tongxi Li
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Jinyang Gu
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China; Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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Wei YH, Lin F. Barcodes based on nucleic acid sequences: Applications and challenges (Review). Mol Med Rep 2025; 32:187. [PMID: 40314098 PMCID: PMC12076290 DOI: 10.3892/mmr.2025.13552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Accepted: 03/04/2025] [Indexed: 05/03/2025] Open
Abstract
Cells are the fundamental structural and functional units of living organisms and the study of these entities has remained a central focus throughout the history of biological sciences. Traditional cell research techniques, including fluorescent protein tagging and microscopy, have provided preliminary insights into the lineage history and clonal relationships between progenitor and descendant cells. However, these techniques exhibit inherent limitations in tracking the full developmental trajectory of cells and elucidating their heterogeneity, including sensitivity, stability and barcode drift. In developmental biology, nucleic acid barcode technology has introduced an innovative approach to cell lineage tracing. By assigning unique barcodes to individual cells, researchers can accurately identify and trace the origin and differentiation pathways of cells at various developmental stages, thereby illuminating the dynamic processes underlying tissue development and organogenesis. In cancer research, nucleic acid barcoding has played a pivotal role in analyzing the clonal architecture of tumor cells, exploring their heterogeneity and resistance mechanisms and enhancing our understanding of cancer evolution and inter‑clonal interactions. Furthermore, nucleic acid barcodes play a crucial role in stem cell research, enabling the tracking of stem cells from diverse origins and their derived progeny. This has offered novel perspectives on the mechanisms of stem cell self‑renewal and differentiation. The present review presented a comprehensive examination of the principles, applications and challenges associated with nucleic acid barcode technology.
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Affiliation(s)
- Ying Hong Wei
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Faquan Lin
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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Khan A, Anicet G, Asdullah HU, Hassan MA, Song Y. RNA modification: A contemporary review of pseudouridine (Ψ) and its role in functional plant biology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2025; 356:112522. [PMID: 40287098 DOI: 10.1016/j.plantsci.2025.112522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Revised: 03/14/2025] [Accepted: 04/20/2025] [Indexed: 04/29/2025]
Abstract
Pseudouridine (Ψ) is a modified nucleoside present in diverse RNA species, including mRNA (messenger RNA), snRNA (small nuclear RNA), rRNA (ribosomal RNA) and tRNA (transfer RNA). In plants, Ψ serves a critical function in RNA modification, supporting the stability, structural integrity, and functionality of RNA molecules. This review provides the various roles that Ψ fulfils in the modification of plant RNA biology, encompassing effects on biosynthesis pathways, regulatory mechanisms, stability, and translation efficiency. Additionally, we discuss recent advancements in the dynamic regulation of Ψ deposition in response to environmental stimuli and stressors. Elucidating Ψ's roles contributes to the comprehension of plant biology and may facilitate developments in biotechnology and crop improvement.
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Affiliation(s)
- Ahsan Khan
- School of Agronomy, Anhui Agricultural University, Hefei 230036, Anhui Province, China.
| | - Gatera Anicet
- School of Agronomy, Anhui Agricultural University, Hefei 230036, Anhui Province, China.
| | - Hafiz Umair Asdullah
- School of Agronomy, Anhui Agricultural University, Hefei 230036, Anhui Province, China.
| | - Muhammad Ahmad Hassan
- College of Resource and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Youhong Song
- School of Agronomy, Anhui Agricultural University, Hefei 230036, Anhui Province, China.
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Haran R, Sathyaseelan C, Sumathi E, Sathiya Priya S, Gayathri M, Prathiksha R, Shandeep G, Jayakanthan M. Unveiling the molecular basis of hygienic behavior in Apis cerana indica through antennal proteomics. Biochimie 2025; 234:110-119. [PMID: 40339734 DOI: 10.1016/j.biochi.2025.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 03/17/2025] [Accepted: 05/05/2025] [Indexed: 05/10/2025]
Abstract
Hygienic behavior in honey bees, particularly Apis cerana indica, is essential for the health of the colony as it helps reduce the impact of diseases and parasites. Despite its importance, the underlying molecular mechanisms remain inadequately characterized. Using a label-free quantitative proteomics method, this study investigates the antennal proteome associated with hygienic behavior. We employed Principal Component Analysis, Partial Least Squares Discriminant Analysis, and RT-qPCR to identify significant proteins that are involved in this behavior. Our analysis identified 408 proteins in colonies demonstrating high hygienic behavior and 419 proteins in those with low hygienic behavior, with 219 proteins showing significant differences in abundance. Notably, several odorant-binding proteins were upregulated in high-hygiene colonies. Furthermore, pathway enrichment analysis revealed that RNA transport and various signaling pathways are involved in this behavioral trait. The protein-protein interaction analysis illustrated substantial clustering among the odorant-binding proteins, underscoring their critical role in the mechanisms underlying hygienic behavior. This research enhances our understanding of the molecular basis of hygienic behavior in Apis cerana indica, positioning odorant-binding proteins as potential biomarkers for further studies that aim at improving colony health and resilience against pests and diseases.
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Affiliation(s)
- Ramkumar Haran
- Department of Agricultural Entomology, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India.
| | - Chakkarai Sathyaseelan
- Department of Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
| | - Ettiappan Sumathi
- Department of Agricultural Entomology, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India.
| | - Sundaravadivel Sathiya Priya
- Department of Agricultural Entomology, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
| | - Muthusamy Gayathri
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
| | - Ravichandran Prathiksha
- Department of Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
| | - Ganeshan Shandeep
- Department of Nematology, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
| | - Mannu Jayakanthan
- Department of Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore, 641 003, Tamil Nadu, India
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49
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Parimita S, Das A, Samanta S. Vestigial-like family member 1 (VGLL1): An emerging candidate in tumor progression. Biochem Biophys Res Commun 2025; 766:151889. [PMID: 40300335 DOI: 10.1016/j.bbrc.2025.151889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2025] [Revised: 04/19/2025] [Accepted: 04/23/2025] [Indexed: 05/01/2025]
Abstract
Vestigial-like family member 1 (VGLL1), a product of an X-linked gene (VGLL1), belongs to a family of transcriptional co-activators including VGLL2, VGLL3 and VGLL4. These proteins are called vestigial-like because of the structural and functional similarities with the Drosophila ortholog vestigial (vg). VGLL1 is usually expressed in human placenta, and has also been detected in many aggressive cancers. For this reason, it is called an onco-placental protein. It can bind and activate the TEA-domain containing transcription factors TEAD1-4, and the interaction is mediated through a conserved 'valine-x-x-histidine-phenylalanine' domain (VxxHF, x denotes any amino acid) present in VGLL1 protein. Prior studies indicate a pro-tumorigenic role for this protein in several cancers including carcinoma of the breast. This review aims at summarizing our present knowledge about the functions of VGLL1, and the mechanisms that regulate its expression in cancer.
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Affiliation(s)
- Shubhashree Parimita
- Department of Applied Biology, Council of Scientific & Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Uppal Road, Tarnaka, Hyderabad, TS, 500007, India; Academy of Scientific and Innovative Research, Ghaziabad, 201002, India
| | - Amitava Das
- Department of Applied Biology, Council of Scientific & Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Uppal Road, Tarnaka, Hyderabad, TS, 500007, India; Academy of Scientific and Innovative Research, Ghaziabad, 201002, India
| | - Sanjoy Samanta
- Department of Applied Biology, Council of Scientific & Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Uppal Road, Tarnaka, Hyderabad, TS, 500007, India; Academy of Scientific and Innovative Research, Ghaziabad, 201002, India.
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50
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Huang X, Li F, Liu L, Li Y, Zhang M, Ma G, Gao Y, Shan B, Liang X, Yuan J, Pan H. PARP12-mediated mono-ADP-ribosylation as a checkpoint for necroptosis and apoptosis. Proc Natl Acad Sci U S A 2025; 122:e2426660122. [PMID: 40489618 DOI: 10.1073/pnas.2426660122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Accepted: 04/29/2025] [Indexed: 06/11/2025] Open
Abstract
Necroptosis and apoptosis are two alternatively regulated cell death pathways. Activation of RIPK1 upon engagement of TNFR1 by TNFα may promote necroptosis by interacting with RIPK3 or apoptosis by activating caspases. RIPK1 is extensively regulated by a variety of dynamic posttranslational modifications which control its kinase activity and formation of downstream complexes to mediate necroptosis and apoptosis. Here, we investigate the functional significance and mechanism by which PARP12, a mono-ADP-ribosyltransferase, interacts with RIPK1 and RIPK3 in cells stimulated by IFNγ and TNFα. We show that PARP12 catalyzes the mono-ADP-ribosylation (MARylation) of RIPK1 in both the intermediate domain and the kinase domain, as well as the MARylation of RIPK3. PARP12 deficiency reduces necroptosis by inhibiting the activation of RIPK1 kinase and its interaction with RIPK3, as well as sensitizes to apoptosis by promoting the binding of RIPK1 with caspase-8. Thus, upon induction by IFNs, PARP12 may function as a cellular checkpoint that controls RIPK1 to promote necroptosis and inhibit apoptosis. Importantly, while PARP12 is a known interferon-stimulated gene (ISG), PARP12 deficiency promotes the expression of a subset of ISGs and confers protection against influenza A virus-induced mortality in mice. Our study demonstrates that PARP12 is an important modulator of cellular antiviral response.
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Affiliation(s)
- Xin Huang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Key Laboratory of Aging Studies, Shanghai 201210, China
| | - Fangxia Li
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lin Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Key Laboratory of Aging Studies, Shanghai 201210, China
| | - Yanxia Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mengmeng Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Guoming Ma
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ying Gao
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bing Shan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
- Shanghai Key Laboratory of Aging Studies, Shanghai 201210, China
| | - Xiaozhen Liang
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junying Yuan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Key Laboratory of Aging Studies, Shanghai 201210, China
| | - Heling Pan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
- Shanghai Key Laboratory of Aging Studies, Shanghai 201210, China
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