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Jia L, Zhu S, Zhu M, Nie R, Huang L, Xu S, Luo Y, Su H, Huang S, Tan Q. Celastrol inhibits angiogenesis and the biological processes of MDA-MB-231 cells via the DEGS1/S1P signaling pathway. Biol Chem 2024; 405:267-281. [PMID: 38081222 DOI: 10.1515/hsz-2023-0324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/25/2023] [Indexed: 04/02/2024]
Abstract
Celastrol (Cel) shows potent antitumor activity in various experimental models. This study examined the relationship between Cel's antivascular and antitumor effects and sphingolipids. CCK-8 assay, transwell assay, Matrigel, PCR-array/RT-PCR/western blotting/immunohistochemistry assay, ELISA and HE staining were used to detect cell proliferation, migration and invasion, adhesion and angiogenesis, mRNA and protein expression, S1P production and tumor morphology. The results showed that Cel could inhibit proliferation, migration or invasion, adhesion and angiogenesis of human umbilical vein endothelial cells (HUVECs) and MDA-MB-231 cells by downregulating the expression of degenerative spermatocyte homolog 1 (DEGS1). Transfection experiments showed that downregulation of DEGS1 inhibited the above processes and sphingosine-1-phosphate (S1P) production of HUVECs and MDA-MB-231 cells, while upregulation of DEGS1 had the opposite effects. Coculture experiments showed that HUVECs could promote proliferation, migration and invasion of MDA-MB-231 cells through S1P/sphingosine-1-phosphate receptor (S1PR) signaling pathway, while Cel inhibited these processes in MDA-MB-231 cells induced by HUVECs. Animal experiments showed that Cel could inhibit tumor growth in nude mice. Western blotting, immunohistochemistry and ELISA assay showed that Cel downregulated the expression of DEGS1, CD146, S1PR1-3 and S1P production. These data confirm that DEGS1/S1P signaling pathway may be related to the antivascular and antitumor effects of cel.
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Affiliation(s)
- Lulu Jia
- Clinical Pharmacy & Pharmacology Research Institute, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
| | - Shengnan Zhu
- Clinical Pharmacy & Pharmacology Research Institute, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
| | - Mingfei Zhu
- Clinical Pharmacy & Pharmacology Research Institute, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
| | - Rongrong Nie
- Rehabilitation Department, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
| | - Lingyue Huang
- Clinical Pharmacy & Pharmacology Research Institute, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
| | - Siyuan Xu
- Clinical Pharmacy & Pharmacology Research Institute, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
| | - Yuqin Luo
- Clinical Pharmacy & Pharmacology Research Institute, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
| | - Huazhen Su
- Clinical Pharmacy & Pharmacology Research Institute, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
| | - Shaoyuan Huang
- Clinical Pharmacy & Pharmacology Research Institute, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
| | - Qinyou Tan
- Clinical Pharmacy & Pharmacology Research Institute, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- Guangxi Health Commission Key Laboratory of Basic Research in Sphingolipid Metabolism Related Diseases, Affiliated Hospital of Guilin Medical University, 541001 Guilin, Guangxi Province, China
- China-USA Lipids in Health and Disease Research Center, Guilin Medical University, 541001 Guilin, Guangxi Province, China
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Zhu G, Zhang H, Xia M, Liu Y, Li M. EH domain-containing protein 2 (EHD2): Overview, biological function, and therapeutic potential. Cell Biochem Funct 2024; 42:e4016. [PMID: 38613224 DOI: 10.1002/cbf.4016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
EH domain-containing protein 2 (EHD2) is a member of the EHD protein family and is mainly located in the plasma membrane, but can also be found in the cytoplasm and endosomes. EHD2 is also a nuclear-cytoplasmic shuttle protein. After entering the cell nuclear, EHD2 acts as a corepressor of transcription to inhibit gene transcription. EHD2 regulates a series of biological processes. As a key regulator of endocytic transport, EHD2 is involved in the formation and maintenance of endosomal tubules and vesicles, which are critical for the intracellular transport of proteins and other substances. The N-terminal of EHD2 is attached to the cell membrane, while its C-terminal binds to the actin-binding protein. After binding, EHD2 connects with the actin cytoskeleton, forming the curvature of the membrane and promoting cell endocytosis. EHD2 is also associated with membrane protein trafficking and receptor signaling, as well as in glucose metabolism and lipid metabolism. In this review, we highlight the recent advances in the function of EHD2 in various cellular processes and its potential implications in human diseases such as cancer and metabolic disease. We also discussed the prospects for the future of EHD2. EHD2 has a broad prospect as a therapeutic target for a variety of diseases. Further research is needed to explore its mechanism, which could pave the way for the development of targeted treatments.
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Affiliation(s)
- Guoqiang Zhu
- Department of Urology, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Hu Zhang
- Department of Urology, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Min Xia
- Hengyang Medical School, Institute of Clinical Medicine, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
- Hengyang Medical School, Cancer Research Institute, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Yiqi Liu
- Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Mingyong Li
- Department of Urology, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
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Zhang C, Chen L, Hou S. The emerging roles of clathrin-mediated endocytosis in plant development and stress responses. J Plant Physiol 2024; 295:154189. [PMID: 38432037 DOI: 10.1016/j.jplph.2024.154189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/22/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
Clathrin-mediated endocytosis (CME) is a highly conserved pathway that plays a crucial role in the endocytosis of plasma membrane proteins in eukaryotic cells. The pathway is initiated when the adaptor protein complex 2 (AP2) and TPLATE complex (TPC) work together to recognize cargo proteins and recruit clathrin. This review provides a concise overview of the functions of each subunit of AP2 and TPC, and highlights the involvement of CME in various biological processes, such as pollen development, root development, nutrient transport, extracellular signal transduction, auxin polar transport, hyperosmotic stress, salinity stress, high ammonium stress, and disease resistance. Additionally, the review explores the regulation of CME by phytohormones, clathrin-mediated exocytosis (CMX), and AP2M phosphorylation. It also suggests potential future research directions for CME.
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Affiliation(s)
- Chi Zhang
- Key Laboratory of Gene Editing for Breeding, Gansu Province, Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Liang Chen
- Key Laboratory of Gene Editing for Breeding, Gansu Province, Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Suiwen Hou
- Key Laboratory of Gene Editing for Breeding, Gansu Province, Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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Hashimoto U, Fujitani N, Uehara Y, Okamoto H, Saitou A, Ito F, Ariki S, Shiratsuchi A, Hasegawa Y, Takahashi M. N-glycan on N262 of FGFR3 regulates the intracellular localization and phosphorylation of the receptor. Biochim Biophys Acta Gen Subj 2024; 1868:130565. [PMID: 38244702 DOI: 10.1016/j.bbagen.2024.130565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/12/2024] [Accepted: 01/14/2024] [Indexed: 01/22/2024]
Abstract
N-glycosylation and proper processing of N-glycans are required for the function of membrane proteins including cell surface receptors. Fibroblast growth factor receptor (FGFR) is involved in a wide variety of biological processes including embryonic development, osteogenesis, angiogenesis, and cell proliferation. Human FGFR3 contains six potential N-glycosylation sites, however, the roles of glycosylation have not been elucidated. The site-specific profiles of N-glycans of the FGFR3 extracellular domain expressed and secreted by CHO-K1 cells were examined, and glycan occupancies and structures of four sites were determined. The results indicated that most sites were fully occupied by glycans, and the dominant populations were the complex type. By examining single N-glycan deletion mutants of FGFR3, it was found that N262Q mutation significantly increased the population with oligomannose-type N-glycans, which was localized in the endoplasmic reticulum. Protein stability assay suggested that fraction with oligomannose-type N-glycans in the N262Q mutant is more stable than those in the wild type and other mutants. Furthermore, it was found that ligand-independent phosphorylation was significantly upregulated in N262Q mutants with complex type N-glycans. The findings suggest that N-glycans on N262 of FGFR3 affect the intracellular localization and phosphorylation status of the receptor.
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Affiliation(s)
- Ukichiro Hashimoto
- Department of Biochemistry, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Naoki Fujitani
- Department of Biochemistry, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yasuaki Uehara
- Department of Biochemistry, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiromi Okamoto
- Department of Biochemistry, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Atsushi Saitou
- Department of Biochemistry, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Fumie Ito
- Department of Biochemistry, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shigeru Ariki
- Department of Biochemistry, Sapporo Medical University School of Medicine, Sapporo, Japan; Department of Chemistry, Center for Medical Education, Sapporo Medical University, Japan
| | - Akiko Shiratsuchi
- Department of Chemistry, Center for Medical Education, Sapporo Medical University, Japan
| | - Yoshihiro Hasegawa
- Department of Biochemistry, Sapporo Medical University School of Medicine, Sapporo, Japan.
| | - Motoko Takahashi
- Department of Biochemistry, Sapporo Medical University School of Medicine, Sapporo, Japan.
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Kaizuka T, Suzuki T, Kishi N, Tamada K, Kilimann MW, Ueyama T, Watanabe M, Shimogori T, Okano H, Dohmae N, Takumi T. Remodeling of the postsynaptic proteome in male mice and marmosets during synapse development. Nat Commun 2024; 15:2496. [PMID: 38548776 PMCID: PMC10979008 DOI: 10.1038/s41467-024-46529-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 02/29/2024] [Indexed: 04/01/2024] Open
Abstract
Postsynaptic proteins play crucial roles in synaptic function and plasticity. During brain development, alterations in synaptic number, shape, and stability occur, known as synapse maturation. However, the postsynaptic protein composition changes during development are not fully understood. Here, we show the trajectory of the postsynaptic proteome in developing male mice and common marmosets. Proteomic analysis of mice at 2, 3, 6, and 12 weeks of age shows that proteins involved in synaptogenesis are differentially expressed during this period. Analysis of published transcriptome datasets shows that the changes in postsynaptic protein composition in the mouse brain after 2 weeks of age correlate with gene expression changes. Proteomic analysis of marmosets at 0, 2, 3, 6, and 24 months of age show that the changes in the marmoset brain can be categorized into two parts: the first 2 months and after that. The changes observed in the first 2 months are similar to those in the mouse brain between 2 and 12 weeks of age. The changes observed in marmoset after 2 months old include differential expression of synaptogenesis-related molecules, which hardly overlap with that in mice. Our results provide a comprehensive proteomic resource that underlies developmental synapse maturation in rodents and primates.
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Affiliation(s)
- Takeshi Kaizuka
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
- Department Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, 650-0117, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Noriyuki Kishi
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
| | - Kota Tamada
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
- Department Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, 650-0117, Japan
| | - Manfred W Kilimann
- Max Planck Institute for Experimental Medicine, Göttingen, 37075, Germany
| | - Takehiko Ueyama
- Laboratory of Molecular Pharmacology, Biosignal Research Center, Kobe University, Nada, Kobe, 657-8501, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Kita, Sapporo, 060-8638, Japan
| | | | - Hideyuki Okano
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo, 160-8585, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan.
- Department Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, 650-0117, Japan.
- RIKEN Center for Biosystems Dynamics Research, Chuo, Kobe, 650-0047, Japan.
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6
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Shu X, Wang J, Zeng H, Shao L. Progression of Notch signaling regulation of B cells under radiation exposure. Front Immunol 2024; 15:1339977. [PMID: 38524139 PMCID: PMC10957566 DOI: 10.3389/fimmu.2024.1339977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/14/2024] [Indexed: 03/26/2024] Open
Abstract
With the continuous development of nuclear technology, the radiation exposure caused by radiation therapy is a serious health hazard. It is of great significance to further develop effective radiation countermeasures. B cells easily succumb to irradiation exposure along with immunosuppressive response. The approach to ameliorate radiation-induced B cell damage is rarely studied, implying that the underlying mechanisms of B cell damage after exposure are eager to be revealed. Recent studies suggest that Notch signaling plays an important role in B cell-mediated immune response. Notch signaling is a critical regulator for B cells to maintain immune function. Although accumulating studies reported that Notch signaling contributes to the functionality of hematopoietic stem cells and T cells, its role in B cells is scarcely appreciated. Presently, we discussed the regulation of Notch signaling on B cells under radiation exposure to provide a scientific basis to prevent radiation-induced B cell damage.
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Affiliation(s)
- Xin Shu
- Department of Occupational Health and Toxicology, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, School of Public Health, Nanchang University, Nanchang, China
| | - Jie Wang
- Department of Histology and Embryology, School of Basic Medicine Sciences, Nanchang University, Nanchang, China
| | - Huihong Zeng
- Department of Histology and Embryology, School of Basic Medicine Sciences, Nanchang University, Nanchang, China
| | - Lijian Shao
- Department of Occupational Health and Toxicology, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, School of Public Health, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Interdisciplinary Science, Nanchang University, Nanchang, China
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7
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Xu H, Jiang Y, Lu Y, Hu Z, Du R, Zhou Y, Liu Y, Zhao X, Tian Y, Yang C, Zhang Z, Qiu M, Wang Y. Thiram exposure induces tibial dyschondroplasia in broilers via the regulation effect of circ_003084/miR-130c-5p/BMPR1A crosstalk on chondrocyte proliferation and differentiation. J Hazard Mater 2024; 465:133071. [PMID: 38008051 DOI: 10.1016/j.jhazmat.2023.133071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/20/2023] [Accepted: 11/21/2023] [Indexed: 11/28/2023]
Abstract
Thiram, an agricultural insecticide, has been demonstrated to induce tibial dyschondroplasia (TD) in avian species. Circular RNA (circRNAs), a novel class of functional biological macromolecules characterized by their distinct circular structure, play crucial roles in various biological processes and diseases. Nevertheless, the precise regulatory mechanism underlying non-coding RNA involvement in thiram-induced broiler tibial chondrodysplasia remains elusive. In this study, we established a broiler model of thiram exposure for 10 days to assess TD and obtain a ceRNA network by RNA sequencing. By analyzing the differentially expressed circRNAs network, we id entify that circ_003084 was significantly upregulated in TD cartilage. Elevated circ_003084 inhibited TD chondrocytes proliferation and differentiation in vitro but promote apoptosis. Mechanistically, circ_003084 competitively binds to miR-130c-5p and prevents miR-130c-5p to decrease the level of BMPR1A, which upregulates the expression of apoptosis genes Caspase 3, Caspase 9, Bax and Bcl2, and finally facilitates cell apoptosis. Taken together, these findings imply that circ_003084/miR-130c-5p/BMPR1A interaction regulated TD chicken chondrocyte proliferation, apoptosis, and differentiation. This is the first work to reveal the mechanism of regulation of circRNA-related ceRNA on thiram-induced TD, offering a key reference for environmental toxicology.
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Affiliation(s)
- Hengyong Xu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuru Jiang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuxiang Lu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhi Hu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Ranran Du
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuxin Zhou
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yiping Liu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoling Zhao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yaofu Tian
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Chaowu Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Zengrong Zhang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Mohan Qiu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Yan Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; State Key Laboratory of Swine and Poultry Breeding Industry, Sichuan Agricultural University, Chengdu 611130, China.
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8
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Green HE, Oliveira HRD, Alvarenga AB, Scramlin-Zuelly S, Grossi D, Schinckel AP, Brito LF. Genomic background of biotypes related to growth, carcass and meat quality traits in Duroc pigs based on principal component analysis. J Anim Breed Genet 2024; 141:163-178. [PMID: 37902119 DOI: 10.1111/jbg.12831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/14/2023] [Accepted: 10/14/2023] [Indexed: 10/31/2023]
Abstract
As the swine industry continues to explore pork quality traits alongside growth, feed efficiency and carcass leanness traits, it becomes imperative to understand their underlying genetic relationships. Due to this increase in the number of desirable traits, animal breeders must also consider methods to efficiently perform direct genetic changes for each trait and evaluate alternative selection indexes with different sets of phenotypic measurements. Principal component analysis (PCA) and genome-wide association studies (GWAS) can be combined to understand the genetic architecture and biological mechanisms by defining biological types (biotypes) that relate these valuable traits. Therefore, the main objectives of this study were to: (1) estimate genomic-based genetic parameters; (2) define animal biotypes utilizing PCA; and (3) utilize GWAS to link the biotypes to candidate genes and quantitative trait loci (QTL). The phenotypic dataset included 2583 phenotypic records from female Duroc pigs from a terminal sire line. The pedigree file contained 193,764 animals and the genotype file included 21,309 animals with 35,651 single nucleotide polymorphisms (SNPs). Eight principal components (PCs), accounting for a total of 99.7% of the population variation, were defined for three growth, eight conventional carcass, 10 pork quality and 18 novel carcass traits. The eight biotypes defined from the PCs were found to be related to growth rate, maturity, meat quality and body structure, which were then related to candidate genes. Of the 175 candidate genes found, six of them [LDHA (SSC1), PIK3C3 (SSC6), PRKAG3 (SSC15), VRTN (SSC7), DLST (SSC7) and PAPPA (SSC1)] related to four PCs were found to be associated with previously defined QTL, linking the biotypes with biological processes involved with muscle growth, fat deposition, glycogen levels and skeletal development. Further functional analyses helped to make connections between biotypes, relating them through common KEGG pathways and gene ontology (GO) terms. These findings contribute to a better understanding of the genetic relationships between growth, carcass and meat quality traits in Duroc pigs, enabling breeders to better understand the biological mechanisms underlying the phenotypic expression of these traits.
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Affiliation(s)
- Hannah E Green
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
- Fast Genetics, Saskatoon, Saskatchewan, Canada
| | | | | | | | | | - Allan P Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
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9
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Wang M, Li S, Li H, Song C, Xie W, Zuo S, Zhou X, Zhou C, Ji Z, Zhou H. Genome editing of a dominant resistance gene for broad-spectrum resistance to bacterial diseases in rice without growth penalty. Plant Biotechnol J 2024; 22:529-531. [PMID: 37997505 PMCID: PMC10893933 DOI: 10.1111/pbi.14233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/15/2023] [Accepted: 11/04/2023] [Indexed: 11/25/2023]
Affiliation(s)
- Meixia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
- Citrus Research Institute, Southwest UniversityChongqingChina
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural SciencesSanyaChina
| | - Shaofang Li
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry ScienceBeijingChina
| | - Huayang Li
- Institute of Botany, The Chinese Academy of SciencesBeijingChina
| | - Congfeng Song
- College of Plant Protection, Nanjing Agricultural UniversityNanjingChina
| | - Wenya Xie
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou UniversityYangzhouChina
| | - Shimin Zuo
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou UniversityYangzhouChina
| | - Xueping Zhou
- Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
- Institute of Biotechnology, Zhejiang UniversityHangzhouChina
| | - Changyong Zhou
- Citrus Research Institute, Southwest UniversityChongqingChina
| | - Zhiyuan Ji
- Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Huanbin Zhou
- Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural SciencesSanyaChina
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10
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He K, Nie L, Yang C, Liu Z, Huang X, Li S, Yang X. Exhaustive exercise decreases tau phosphorylation and modifies biological processes associated with the protein translation and electron transport chain in P301L tau transgenic mice. Exp Gerontol 2024; 187:112375. [PMID: 38320733 DOI: 10.1016/j.exger.2024.112375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/13/2024]
Abstract
Stress response is a fundamental mechanism for cell survival, providing protection under unfavorable conditions. Mitochondrial stress, in particular, can trigger mitophagy, a process that restores cellular health. Exhaustive exercise (EE) is a form of acute mitochondrial stress. The objective of this current study is to investigate the impact of EE on tau pathology in pR5 mice, as well as the potential underlying mechanisms. To evaluate this, we examined the levels of total and phosphorylated tau in the hippocampus of pR5 mice, both with and without EE treatment. Furthermore, the application of weighted correlation network analysis (WGCNA) was employed to identify protein modules associated with the phenotype following the proteomic experiment. The findings of our study demonstrated a significant decrease in tau phosphorylation levels upon EE treatment, in comparison to the pR5 group. Moreover, the proteomic analysis provided additional insights, revealing that the mitigation of tau pathology was primarily attributed to the modulation of various pathways, such as translation factors and oxidative phosphorylation. Additionally, the analysis of heatmaps revealed a significant impact of EE treatment on the translation process and electron transport chain in pR5 mice. Furthermore, biochemical analysis provided further confirmation that EE treatment effectively modulated the ATP level in pR5 mice. In conclusion, our study suggests that the observed decrease in tau phosphorylation resulting from EE treatment may primarily be attributed to its regulation of the translation process and enhancement of mitochondrial function.
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Affiliation(s)
- Kaiwu He
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China; Department of Anesthesiology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), No. 1017, Dongmen North Road, Shenzhen 518020, China; Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, China
| | - Lulin Nie
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China; Institute of New Drug Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education, Jinan University College of Pharmacy, Jinan University, Guangzhou, China
| | - Chen Yang
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Zizhen Liu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Xinfeng Huang
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Shupeng Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Xifei Yang
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China.
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11
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Brasileiro-Martins LM, Cavalcante SA, Nascimento TP, Silva-Neto AV, Mariano Santos MD, Camillo-Andrade AC, da Gama Fischer JDS, Ferreira CC, Oliveira LB, Sartim MA, Costa AG, Pucca MB, Wen FH, Moura-da-Silva AM, Sachett J, Carvalho PC, de Aquino PF, Monteiro WM. Urinary proteomics reveals biological processes related to acute kidney injury in Bothrops atrox envenomings. PLoS Negl Trop Dis 2024; 18:e0012072. [PMID: 38536893 PMCID: PMC11020875 DOI: 10.1371/journal.pntd.0012072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/16/2024] [Accepted: 03/14/2024] [Indexed: 04/18/2024] Open
Abstract
Acute kidney injury (AKI) is a critical systemic complication caused by Bothrops envenoming, a neglected health problem in the Brazilian Amazon. Understanding the underlying mechanisms leading to AKI is crucial for effectively mitigating the burden of this complication. This study aimed to characterize the urinary protein profile of Bothrops atrox snakebite victims who developed AKI. We analyzed three groups of samples collected on admission: healthy subjects (controls, n = 10), snakebite victims who developed AKI (AKI, n = 10), and those who did not evolve to AKI (No-AKI, n = 10). Using liquid-chromatography tandem mass spectrometry, we identified and quantified (label-free) 1190 proteins. A panel of 65 proteins was identified exclusively in the urine of snakebite victims, with 32 exclusives to the AKI condition. Proteins more abundant or exclusive in AKI's urine were associated with acute phase response, endopeptidase inhibition, complement cascade, and inflammation. Notable proteins include serotransferrin, SERPINA-1, alpha-1B-glycoprotein, and NHL repeat-containing protein 3. Furthermore, evaluating previously reported biomarkers candidates for AKI and renal injury, we found retinol-binding protein, beta-2-microglobulin, cystatin-C, and hepcidin to be significant in cases of AKI induced by Bothrops envenoming. This work sheds light on physiological disturbances caused by Bothrops envenoming, highlighting potential biological processes contributing to AKI. Such insights may aid in better understanding and managing this life-threatening complication.
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Affiliation(s)
- Lisele Maria Brasileiro-Martins
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
| | | | - Thaís Pinto Nascimento
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
- Leonidas and Maria Deane Institute, Oswaldo Cruz Foundation, Manaus, Brazil
| | - Alexandre Vilhena Silva-Neto
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
| | - Marlon Dias Mariano Santos
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Brazil
| | - Amanda C. Camillo-Andrade
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Brazil
| | | | | | | | - Marco Aurelio Sartim
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
- Department of Research, Nilton Lins University, Manaus, Brazil
| | - Allyson Guimarães Costa
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
- Nursing School, Amazonas Federal University, Manaus, Brazil
| | - Manuela B. Pucca
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University, Araraquara, Brazil
| | - Fan Hui Wen
- Immunopathology Laboratory, Butantan Institute, São Paulo, Brazil
| | | | - Jacqueline Sachett
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- Immunopathology Laboratory, Butantan Institute, São Paulo, Brazil
| | - Paulo Costa Carvalho
- Structural and Computational Proteomics Laboratory, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Brazil
| | | | - Wuelton M. Monteiro
- Department of Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Brazil
- School of Health Sciences, Amazonas State University, Manaus, Brazil
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12
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Jia X, He X, Huang C, Li J, Dong Z, Liu K. Protein translation: biological processes and therapeutic strategies for human diseases. Signal Transduct Target Ther 2024; 9:44. [PMID: 38388452 PMCID: PMC10884018 DOI: 10.1038/s41392-024-01749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Protein translation is a tightly regulated cellular process that is essential for gene expression and protein synthesis. The deregulation of this process is increasingly recognized as a critical factor in the pathogenesis of various human diseases. In this review, we discuss how deregulated translation can lead to aberrant protein synthesis, altered cellular functions, and disease progression. We explore the key mechanisms contributing to the deregulation of protein translation, including functional alterations in translation factors, tRNA, mRNA, and ribosome function. Deregulated translation leads to abnormal protein expression, disrupted cellular signaling, and perturbed cellular functions- all of which contribute to disease pathogenesis. The development of ribosome profiling techniques along with mass spectrometry-based proteomics, mRNA sequencing and single-cell approaches have opened new avenues for detecting diseases related to translation errors. Importantly, we highlight recent advances in therapies targeting translation-related disorders and their potential applications in neurodegenerative diseases, cancer, infectious diseases, and cardiovascular diseases. Moreover, the growing interest lies in targeted therapies aimed at restoring precise control over translation in diseased cells is discussed. In conclusion, this comprehensive review underscores the critical role of protein translation in disease and its potential as a therapeutic target. Advancements in understanding the molecular mechanisms of protein translation deregulation, coupled with the development of targeted therapies, offer promising avenues for improving disease outcomes in various human diseases. Additionally, it will unlock doors to the possibility of precision medicine by offering personalized therapies and a deeper understanding of the molecular underpinnings of diseases in the future.
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Affiliation(s)
- Xuechao Jia
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Xinyu He
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Chuntian Huang
- Department of Pathology and Pathophysiology, Henan University of Chinese Medicine, Zhengzhou, Henan, 450000, China
| | - Jian Li
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, 450000, China.
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13
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Viktorsson C, Portugal AM, Falck-Ytter T. Genetic and environmental contributions to gaze lateralization across social and non-social stimuli in human infants. Sci Rep 2024; 14:3668. [PMID: 38351309 PMCID: PMC10864339 DOI: 10.1038/s41598-024-54373-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/12/2024] [Indexed: 02/16/2024] Open
Abstract
A tendency to look at the left side of faces from the observer's point of view has been found in older children and adults, but it is not known when this face-specific left gaze bias develops and what factors may influence individual differences in gaze lateralization. Therefore, the aims of this study were to estimate gaze lateralization during face observation and to more broadly estimate lateralization tendencies across a wider set of social and non-social stimuli, in early infancy. In addition, we aimed to estimate the influence of genetic and environmental factors on lateralization of gaze. We studied gaze lateralization in 592 5-month-old twins (282 females, 330 monozygotic twins) by recording their gaze while viewing faces and two other types of stimuli that consisted of either collections of dots (non-social stimuli) or faces interspersed with objects (mixed stimuli). A right gaze bias was found when viewing faces, and this measure was moderately heritable (A = 0.38, 95% CI 0.24; 0.50). A left gaze bias was observed in the non-social condition, while a right gaze bias was found in the mixed condition, suggesting that there is no general left gaze bias at this age. Genetic influence on individual differences in gaze lateralization was only found for the tendency to look at the right versus left side of faces, suggesting genetic specificity of lateralized gaze when viewing faces.
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Affiliation(s)
- Charlotte Viktorsson
- Development and Neurodiversity Lab, Department of Psychology, Uppsala University, Uppsala, Sweden.
| | - Ana Maria Portugal
- Development and Neurodiversity Lab, Department of Psychology, Uppsala University, Uppsala, Sweden
- Division of Neuropsychiatry, Department of Women's and Children's Health, Center of Neurodevelopmental Disorders (KIND), Karolinska Institutet, Stockholm, Sweden
| | - Terje Falck-Ytter
- Development and Neurodiversity Lab, Department of Psychology, Uppsala University, Uppsala, Sweden
- Division of Neuropsychiatry, Department of Women's and Children's Health, Center of Neurodevelopmental Disorders (KIND), Karolinska Institutet, Stockholm, Sweden
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14
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Kato S, Hotta K. Automatic enhancement preprocessing for segmentation of low quality cell images. Sci Rep 2024; 14:3619. [PMID: 38351053 PMCID: PMC10864346 DOI: 10.1038/s41598-024-53411-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
We present a novel automatic preprocessing and ensemble learning technique for the segmentation of low-quality cell images. Capturing cells subjected to intense light is challenging due to their vulnerability to light-induced cell death. Consequently, microscopic cell images tend to be of low quality and it causes low accuracy for semantic segmentation. This problem can not be satisfactorily solved by classical image preprocessing methods. Therefore, we propose a novel approach of automatic enhancement preprocessing (AEP), which translates an input image into images that are easy to recognize by deep learning. AEP is composed of two deep neural networks, and the penultimate feature maps of the first network are employed as filters to translate an input image with low quality into images that are easily classified by deep learning. Additionally, we propose an automatic weighted ensemble learning (AWEL), which combines the multiple segmentation results. Since the second network predicts segmentation results corresponding to each translated input image, multiple segmentation results can be aggregated by automatically determining suitable weights. Experiments on two types of cell image segmentation confirmed that AEP can translate low-quality cell images into images that are easy to segment and that segmentation accuracy improves using AWEL.
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Affiliation(s)
- Sota Kato
- Department of Electrical, Information, Materials and Materials Engineering, Graduate School of Science and Engineering, Meijo University, Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan.
| | - Kazuhiro Hotta
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Meijo University, Nagoya, Aichi, Japan
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15
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Liu D, Zhao X, Zhang Q, Zhou F, Tong X. Bone marrow mesenchymal stem cell-derived exosomes promote osteoblast proliferation, migration and inhibit apoptosis by regulating KLF3-AS1/miR-338-3p. BMC Musculoskelet Disord 2024; 25:122. [PMID: 38336637 PMCID: PMC10854165 DOI: 10.1186/s12891-024-07236-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
AIM This study aimed to investigate the effect and mechanism of bone marrow mesenchymal stem cell-derived exosomes on osteoblast function. METHODS The expression of KLF3-AS1 and miR-338-3p in serum of fracture patients was detected by qRT-PCR. Exosomes from BMSCs were isolated by ultrafast centrifugation. MC3T3-E1 cells were cultured in vitro as experimental cells. Intracellular gene expression was regulated by transfection of si-KLF3-AS1 or miR-338-3p inhibitors. MTT assay, Transwell assay and flow cytometry were used to evaluate cell viability, migration, and apoptosis. The luciferase reporter gene was used to verify the targeting relationship between KLF3-AS1 and miR-338-3p. Bioinformatics analysis was used to identify the basic functions and possible enrichment pathways of miR-338-3p target genes. RESULTS The expressions of KLF3-AS1 and miR-338-3p in the serum of fracture patients were down-regulated and up-regulated, respectively. The expression of KLF3-AS1 was increased in MC3T3-E1 cells cultured with BMSCs-Exo, while the viability and migration ability of MC3T3-E1 cells were enhanced, and the apoptosis ability was weakened. Further analysis revealed miR-338-3p was the target gene of KLF3-AS1. The expression of miR-338-3p was downregulated in MC3T3-E1 cells cultured with BMSCs-Exo. Inhibition of miR-338-3p in MC3T3-E1 cells enhanced the viability and migration ability of MC3T3-E1 cells when cultured with BMSCs-Exo, while suppressing apoptosis. Bioinformatics analysis demonstrated that the target genes of miR-338-3p were predominantly localized at the axon's initiation site, involved in biological processes such as development and growth regulation, and mainly enriched in MAPK and ErbB signaling pathways. CONCLUSION In vitro, BMSCs-Exo exhibits the capacity to enhance proliferation and migration while inhibiting apoptosis of MC3T3-E1 cells, potentially achieved through modulation of KLF3-AS1 and miR-338-3p expression in MC3T3-E1 cells.
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Affiliation(s)
- Dacheng Liu
- Department of Orthopedics, Xuzhou Municipal Hospital Affiliated to Xuzhou Medical University, 269 University Road, Tongshan District, Xuzhou, 221100, Jiangsu, China
| | - Xuechao Zhao
- Department of Orthopedics, Xuzhou Municipal Hospital Affiliated to Xuzhou Medical University, 269 University Road, Tongshan District, Xuzhou, 221100, Jiangsu, China
| | - Qiang Zhang
- Department of Orthopedics, Xuzhou Municipal Hospital Affiliated to Xuzhou Medical University, 269 University Road, Tongshan District, Xuzhou, 221100, Jiangsu, China
| | - Fei Zhou
- Operating Room, Xuzhou Central Hospital, Xuzhou, 221006, China
| | - Xiangyang Tong
- Department of Orthopedics, Xuzhou Municipal Hospital Affiliated to Xuzhou Medical University, 269 University Road, Tongshan District, Xuzhou, 221100, Jiangsu, China.
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16
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Ren H, Zhang D. Lactylation constrains OXPHOS under hypoxia. Cell Res 2024; 34:91-92. [PMID: 38163845 PMCID: PMC10837435 DOI: 10.1038/s41422-023-00872-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Affiliation(s)
- Haowen Ren
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Di Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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17
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Li Z, Nie Q, Nie SP. Comprehensive insights: unraveling the mechanisms of gut commensals in glucose metabolism regulation. Sci China Life Sci 2024; 67:414-417. [PMID: 38155278 DOI: 10.1007/s11427-023-2455-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/19/2023] [Indexed: 12/30/2023]
Affiliation(s)
- Zhipeng Li
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, 330047, China
| | - Qixing Nie
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, 330047, China
| | - Shao-Ping Nie
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, 330047, China.
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18
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Stables RG, Hannon MP, Costello NB, McHaffie SJ, Sodhi JS, Close GL, Morton JP. Acute fuelling and recovery practices of academy soccer players: implications for growth, maturation, and physical performance. SCI MED FOOTBALL 2024; 8:37-51. [PMID: 36351858 DOI: 10.1080/24733938.2022.2146178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/07/2022] [Indexed: 11/11/2022]
Abstract
Academy soccer players frequently train in the evening (i.e. 1700-2000 h), hence limited time to nutritionally prepare and recover due to schooling, travel and sleep schedules. Accordingly, we assessed timing and quantity of energy intake in the pre-training and post-training period. Over a 3-day in-season training period, male players (n=48; n=8 from under (U) 12, 13, 14, 15/16, 18 and 23 players) from an English Premier League academy self-reported dietary intake and physical activity levels (via the remote food photography method and activity diary, respectively) in the four hours pre- and post-training. Timing of pre-training energy intake ranged from 40 ± 28 mins (U15/U16 players) to 114 ± 71 mins (U18) before training and mean carbohydrate (CHO) intake ranged from 0.8±0.4 g.kg-1 (U23) to 1.5±0.9 g.kg-1 (U12). Timing of post-training energy intake ranged from 39 ± 27 mins (U14) to 70 ± 84 mins (U23) and mean CHO intake ranged from 1.6±0.8 g.kg-1 (U12) to 0.9±0.5 g.kg-1 (U14). In contrast to CHO, all age groups consumed sufficient protein intake in the post-training period (i.e. > 0.3 g.kg-1). We conclude academy soccer players habitually practice sub-optimal fuelling and recovery strategies, the consequence of which could impair growth, maturation and physical performance.
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Affiliation(s)
- Reuben G Stables
- Research Institute for Sport and Exercise Sciences (RISES), Liverpool John Moores University, Liverpool, UK
| | - Marcus P Hannon
- Research Institute for Sport and Exercise Sciences (RISES), Liverpool John Moores University, Liverpool, UK
| | - Nessan B Costello
- Carnegie Faculty, Institute for Sport, Physical Activity and Leisure, Leeds Beckett University, Leeds, UK
| | - Sam J McHaffie
- Research Institute for Sport and Exercise Sciences (RISES), Liverpool John Moores University, Liverpool, UK
| | - Jazz S Sodhi
- Aston Villa Football Club, Bodymoor Heath Training Ground, Tamworth, UK
| | - Graeme L Close
- Research Institute for Sport and Exercise Sciences (RISES), Liverpool John Moores University, Liverpool, UK
| | - James P Morton
- Research Institute for Sport and Exercise Sciences (RISES), Liverpool John Moores University, Liverpool, UK
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19
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Sun D, Yu H, Kong L, Liu S, Xu C, Li Q. The role of DNA methylation reprogramming during sex determination and sex reversal in the Pacific oyster Crassostrea gigas. Int J Biol Macromol 2024; 259:128964. [PMID: 38219938 DOI: 10.1016/j.ijbiomac.2023.128964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/19/2023] [Accepted: 12/14/2023] [Indexed: 01/16/2024]
Abstract
DNA methylation is instrumental in vertebrate sex reversal. However, the mechanism of DNA methylation regulation regarding sex reversal in invertebrates is unclear. In this study, we used whole genome bisulfite sequencing (WGBS) to map single-base resolution methylation profiles of the Pacific oyster, including female-to-male (FMa-to-FMb) and male-to-female (MFa-to-MFb) sex reversal, as well as sex non-reversed males and females (MMa-to-MMb and FFa-to-FFb). The results showed that global DNA methylation levels increase during female-to-male sex reversals, with a particular increase in the proportion of high methylation levels (mCGs >0.75) and a decrease in the proportion of intermediate methylation levels (0.25 < mCGs <0.75). This increase in DNA methylation was mainly associated with the elevated expression of DNA methylase genes. Genome-wide methylation patterns of females were accurately remodeled to those of males after sex reversal, while the opposite was true for the male-to-female reversal. Those findings directly indicate that alterations in DNA methylation play a significant role in sex reversal in Pacific oysters. Comparative analysis of the DNA methylomes of pre- and post- sex reversal gonadal tissues (FMb-vs-FMa or MFb-vs-MFa) revealed that differentially methylated genes were mainly involved in the biological processes of sex determination or gonadal development. However critical genes such as Dmrt1, Foxl2 and Sox-like, which are involved in the putative sex determination pathway in Pacific oysters, showed almost an absence of methylation modifications, varying greatly from vertebrates. Additionally, comparative analysis of the DNA methylomes of sexual reversal and sex non-reversal (FMa-vs-FFa or MFa-vs-MMa) revealed that heat shock protein genes, such as Hsp68-like and Hsp70B, were important for the occurrence of sex reversal. These findings shed light on the epigenetic mechanisms underlying the maintenance of gonadal plasticity and the reversal of organ architecture in oysters.
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Affiliation(s)
- Dongfang Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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20
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Tamaki A, Kato T, Sakurai Y, Sato K, Adachi K, Tadehara M, Kogami T, Matsushita M, Hoshino A, Sanoyama I, Numata Y, Umezawa A, Ichinoe M, Ichihara M, Kusano C, Murakumo Y. REV7 is involved in outcomes of platinum-based chemotherapy in pancreatic cancer by controlling the DNA damage response. Cancer Sci 2024; 115:660-671. [PMID: 38130032 PMCID: PMC10859597 DOI: 10.1111/cas.16044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
REV7 is a multifunctional protein implicated in various biological processes, including DNA damage response. REV7 expression in human cancer cells affects their sensitivity to DNA-damaging agents. In the present study, we investigated the significance of REV7 in pancreatic ductal adenocarcinoma (PDAC). REV7 expression was immunohistochemically examined in 92 resected PDAC specimens and 60 endoscopic ultrasound-guided fine-needle aspiration biopsy (EUS-FNAB) specimens of unresectable PDAC treated with platinum-based chemotherapy, and its association with clinicopathologic features was analyzed. Although REV7 expression was not significantly associated with the progression of primary tumors (T-factor and Stage) in either resected or unresectable PDAC, decreased levels of REV7 expression in EUS-FNAB specimens of unresectable PDAC were significantly associated with better outcomes of platinum-based chemotherapy and a favorable prognosis. REV7-deficient PDAC cell lines showed suppressed cell growth and enhanced sensitivity to cisplatin in vitro. Tumor-bearing mice generated using REV7-deficient PDAC cell lines also showed enhanced sensitivity to cisplatin in vivo. RNA sequencing analysis using WT and REV7-deficient PDAC cell lines revealed that REV7 inactivation promoted the downregulation of genes involved in the DNA repair and the upregulation of genes involved in apoptosis. Our results indicate that decreased expression of REV7 is associated with better outcomes of platinum-based chemotherapy in PDAC by suppressing the DNA damage response. It is also suggested that REV7 is a useful biomarker for predicting the outcome of platinum-based chemotherapy and the prognosis of unresectable PDAC and is a potential target for PDAC treatment.
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Affiliation(s)
- Akihiro Tamaki
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
- Department of GastroenterologyKitasato University School of MedicineSagamiharaJapan
| | - Takuya Kato
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
| | - Yasutaka Sakurai
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
| | - Keita Sato
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
| | - Kai Adachi
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
- Department of GastroenterologyKitasato University School of MedicineSagamiharaJapan
| | - Masayoshi Tadehara
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
- Department of GastroenterologyKitasato University School of MedicineSagamiharaJapan
| | - Taro Kogami
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
- Department of GastroenterologyKitasato University School of MedicineSagamiharaJapan
| | - Masahiro Matsushita
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
- Department of GastroenterologyKitasato University School of MedicineSagamiharaJapan
| | - Akiyoshi Hoshino
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
| | - Itaru Sanoyama
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
| | - Yoshiko Numata
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
| | - Atsuko Umezawa
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
| | - Masaaki Ichinoe
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
| | - Masatoshi Ichihara
- Department of Biomedical Sciences, College of Life and Health SciencesChubu UniversityKasugaiJapan
| | - Chika Kusano
- Department of GastroenterologyKitasato University School of MedicineSagamiharaJapan
| | - Yoshiki Murakumo
- Department of PathologyKitasato University School of MedicineSagamiharaJapan
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21
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Lalechère E, Monnet JM, Breen J, Fuhr M. Assessing the potential of remote sensing-based models to predict old-growth forests on large spatiotemporal scales. J Environ Manage 2024; 351:119865. [PMID: 38159307 DOI: 10.1016/j.jenvman.2023.119865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/20/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
Old-growth forests provide a broad range of ecosystem services. However, due to poor knowledge of their spatiotemporal distribution, implementing conservation and restoration strategies is challenging. The goal of this study is to compare the predictive ability of socioecological factors and different sources of remotely sensed data that determine the spatiotemporal scales at which forest maturity attributes can be predicted. We evaluated various remotely sensed data that cover a broad range of spatial (from local to global) and temporal (from current to decades) extents, from Airborne Laser Scanning (ALS), aerial multispectral and stereo-imagery, Sentinel-1, Sentinel-2 and Landsat data. Using random forests, remotely sensed data were related to a forest maturity index available in 688 forest plots across four ranges of the French Alps. Each model also includes socioecological predictors related to topography, socioeconomy, pedology and climatology. We found that the different remotely sensed data provide information on the main forest structural characteristics as defined by ALS, except for Landsat, which has a too coarse resolution, and Sentinel-1, which responds differently to vegetation structure. The predictions were quite similar considering aerial remotely sensed data, on the one hand, and satellite remotely sensed data, on the other hand. Socioecological variables are the most important predictors compared to the remote sensing metrics. In conclusion, our results indicate that a wide range of remotely sensed data can be used to study old-growth forests beyond the use of ALS and despite different abilities to predict forest structure. Accounting for socioecological predictors is indispensable to avoid a significant loss of predictive accuracy. Remotely sensed data can allow for predictions to be made at different spatiotemporal resolutions and extents. This study paves the way to large-scale monitoring of forest maturity, as well as for retrospective analyses which will show to what extent predicted maturity change at different dates.
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Affiliation(s)
- Etienne Lalechère
- Université de Picardie Jules Verne, EDYSAN (UMR CNRS-UPJV 7058), 1 rue des Louvels, 80037, Amiens Cedex, France.
| | - Jean-Matthieu Monnet
- INRAE, UR LESSEM, 2 rue de la Papeterie, BP 76 38402, Saint Martin d'Hères Cedex, France.
| | - Juliette Breen
- INRAE, UR LESSEM, 2 rue de la Papeterie, BP 76 38402, Saint Martin d'Hères Cedex, France.
| | - Marc Fuhr
- INRAE, UR LESSEM, 2 rue de la Papeterie, BP 76 38402, Saint Martin d'Hères Cedex, France.
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22
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Kudal P, Patnaik A, Dawar S, Satankar RK, Dawar P. Segmentation of OECD countries on the basis of selected global environmental indicators using k-means non-hierarchical clustering. Environ Sci Pollut Res Int 2024; 31:10334-10345. [PMID: 37067703 DOI: 10.1007/s11356-023-26679-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
In order to allocate resources and describe progress, frequently nations are grouped together by many international authorities. A variety of pertinent indicators can provide a more useful basis for classification for each specific area of interest. Based on commonalities between various variables connected to the global environmental sector, we developed a novel typology of country clusters. Four indicators were chosen after a review of the literature. In order to optimize data availability across as many OECD nations as feasible, indicators were chosen based on their relevance for all the OECD countries. Countries were arranged into a natural cluster using the hierarchical clustering method. Four groups, covering 31 countries, were the result of two stages of grouping. These four clusters were found to be more compact and clearly divided which gives policymakers a clear-cut idea as to how these environmental indicators are deteriorating day by day and year by year and what needs to be done to be more environmentally sustainable and responsible.
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Affiliation(s)
- Pallavi Kudal
- Balaji Institute of International Business (BIIB), Sri Balaji University, Pune, Maharashtra, India
| | - Amitabh Patnaik
- Dr. D.Y. Patil Institute of Management Studies, Pune, Maharashtra, India
| | - Sunny Dawar
- Faculty of Management & Commerce, Manipal University Jaipur, Jaipur, Rajasthan, India.
| | | | - Prince Dawar
- Poornima Group of Colleges, Jaipur, Rajasthan, India
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23
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Wang K, Armour CH, Gibbs RGJ, Xu XY. A numerical study of the effect of thrombus breakdown on predicted thrombus formation and growth. Biomech Model Mechanobiol 2024; 23:61-71. [PMID: 37566172 PMCID: PMC10901920 DOI: 10.1007/s10237-023-01757-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/22/2023] [Indexed: 08/12/2023]
Abstract
Thrombosis is a complex biological process which involves many biochemical reactions and is influenced by blood flow. Various computational models have been developed to simulate natural thrombosis in diseases such as aortic dissection (AD), and device-induced thrombosis in blood-contacting biomedical devices. While most hemodynamics-based models consider the role of low shear stress in the initiation and growth of thrombus, they often ignore the effect of thrombus breakdown induced by elevated shear stress. In this study, a new shear stress-induced thrombus breakdown function is proposed and implemented in our previously published thrombosis model. The performance of the refined model is assessed by quantitative comparison with experimental data on thrombus formation in a backward-facing step geometry, and qualitative comparison with in vivo data obtained from an AD patient. Our results show that incorporating thrombus breakdown improves accuracy in predicted thrombus volume and captures the same pattern of thrombus evolution as measured experimentally and in vivo. In the backward-facing step geometry, thrombus breakdown impedes growth over the step and downstream, allowing a stable thrombus to be reached more quickly. Moreover, the predicted thrombus volume, height and length are in better agreement with the experimental measurements compared to the original model which does not consider thrombus breakdown. In the patient-specific AD, the refined model outperforms the original model in predicting the extent and location of thrombosis. In conclusion, the effect of thrombus breakdown is not negligible and should be included in computational models of thrombosis.
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Affiliation(s)
- Kaihong Wang
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Chlöe H Armour
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Richard G J Gibbs
- Regional Vascular Unit, St Mary's Hospital, Imperial College Healthcare National Health Service Trust, Imperial College London, London, UK
| | - Xiao Yun Xu
- Department of Chemical Engineering, Imperial College London, London, UK.
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24
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Abstract
Complement has long been considered a key innate immune effector system that mediates host defence and tissue homeostasis. Yet, growing evidence has illuminated a broader involvement of complement in fundamental biological processes extending far beyond its traditional realm in innate immunity. Complement engages in intricate crosstalk with multiple pattern-recognition and signalling pathways both in the extracellular and intracellular space. Besides modulating host-pathogen interactions, this crosstalk guides early developmental processes and distinct cell trajectories, shaping tissue immunometabolic and regenerative programmes in different physiological systems. This Review provides a guide to the system-wide functions of complement. It highlights illustrative paradigm shifts that have reshaped our understanding of complement pathobiology, drawing examples from evolution, development of the central nervous system, tissue regeneration and cancer immunity. Despite its tight spatiotemporal regulation, complement activation can be derailed, fuelling inflammatory tissue pathology. The pervasive contribution of complement to disease pathophysiology has inspired a resurgence of complement therapeutics with major clinical developments, some of which have challenged long-held dogmas. We thus highlight major therapeutic concepts and milestones in clinical complement intervention.
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Affiliation(s)
| | - George Hajishengallis
- Department of Basic and Translational Sciences, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John D Lambris
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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25
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Robil JM. The pollen tube's secret to slick growth? A dab of pectate lyase-like enzyme. Plant Physiol 2024; 194:606-608. [PMID: 37788566 PMCID: PMC10828198 DOI: 10.1093/plphys/kiad522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/05/2023]
Affiliation(s)
- Janlo M Robil
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Department of Biology, School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
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26
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Yokoyama R. Sense or nonsense? The role of protein acetylation in cyanobacterial photosynthesis and growth. Plant Physiol 2024; 194:595-597. [PMID: 37823417 PMCID: PMC10828185 DOI: 10.1093/plphys/kiad545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023]
Affiliation(s)
- Ryo Yokoyama
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
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27
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Kines KJ, Sokolowski M, DeFreece C, Shareef A, deHaro DL, Belancio VP. Large Deletions, Cleavage of the Telomeric Repeat Sequence, and Reverse Transcriptase-Mediated DNA Damage Response Associated with Long Interspersed Element-1 ORF2p Enzymatic Activities. Genes (Basel) 2024; 15:143. [PMID: 38397133 PMCID: PMC10887698 DOI: 10.3390/genes15020143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
L1 elements can cause DNA damage and genomic variation via retrotransposition and the generation of endonuclease-dependent DNA breaks. These processes require L1 ORF2p protein that contains an endonuclease domain, which cuts genomic DNA, and a reverse transcriptase domain, which synthesizes cDNA. The complete impact of L1 enzymatic activities on genome stability and cellular function remains understudied, and the spectrum of L1-induced mutations, other than L1 insertions, is mostly unknown. Using an inducible system, we demonstrate that an ORF2p containing functional reverse transcriptase is sufficient to elicit DNA damage response even in the absence of the functional endonuclease. Using a TK/Neo reporter system that captures misrepaired DNA breaks, we demonstrate that L1 expression results in large genomic deletions that lack any signatures of L1 involvement. Using an in vitro cleavage assay, we demonstrate that L1 endonuclease efficiently cuts telomeric repeat sequences. These findings support that L1 could be an unrecognized source of disease-promoting genomic deletions, telomere dysfunction, and an underappreciated source of chronic RT-mediated DNA damage response in mammalian cells. Our findings expand the spectrum of biological processes that can be triggered by functional and nonfunctional L1s, which have impactful evolutionary- and health-relevant consequences.
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Affiliation(s)
- Kristine J. Kines
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Mark Sokolowski
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Cecily DeFreece
- Department of Biology, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Afzaal Shareef
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Dawn L. deHaro
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Victoria P. Belancio
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
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28
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Jumde G, Spanjaard B, Junker JP. Inference of differentiation trajectories by transfer learning across biological processes. Cell Syst 2024; 15:75-82.e5. [PMID: 38128536 DOI: 10.1016/j.cels.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/28/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Stem cells differentiate into distinct fates by transitioning through a series of transcriptional states. Current computational approaches allow reconstruction of differentiation trajectories from single-cell transcriptomics data, but it remains unknown to what degree differentiation can be predicted across biological processes. Here, we use transfer learning to infer differentiation processes and quantify predictability in early embryonic development and adult hematopoiesis. Overall, we find that non-linear methods outperform linear approaches, and we achieved the best predictions with a custom variational autoencoder that explicitly models changes in transcriptional variance. We observed a high accuracy of predictions in embryonic development, but we found somewhat lower agreement with the real data in adult hematopoiesis. We demonstrate that this discrepancy can be explained by a higher degree of concordant transcriptional processes along embryonic differentiation compared with adult homeostasis. In summary, we establish a framework for quantifying and exploiting predictability of cellular differentiation trajectories.
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Affiliation(s)
- Gaurav Jumde
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany; Humboldt Universität zu Berlin, Faculty of Life Sciences, Department of Biology, 10115 Berlin, Germany
| | - Bastiaan Spanjaard
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany; Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany; Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
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29
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Liu S, Zhang C, Li L, Deng X, Hu C, Yang F, Liu Q, Tan W. Organization of an Artificial Multicellular System with a Tunable DNA Patch on a Membrane Surface. Nano Lett 2024; 24:433-440. [PMID: 38112415 DOI: 10.1021/acs.nanolett.3c04249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Coordinating multiple artificial cellular compartments into a well-organized artificial multicellular system (AMS) is of great interest in bottom-up synthetic biology. However, developing a facile strategy for fabricating an AMS with a controlled arrangement remains a challenge. Herein, utilizing in situ DNA hybridization chain reaction on the membrane surface, we developed a DNA patch-based strategy to direct the interconnection of vesicles. By tuning the DNA patch that generates heterotrophic adhesion for the attachment of vesicles, we could produce an AMS with higher-order structures straightforwardly and effectively. Furthermore, a hybrid AMS comprising live cells and vesicles was fabricated, and we found the hybrid AMS with higher-order structures arouses efficient molecular transportation from vesicles to living cells. In brief, our work provides a versatile strategy for modulating the self-assembly of AMSs, which could expand our capability to engineer synthetic biological systems and benefit synthetic cell research in programmable manipulation of intercellular communications.
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Affiliation(s)
- Shuang Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, FuRong Laboratory, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Chunjuan Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, FuRong Laboratory, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Lexun Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, FuRong Laboratory, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Xiaodan Deng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, FuRong Laboratory, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Canqiong Hu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, FuRong Laboratory, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Fan Yang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, FuRong Laboratory, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, FuRong Laboratory, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, FuRong Laboratory, College of Biology, Hunan University, Changsha, Hunan 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Materials Science and Engineering, Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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30
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Oikonomou VK, Huerta M, Sandéhn A, Dreier T, Daguerre Y, Lim H, Berggren M, Pavlopoulou E, Näsholm T, Bech M, Stavrinidou E. eSoil: A low-power bioelectronic growth scaffold that enhances crop seedling growth. Proc Natl Acad Sci U S A 2024; 121:e2304135120. [PMID: 38147542 PMCID: PMC10786271 DOI: 10.1073/pnas.2304135120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 11/15/2023] [Indexed: 12/28/2023] Open
Abstract
Active hydroponic substrates that stimulate on demand the plant growth have not been demonstrated so far. Here, we developed the eSoil, a low-power bioelectronic growth scaffold that can provide electrical stimulation to the plants' root system and growth environment in hydroponics settings. eSoil's active material is an organic mixed ionic electronic conductor while its main structural component is cellulose, the most abundant biopolymer. We demonstrate that barley seedlings that are widely used for fodder grow within the eSoil with the root system integrated within its porous matrix. Simply by polarizing the eSoil, seedling growth is accelerated resulting in increase of dry weight on average by 50% after 15 d of growth. The effect is evident both on root and shoot development and occurs during the growth period after the stimulation. The stimulated plants reduce and assimilate NO3- more efficiently than controls, a finding that may have implications on minimizing fertilizer use. However, more studies are required to provide a mechanistic understanding of the physical and biological processes involved. eSoil opens the pathway for the development of active hydroponic scaffolds that may increase crop yield in a sustainable manner.
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Affiliation(s)
- Vasileios K. Oikonomou
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-60174Norrköping, Sweden
- Wallenberg Wood Science Center, Department of Science and Technology, Linköping University, SE-60174Norrköping, Sweden
| | - Miriam Huerta
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-60174Norrköping, Sweden
| | - Alexandra Sandéhn
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-60174Norrköping, Sweden
- Wallenberg Wood Science Center, Department of Science and Technology, Linköping University, SE-60174Norrköping, Sweden
| | - Till Dreier
- Department for Medical Radiation Physics, Clinical Sciences Lund, Lund University, SE-22242Lund, Sweden
- Excillum AB, SE-16440Kista, Sweden
| | - Yohann Daguerre
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183Umeå, Sweden
| | - Hyungwoo Lim
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-90183Umeå, Sweden
| | - Magnus Berggren
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-60174Norrköping, Sweden
- Wallenberg Wood Science Center, Department of Science and Technology, Linköping University, SE-60174Norrköping, Sweden
| | - Eleni Pavlopoulou
- Institute of Electronic Structure and Laser, Foundation for Research and Technology—Hellas, 71110Heraklion, Crete, Greece
| | - Torgny Näsholm
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-90183Umeå, Sweden
| | - Martin Bech
- Department for Medical Radiation Physics, Clinical Sciences Lund, Lund University, SE-22242Lund, Sweden
| | - Eleni Stavrinidou
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-60174Norrköping, Sweden
- Wallenberg Wood Science Center, Department of Science and Technology, Linköping University, SE-60174Norrköping, Sweden
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183Umeå, Sweden
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Chen B, Yu P, Chan WN, Xie F, Zhang Y, Liang L, Leung KT, Lo KW, Yu J, Tse GMK, Kang W, To KF. Cellular zinc metabolism and zinc signaling: from biological functions to diseases and therapeutic targets. Signal Transduct Target Ther 2024; 9:6. [PMID: 38169461 PMCID: PMC10761908 DOI: 10.1038/s41392-023-01679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/15/2023] [Accepted: 10/10/2023] [Indexed: 01/05/2024] Open
Abstract
Zinc metabolism at the cellular level is critical for many biological processes in the body. A key observation is the disruption of cellular homeostasis, often coinciding with disease progression. As an essential factor in maintaining cellular equilibrium, cellular zinc has been increasingly spotlighted in the context of disease development. Extensive research suggests zinc's involvement in promoting malignancy and invasion in cancer cells, despite its low tissue concentration. This has led to a growing body of literature investigating zinc's cellular metabolism, particularly the functions of zinc transporters and storage mechanisms during cancer progression. Zinc transportation is under the control of two major transporter families: SLC30 (ZnT) for the excretion of zinc and SLC39 (ZIP) for the zinc intake. Additionally, the storage of this essential element is predominantly mediated by metallothioneins (MTs). This review consolidates knowledge on the critical functions of cellular zinc signaling and underscores potential molecular pathways linking zinc metabolism to disease progression, with a special focus on cancer. We also compile a summary of clinical trials involving zinc ions. Given the main localization of zinc transporters at the cell membrane, the potential for targeted therapies, including small molecules and monoclonal antibodies, offers promising avenues for future exploration.
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Affiliation(s)
- Bonan Chen
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
- CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Peiyao Yu
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Wai Nok Chan
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
- CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Fuda Xie
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
- CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yigan Zhang
- Institute of Biomedical Research, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Li Liang
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, China
| | - Kam Tong Leung
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwok Wai Lo
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Gary M K Tse
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.
- CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
| | - Ka Fai To
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China.
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Curcio R, Frattaruolo L, Marra F, Pesole G, Vozza A, Cappello AR, Fiorillo M, Lauria G, Ahmed A, Fiermonte G, Capobianco L, Dolce V. Two functionally different mitochondrial phosphate carriers support Drosophila melanogaster OXPHOS throughout distinct developmental stages. Biochim Biophys Acta Mol Cell Res 2024; 1871:119615. [PMID: 37898376 DOI: 10.1016/j.bbamcr.2023.119615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Affiliation(s)
- Rosita Curcio
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Luca Frattaruolo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Federica Marra
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Graziano Pesole
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Angelo Vozza
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Anna Rita Cappello
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Marco Fiorillo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Graziantonio Lauria
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Amer Ahmed
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Giuseppe Fiermonte
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy.
| | - Loredana Capobianco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy.
| | - Vincenza Dolce
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy.
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Mathur S, Haynes E, Allender MC, Gibbs HL. Genetic mechanisms and biological processes underlying host response to ophidiomycosis (snake fungal disease) inferred from tissue-specific transcriptome analyses. Mol Ecol 2024; 33:e17210. [PMID: 38010927 DOI: 10.1111/mec.17210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/28/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023]
Abstract
Emerging infectious diseases in wildlife species caused by pathogenic fungi are of growing concern, yet crucial knowledge gaps remain for diseases with potentially large impacts. For example, there is detailed knowledge about host pathology and mechanisms underlying response for chytridiomycosis in amphibians and white-nose syndrome in bats, but such information is lacking for other more recently described fungal infections. One such disease is ophidiomycosis, caused by the fungus Ophidiomyces ophidiicola, which has been identified in many species of snakes, yet the biological mechanisms and molecular changes occurring during infection are unknown. To gain this information, we performed a controlled experimental infection in captive Prairie rattlesnakes (Crotalus viridis) with O. ophidiicola at two different temperatures: 20 and 26°C. We then compared liver, kidney, and skin transcriptomes to assess tissue-specific genetic responses to O. ophidiicola infection. Given previous histopathological studies and the fact that snakes are ectotherms, we expected highest fungal activity on skin and a significant impact of temperature on host response. Although we found fungal activity to be localized on skin, most of the differential gene expression occurred in internal tissues. Infected snakes at the lower temperature had the highest host mortality whereas two-thirds of the infected snakes at the higher temperature survived. Our results suggest that ophidiomycosis is likely a systemic disease with long-term effects on host response. Our analysis also identified candidate protein coding genes that are potentially involved in host response, providing genetic tools for studies of host response to ophidiomycosis in natural populations.
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Affiliation(s)
- Samarth Mathur
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| | - Ellen Haynes
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, USA
| | - Matthew C Allender
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Brookfield Zoo, Chicago Zoological Society, Brookfield, Illinois, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
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Hammond LR, White ML, Eswara PJ. Probing Bacterial Cell Division and Cell Envelope Biogenesis with Live-Cell Fluorescence Microscopy. Methods Mol Biol 2024; 2727:205-214. [PMID: 37815719 DOI: 10.1007/978-1-0716-3491-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The development of advanced microscopy techniques has ushered in a new era of research as it helps understand biological processes on a deeper, mechanistic, and molecular level like never before. Live-cell fluorescence microscopy has importantly allowed us to visualize subcellular protein localization and incorporation of various fluorophores compatible with living cells in real time. As such, this technique offers valuable insights at the single-cell level and enables us to monitor phenotypic differences that were easily overlooked at a population level. One area of research that has benefited greatly from these advances is the study of the bacterial cell envelope biogenesis and cell division process. In this report, we provide detailed protocols, optimized in our lab, for imaging these processes in the Gram-positive organisms Bacillus subtilis and Staphylococcus aureus.
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Affiliation(s)
- Lauren R Hammond
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
| | - Maria L White
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
| | - Prahathees J Eswara
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA.
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Morabia A. Public Health Workforce: Retention, Enumeration, and Safety. Am J Public Health 2024; 114:42-43. [PMID: 38091562 PMCID: PMC10726925 DOI: 10.2105/ajph.2023.307524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2023] [Indexed: 12/18/2023]
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Zhang H, Li M, Mo L, Luo J, Shen Q, Quan W. Association between Western Dietary Patterns, Typical Food Groups, and Behavioral Health Disorders: An Updated Systematic Review and Meta-Analysis of Observational Studies. Nutrients 2023; 16:125. [PMID: 38201955 PMCID: PMC10780533 DOI: 10.3390/nu16010125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/07/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Western dietary patterns (WDP) and typical food groups may play a major role in the risk of behavioral health disorders. Nevertheless, the relationships between WDP, common food categories, and mental health disorders lack consistency and remain incompletely understood in relation to potential mechanisms. Therefore, the objective of the present study was conducted to synthesize available evidence linking WDP and typical food groups to these outcomes. Web of Science, PubMed, EMBASE, and MEDLINE were searched up to August 2023. Random effect meta-analyses were performed to obtain pooled odds ratio and the relative risk for the prevalence of outcomes and the incidence of outcomes, respectively. A total of 54 articles were included. WDP was associated with increased risk of both depression (1.19; 95% CI: 1.06-1.32) and depressive symptoms (1.20; 95% CI: 1.08-1.34). Except for high-fat dairy products, food groups are associated with an increased risk of anxiety, depression, and depressive symptoms. This review presents evidence to further understand the relationship between WDP, typical food groups, and the incidence of behavioral health disorders, and more randomized controlled trials and cohort studies are urgently required to confirm these findings and elucidate potential mechanisms.
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Affiliation(s)
- Huang Zhang
- School of Food Science and Bioengineering, Henan University of Animal Husbandry and Economy, No. 6, Longzihu North Road, Zhengzhou 450046, China;
| | - Maiquan Li
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.L.); (L.M.); (J.L.)
| | - Lan Mo
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.L.); (L.M.); (J.L.)
| | - Jie Luo
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.L.); (L.M.); (J.L.)
| | - Qingwu Shen
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.L.); (L.M.); (J.L.)
| | - Wei Quan
- School of Food Science and Bioengineering, Henan University of Animal Husbandry and Economy, No. 6, Longzihu North Road, Zhengzhou 450046, China;
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China; (M.L.); (L.M.); (J.L.)
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Zakaria MN, Salim R, Abdul Wahat NH, Md Daud MK, Wan Mohamad WN. Cervical vestibular evoked myogenic potential (cVEMP) findings in adults with sensorineural hearing loss (SNHL): comparisons between 500 Hz tone burst and narrowband CE-Chirp stimuli. Sci Rep 2023; 13:22842. [PMID: 38129442 PMCID: PMC10739870 DOI: 10.1038/s41598-023-48810-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
There has been a growing interest in studying the usefulness of chirp stimuli in recording cervical vestibular evoked myogenic potential (cVEMP) waveforms. Nevertheless, the study outcomes are debatable and require verification. In view of this, the aim of the present study was to compare cVEMP results when elicited by 500 Hz tone burst and narrowband (NB) CE-Chirp stimuli in adults with sensorineural hearing loss (SNHL). Fifty adults with bilateral SNHL (aged 20-65 years) underwent the cVEMP testing based on the established protocol. The 500 Hz tone burst and NB CE-Chirp (centred at 500 Hz) stimuli were presented to each ear at an intensity level of 120.5 dB peSPL. P1 latency, N1 latency, and P1-N1 amplitude values were analysed accordingly. The NB CE-Chirp stimulus produced significantly shorter P1 and N1 latencies (p < 0.001) with large effect sizes (d > 0.80). In contrast, both stimuli elicited cVEMP responses with P1-N1 amplitude values that were not statistically different from one another (p = 0.157, d = 0.15). Additionally, age and hearing level were found to be significantly correlated (r = 0.56, p < 0.001), as were age and cVEMP amplitude for each stimulus (p < 0.001). To conclude, since both stimuli were presented at an equivalent intensity level (in dB peSPL), the shorter P1 and N1 latencies of cVEMP produced by the NB CE-Chirp stimulus (centred at 500 Hz) were unlikely due to enhanced saccular stimulation. Another more sensible reason is the temporal adjustment of the chirp stimulus.
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Affiliation(s)
- Mohd Normani Zakaria
- Audiology Programme, School of Health Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Rosdan Salim
- Department of Otorhinolaryngology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Nor Haniza Abdul Wahat
- Centre for Rehabilitation and Special Needs, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, 50300, Kuala Lumpur, Malaysia
| | - Mohd Khairi Md Daud
- Department of Otorhinolaryngology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Wan Najibah Wan Mohamad
- Audiology Programme, School of Health Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
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Liu J, Du C, Huang W, Lei Y. Injectable smart stimuli-responsive hydrogels: pioneering advancements in biomedical applications. Biomater Sci 2023; 12:8-56. [PMID: 37969066 DOI: 10.1039/d3bm01352a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Hydrogels have established their significance as prominent biomaterials within the realm of biomedical research. However, injectable hydrogels have garnered greater attention compared with their conventional counterparts due to their excellent minimally invasive nature and adaptive behavior post-injection. With the rapid advancement of emerging chemistry and deepened understanding of biological processes, contemporary injectable hydrogels have been endowed with an "intelligent" capacity to respond to various endogenous/exogenous stimuli (such as temperature, pH, light and magnetic field). This innovation has spearheaded revolutionary transformations across fields such as tissue engineering repair, controlled drug delivery, disease-responsive therapies, and beyond. In this review, we comprehensively expound upon the raw materials (including natural and synthetic materials) and injectable principles of these advanced hydrogels, concurrently providing a detailed discussion of the prevalent strategies for conferring stimulus responsiveness. Finally, we elucidate the latest applications of these injectable "smart" stimuli-responsive hydrogels in the biomedical domain, offering insights into their prospects.
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Affiliation(s)
- Jiacheng Liu
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
| | - Chengcheng Du
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
| | - Wei Huang
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
| | - Yiting Lei
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
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Ahmad SF, Valente GT, Martins C. Response to correspondence on "B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes". BMC Genomics 2023; 24:779. [PMID: 38105226 PMCID: PMC10726491 DOI: 10.1186/s12864-023-09881-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023] Open
Affiliation(s)
- Syed F Ahmad
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, 18618-689, SP, Brazil
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Guilherme T Valente
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, 18618-689, SP, Brazil
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, 18618-689, SP, Brazil.
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Mohammad Nezhady MA, Modaresinejad M, Zia A, Chemtob S. Versatile lactate signaling via HCAR1: a multifaceted GPCR involved in many biological processes. Am J Physiol Cell Physiol 2023; 325:C1502-C1515. [PMID: 37899751 DOI: 10.1152/ajpcell.00346.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/31/2023]
Abstract
G-coupled protein receptors (GPCRs) are the ultimate refuge of pharmacology and medicine as more than 40% of all marketed drugs are directly targeting these receptors. Through cell surface expression, they are at the forefront of cellular communication with the outside world. Metabolites among the conveyors of this communication are becoming more prominent with the recognition of them as ligands for GPCRs. HCAR1 is a GPCR conveyor of lactate. It is a class A GPCR coupled to Gαi which reduces cellular cAMP along with the downstream Gβγ signaling. It was first found to inhibit lipolysis, and lately has been implicated in diverse cellular processes, including neural activities, angiogenesis, inflammation, vision, cardiovascular function, stem cell proliferation, and involved in promoting pathogenesis for different conditions, such as cancer. Other than signaling from the plasma membrane, HCAR1 shows nuclear localization with different location-biased activities therein. Although different functions for HCAR1 are being discovered, its cell and molecular mechanisms are yet ill understood. Here, we provide a comprehensive review on HCAR1, which covers the literature on the subject, and discusses its importance and relevance in various biological phenomena.
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Affiliation(s)
- Mohammad Ali Mohammad Nezhady
- Molecular Biology Program, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
- Research Center of Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Monir Modaresinejad
- Research Center of Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
- Biomedical Sciences Program, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Aliabbas Zia
- Research Center of Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
- Department of Pharmacology, Université de Montréal, Montreal, Quebec, Canada
| | - Sylvain Chemtob
- Molecular Biology Program, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
- Research Center of Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
- Department of Pharmacology, Université de Montréal, Montreal, Quebec, Canada
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41
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Bacete L, Mélida H. Dynamics and mechanics of plant cell walls: insights into plant growth, defence, and stress response. Plant Mol Biol 2023; 113:329-330. [PMID: 38108951 DOI: 10.1007/s11103-023-01395-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Affiliation(s)
- Laura Bacete
- Institute for Biology, Faculty of Natural Sciences, Norwegian University of Science and Technology, 5 Høgskoleringen, Trondheim, 7491, Norway.
- Department of Plant Physiology, Umeå Plant Science Centre (UPSC), Umeå University, Umeå, 901 87, Sweden.
| | - Hugo Mélida
- Área de Fisiología Vegetal, Departamento de Ingeniería y Ciencias Agrarias, Universidad de León, León, Spain.
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Chen XZ, Bai RX, Qin FY, Peng HJ, Ren JF, Hu L, Li YD, He C. Phosphoproteomic Analysis Reveals the Predominating Cellular Processes and the Involved Key Phosphoproteins Essential for the Proliferation of Toxoplasma gondii. Acta Parasitol 2023; 68:820-831. [PMID: 37821727 DOI: 10.1007/s11686-023-00720-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/04/2023] [Indexed: 10/13/2023]
Abstract
PURPOSE To explore the essential roles of phosphorylation in mediating the proliferation of T. gondii in its cell lytic life. METHODS We profiled the phosphoproteome data of T. gondii residing in HFF cells for 2 h and 6 h, representing the early- and late-stages of proliferation (ESP and LSP) within its first generation of division. RESULTS We identified 70 phosphoproteins, among which 8 phosphoproteins were quantified with the phosphorylation level significantly regulated. While only two of the eight phosphoproteins, GRA7 and TGGT1_242070, were significantly down-regulated at the transcriptional level in the group of LSP vs. ESP. Moreover, GO terms correlated with host membrane component were significantly enriched in the category of cellular component, suggesting phosphoprotein played important roles in acquiring essential substance from host cell via manipulating host membrane. Further GO analysis in the categories of molecular function and biological process and pathway analysis revealed that the cellular processes of glucose and lipid metabolism were regulated by T. gondii phosphoproteins such as PMCAA1, LIPIN, Pyk1 and ALD. Additionally, several phosphoproteins were enriched at the central nodes in the protein-protein interaction network, which may have essential roles in T. gondii proliferation including GAP45, MLC1, fructose-1,6-bisphosphate aldolase, GRAs and so on. CONCLUSION This study revealed the main cellular processes and key phosphoproteins crucial for the intracellular proliferation of T. gondii, which would provide clues to explore the roles of phosphorylation in regulating the development of tachyzoites and new insight into the mechanism of T. gondii development in vitro.
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Affiliation(s)
- Xin-Zhu Chen
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu Province, China
| | - Rui-Xue Bai
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu Province, China
| | - Fei-Yu Qin
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu Province, China
| | - Hong-Juan Peng
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jin-Feng Ren
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu Province, China
| | - Lang Hu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu Province, China
| | - Yu-di Li
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu Province, China
| | - Cheng He
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu Province, China.
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Vaz-Rodrigues R, Mazuecos L, Villar M, Contreras M, Artigas-Jerónimo S, González-García A, Gortázar C, de la Fuente J. Multi-omics analysis of zebrafish response to tick saliva reveals biological processes associated with alpha-Gal syndrome. Biomed Pharmacother 2023; 168:115829. [PMID: 37922649 DOI: 10.1016/j.biopha.2023.115829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/17/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023] Open
Abstract
The alpha-Gal syndrome (AGS) is a tick-borne allergy. A multi-omics approach was used to determine the effect of tick saliva and mammalian meat consumption on zebrafish gut transcriptome and proteome. Bioinformatics analysis using R software was focused on significant biological and metabolic pathway changes associated with AGS. Ortholog mapping identified highly concordant human ortholog genes for the detection of disease-enriched pathways. Tick saliva treatment increased zebrafish mortality, incidence of hemorrhagic type allergic reactions and changes in behavior and feeding patterns. Transcriptomics analysis showed downregulation of biological and metabolic pathways correlated with anti-alpha-Gal IgE and allergic reactions to tick saliva affecting blood circulation, cardiac and vascular smooth muscle contraction, behavior and sensory perception. Disease enrichment analysis revealed downregulated orthologous genes associated with human disorders affecting nervous, musculoskeletal, and cardiovascular systems. Proteomics analysis revealed suppression of pathways associated with immune system production of reactive oxygen species and cardiac muscle contraction. Underrepresented proteins were mainly linked to nervous and metabolic human disorders. Multi-omics data revealed inhibition of pathways associated with adrenergic signaling in cardiomyocytes, and heart and muscle contraction. Results identify tick saliva-related biological pathways supporting multisystemic organ involvement and linking α-Gal sensitization with other illnesses for the identification of potential disease biomarkers.
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Affiliation(s)
- Rita Vaz-Rodrigues
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain
| | - Lorena Mazuecos
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain
| | - Margarita Villar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain; Biochemistry Section, Faculty of Science and Chemical Technologies, University of Castilla-La Mancha, 13071 Ciudad Real, Spain
| | - Marinela Contreras
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain
| | - Sara Artigas-Jerónimo
- Biochemistry Section, Faculty of Science and Chemical Technologies, University of Castilla-La Mancha, 13071 Ciudad Real, Spain
| | - Almudena González-García
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain
| | - Christian Gortázar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo 12, 13005 Ciudad Real, Spain; Department of Veterinary Pathobiology, Centre for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
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Konstantinidis I, Sætrom P, Brieuc S, Jakobsen KS, Liedtke H, Pohlmann C, Tsoulia T, Fernandes JMO. DNA hydroxymethylation differences underlie phenotypic divergence of somatic growth in Nile tilapia reared in common garden. Epigenetics 2023; 18:2282323. [PMID: 38010265 PMCID: PMC10732659 DOI: 10.1080/15592294.2023.2282323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023] Open
Abstract
Phenotypic plasticity of metabolism and growth are essential for adaptation to new environmental conditions, such as those experienced during domestication. Epigenetic regulation plays a key role in this process but the underlying mechanisms are poorly understood, especially in the case of hydroxymethylation. Using reduced representation 5-hydroxymethylcytosine profiling, we compared the liver hydroxymethylomes in full-sib Nile tilapia with distinct growth rates (3.8-fold difference) and demonstrated that DNA hydroxymethylation is strongly associated with phenotypic divergence of somatic growth during the early stages of domestication. The 2677 differentially hydroxymethylated cytosines between fast- and slow-growing fish were enriched within gene bodies (79%), indicating a pertinent role in transcriptional regulation. Moreover, they were found in genes involved in biological processes related to skeletal system and muscle structure development, and there was a positive association between somatic growth and 5hmC levels in genes coding for growth factors, kinases and receptors linked to myogenesis. Single nucleotide polymorphism analysis revealed no genetic differentiation between fast- and slow-growing fish. In addition to unveiling a new link between DNA hydroxymethylation and epigenetic regulation of growth in fish during the initial stages of domestication, this study suggests that epimarkers may be applied in selective breeding programmes for superior phenotypes.
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Affiliation(s)
| | - Pål Sætrom
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Computer Science, Norwegian University of Science and Technology, Trondheim, Norway
- Bioinformatics core facility-BioCore, Norwegian University of Science and Technology, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - S.O. Brieuc
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S. Jakobsen
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Hannes Liedtke
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Caroline Pohlmann
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Thomais Tsoulia
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Liu K, Qi A, Ru W, Jiang X, Cao H, Lan X, Huang Y, Lei C, Sun X, Chen H. Insertion/deletions within the bovine FoxO1 gene and their association analysis with growth traits in three Chinese cattle breeds. Anim Biotechnol 2023; 34:2051-2058. [PMID: 35491893 DOI: 10.1080/10495398.2022.2068024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
FOXO1 (FKHR) gene, as a transcription factor, plays a vital role in animal growth and development, participating in many biological processes. The aim of this study was to ascertain Insertion/deletions (Indels) polymorphism within bovine FoxO1 gene in 679 Chinese adult cows and associate them with stature traits. Two Indels (named as Indel-3 and Indel-4, recorded as rs383545622 and rs525318770 in NCBI, respectively) were successfully genotyped by the Once PCR method, which was reliable, rapid and cost effective for simultaneous detection of two or more Indels. Indel-3 and Indel-4 were located at the second intron. All four different haplotypes (H1: D3D4, H2: I3D4, H3: D3I4, H4: I3I4) could be identified, and the D (del-) allele, DD (del-/del-) genotype and D3D4 haplotype retained the highest frequency. However, individuals with DI (D3I3, D4I4 or H1H4/H2H3 genotype) showed significantly better phenotypic traits than those with the other genotypes in Nanyang cattle, showing a hybrid vigor. The results implied that this DI genotype can be applied to early selective breeding to improve the productivity of Nanyang cattle. Our results suggested that these two Indels within the bovine FoxO1 gene might be used as genetic markers for marker-assisted selection (MAS) in cattle breeding and genetics.
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Affiliation(s)
- Kunpeng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ao Qi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wenxiu Ru
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaojun Jiang
- Agriculture and Animal Husbandry Fine Seed Breeding Farm of Shaanxi Province, Fufeng, China
| | - Hui Cao
- Shaanxi Kingbull Livestock Co., LTD, Yangling, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiuzhu Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Wang Y, Mao J, Fan Z, Hang Y, Tang A, Tian Y, Wang X, Hao Z, Han B, Ding J, Chang Y. Transcriptome analysis reveals core lncRNA-mRNA networks regulating melanization and biomineralization in Patinopecten yessoensis shell-infested by Polydora. BMC Genomics 2023; 24:723. [PMID: 38031026 PMCID: PMC10687851 DOI: 10.1186/s12864-023-09837-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Patinopecten yessoensis, a large and old molluscan group, has been one of the most important aquaculture shellfish in Asian countries because of its high economic value. However, the aquaculture of the species has recently been seriously affected by the frequent outbreaks of Polydora disease, causing great economic losses. Long non-coding RNAs (lncRNAs) exhibit exhibit crucial effects on diverse biological processes, but still remain poorly studied in scallops, limiting our understanding of the molecular regulatory mechanism of P. yessoensis in response to Polydora infestation. RESULTS In this study, a high-throughput transcriptome analysis was conducted in the mantles of healthy and Polydora-infected P. yessoensis by RNA sequencing. A total of 19,133 lncRNAs with 2,203 known and 16,930 novel were identified. The genomic characterizations of lncRNAs showed shorter sequence and open reading frame (ORF) length, fewer number of exons and lower expression levels in comparison with mRNAs. There were separately 2280 and 1636 differentially expressed mRNAs and lncRNAs (DEGs and DELs) detected in diseased individuals. The target genes of DELs were determined by both co-location and co-expression analyses. Functional enrichment analysis revealed that DEGs involved in melanization and biomineralization were significantly upregulated; further, obviously increased melanin granules were observed in epithelial cells of the edge mantle in diseased scallops by histological and TEM study, indicating the crucial role of melanizaiton and biomineralization in P. yessoensis to resist against Polydora infestation. Moreover, many key genes, such as Tyrs, Frizzled, Wnts, calmodulins, Pifs, perlucin, laccase, shell matrix protein, mucins and chitins, were targeted by DELs. Finally, a core lncRNA-mRNA interactive network involved in melanization and biomineralization was constructed and validated by qRT-PCR. CONCLUSIONS This work provides valuable resources for studies of lncRNAs in scallops, and adds a new insight into the molecular regulatory mechanisms of P. yessoensis defending against Polydora infestation, which will contribute to Polydora disease control and breeding of disease-resistant varieties in molluscs.
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Affiliation(s)
- Yiying Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Junxia Mao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.
| | - Zhiyue Fan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yunna Hang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - AnQi Tang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Ying Tian
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Xubo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Zhenlin Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Bing Han
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
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47
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Zhou Y, Luo K, Liang L, Chen M, He X. A new Bayesian factor analysis method improves detection of genes and biological processes affected by perturbations in single-cell CRISPR screening. Nat Methods 2023; 20:1693-1703. [PMID: 37770710 PMCID: PMC10630124 DOI: 10.1038/s41592-023-02017-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/18/2023] [Indexed: 09/30/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) screening coupled with single-cell RNA sequencing has emerged as a powerful tool to characterize the effects of genetic perturbations on the whole transcriptome at a single-cell level. However, due to its sparsity and complex structure, analysis of single-cell CRISPR screening data is challenging. In particular, standard differential expression analysis methods are often underpowered to detect genes affected by CRISPR perturbations. We developed a statistical method for such data, called guided sparse factor analysis (GSFA). GSFA infers latent factors that represent coregulated genes or gene modules; by borrowing information from these factors, it infers the effects of genetic perturbations on individual genes. We demonstrated through extensive simulation studies that GSFA detects perturbation effects with much higher power than state-of-the-art methods. Using single-cell CRISPR data from human CD8+ T cells and neural progenitor cells, we showed that GSFA identified biologically relevant gene modules and specific genes affected by CRISPR perturbations, many of which were missed by existing methods, providing new insights into the functions of genes involved in T cell activation and neurodevelopment.
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Affiliation(s)
- Yifan Zhou
- Graduate Program of Biophysical Sciences, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Lifan Liang
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Mengjie Chen
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Department of Medicine, University of Chicago, Chicago, IL, USA.
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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48
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Yuan R, Hascup E, Hascup K, Bartke A. Relationships among Development, Growth, Body Size, Reproduction, Aging, and Longevity - Trade-Offs and Pace-Of-Life. Biochemistry (Mosc) 2023; 88:1692-1703. [PMID: 38105191 PMCID: PMC10792675 DOI: 10.1134/s0006297923110020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 12/19/2023]
Abstract
Relationships of growth, metabolism, reproduction, and body size to the biological process of aging and longevity have been studied for decades and various unifying "theories of aging" have been proposed to account for the observed associations. In general, fast development, early sexual maturation leading to early reproductive effort, as well as production of many offspring, have been linked to shorter lifespans. The relationship of adult body size to longevity includes a remarkable contrast between the positive correlation in comparisons between different species and the negative correlation seen in comparisons of individuals within the same species. We now propose that longevity and presumably also the rate of aging are related to the "pace-of-life." A slow pace-of-life including slow growth, late sexual maturation, and a small number of offspring, predicts slow aging and long life. The fast pace of life (rapid growth, early sexual maturation, and major reproductive effort) is associated with faster aging and shorter life, presumably due to underlying trade-offs. The proposed relationships between the pace-of-life and longevity apply to both inter- and intra-species comparisons as well as to dietary, genetic, and pharmacological interventions that extend life and to evidence for early life programming of the trajectory of aging. Although available evidence suggests the causality of at least some of these associations, much further work will be needed to verify this interpretation and to identify mechanisms that are responsible.
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Affiliation(s)
- Rong Yuan
- Southern Illinois University School of Medicine, Department of Internal Medicine, Springfield, IL 19628, USA.
| | - Erin Hascup
- Southern Illinois University School of Medicine, Department of Medical, Microbial, Cellular Immunology and Biology, Springfield, IL 19628, USA.
| | - Kevin Hascup
- Southern Illinois University School of Medicine, Department of Medical, Microbial, Cellular Immunology and Biology, Springfield, IL 19628, USA.
- Department of Neurology, Dale and Deborah Smith Center for Alzheimer's Research and Treatment, Neuroscience Institute, Southern Illinois University School of Medicine, Springfield, Illinois, USA
| | - Andrzej Bartke
- Southern Illinois University School of Medicine, Department of Internal Medicine, Springfield, IL 19628, USA.
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49
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Wang Z, Liang W, Yan D, Tian H, Dong B, Zhao W, Chang G, Chen G. Identification of genes related to growth traits from transcriptome profiles of duck breast muscle tissue. Anim Biotechnol 2023; 34:1239-1246. [PMID: 34965198 DOI: 10.1080/10495398.2021.2018333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The growth and development of duck skeletal muscle is an important economic trait that is genetically regulated. The internal mechanism underlying the regulation of skeletal muscle growth and development in ducks remains unclear. The purpose of this study was to identify candidate genes related to the growth of duck skeletal muscle. RNA-sequencing technology was used to compare the transcriptome of duck breast muscles in an F2 population with the high breast muscle rate (HB) and the low breast muscle rate (LB). A total of 14,522 genes were confirmed to be expressed in the breast muscle, and 173 differentially expressed genes (DEGs) were identified between the HB and LB groups. Functional analysis showed that these DEGs were mainly involved in biological processes and pathways of fat metabolism and muscle growth, especially the FABP3 and MYL4 involved in the PPAR signaling pathway and cardiac muscle contraction pathway. These findings deepened our understanding of the molecular mechanisms involved in muscle growth in ducks and provided a theoretical basis for improving duck production and breeding of ducks.
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Affiliation(s)
- Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
| | - Wenshuang Liang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
| | - Dan Yan
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
| | - Huiyue Tian
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
| | - Bingqiang Dong
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
| | - Wenming Zhao
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
| | - Guobin Chang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
| | - Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
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50
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Ogawa Y, Lim BC, George S, Oses-Prieto JA, Rasband JM, Eshed-Eisenbach Y, Hamdan H, Nair S, Boato F, Peles E, Burlingame AL, Van Aelst L, Rasband MN. Antibody-directed extracellular proximity biotinylation reveals that Contactin-1 regulates axo-axonic innervation of axon initial segments. Nat Commun 2023; 14:6797. [PMID: 37884508 PMCID: PMC10603070 DOI: 10.1038/s41467-023-42273-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
Axon initial segment (AIS) cell surface proteins mediate key biological processes in neurons including action potential initiation and axo-axonic synapse formation. However, few AIS cell surface proteins have been identified. Here, we use antibody-directed proximity biotinylation to define the cell surface proteins in close proximity to the AIS cell adhesion molecule Neurofascin. To determine the distributions of the identified proteins, we use CRISPR-mediated genome editing for insertion of epitope tags in the endogenous proteins. We identify Contactin-1 (Cntn1) as an AIS cell surface protein. Cntn1 is enriched at the AIS through interactions with Neurofascin and NrCAM. We further show that Cntn1 contributes to assembly of the AIS extracellular matrix, and regulates AIS axo-axonic innervation by inhibitory basket cells in the cerebellum and inhibitory chandelier cells in the cortex.
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Affiliation(s)
- Yuki Ogawa
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Brian C Lim
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Shanu George
- Division of Neuroscience, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Joshua M Rasband
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Yael Eshed-Eisenbach
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hamdan Hamdan
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Physiology and Immunology, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Supna Nair
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Francesco Boato
- Division of Neuroscience, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Elior Peles
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Linda Van Aelst
- Division of Neuroscience, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Matthew N Rasband
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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