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Liu X, Yao X, Chen L. Expanding roles of circRNAs in cardiovascular diseases. Noncoding RNA Res 2024; 9:429-436. [PMID: 38511061 PMCID: PMC10950605 DOI: 10.1016/j.ncrna.2024.02.001] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 03/22/2024] Open
Abstract
CircRNAs are a class of single-stranded RNAs characterized by covalently looped structures. Emerging advances have promoted our understanding of circRNA biogenesis, nuclear export, biological functions, and functional mechanisms. Roles of circRNAs in diverse diseases have been increasingly recognized in the past decade, with novel approaches in bioinformatics analysis and new strategies in modulating circRNA levels, which have made circRNAs the hot spot for therapeutic applications. Moreover, due to the intrinsic features of circRNAs such as high stability, conservation, and tissue-/stage-specific expression, circRNAs are believed to be promising prognostic and diagnostic markers for diseases. Aiming cardiovascular disease (CVD), one of the leading causes of mortality worldwide, we briefly summarize the current understanding of circRNAs, provide the recent progress in circRNA functions and functional mechanisms in CVD, and discuss the future perspectives both in circRNA research and therapeutics based on existing knowledge.
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Affiliation(s)
- Xu Liu
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Xuelin Yao
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Liang Chen
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
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Zhang W, Li H, Li Q, Wang Z, Zeng W, Yin H, Qi K, Zou Y, Hu J, Huang B, Gu P, Qiao X, Zhang S. Genome-wide identification, comparative analysis and functional roles in flavonoid biosynthesis of cytochrome P450 superfamily in pear (Pyrus spp.). BMC Genom Data 2023; 24:58. [PMID: 37789271 PMCID: PMC10548706 DOI: 10.1186/s12863-023-01159-w] [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: 05/24/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND The cytochrome P450 (CYP) superfamily is the largest enzyme metabolism family in plants identified to date, and it is involved in many biological processes, including secondary metabolite biosynthesis, hormone metabolism and stress resistance. However, the P450 gene superfamily has not been well studied in pear (Pyrus spp.). RESULTS Here, the comprehensive identification and a comparative analysis of P450 superfamily members were conducted in cultivated and wild pear genomes. In total, 338, 299 and 419 P450 genes were identified in Chinese white pear, European pear and the wild pear, respectively. Based on the phylogenetic analyses, pear P450 genes were divided into ten clans, comprising 48 families. The motif and gene structure analyses further supported this classification. The expansion of the pear P450 gene family was attributed to whole-genome and single-gene duplication events. Several P450 gene clusters were detected, which have resulted from tandem and proximal duplications. Purifying selection was the major force imposed on the long-term evolution of P450 genes. Gene dosage balance, subfunctionalization and neofunctionalization jointly drove the retention and functional diversification of P450 gene pairs. Based on the association analysis between transcriptome expression profiles and flavonoid content during fruit development, three candidate genes were identified as being closely associated with the flavonoid biosynthesis, and the expression of one gene was further verified using qRT-PCR and its function was validated through transient transformation in pear fruit. CONCLUSIONS The study results provide insights into the evolution and biological functions of P450 genes in pear.
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Affiliation(s)
- Wei Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongxiang Li
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qionghou Li
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zewen Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiwei Zeng
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Yin
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaijie Qi
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Zou
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Hu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Baisha Huang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Gu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin Qiao
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Chen P, Hu J, Han X, Chen Y. Advances in the functional roles of N6-methyladenosine modification in cancer progression: mechanisms and clinical implications. Mol Biol Rep 2022. [PMID: 35025029 DOI: 10.1007/s11033-022-07126-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/04/2022] [Indexed: 12/24/2022]
Abstract
N6-methyladenosine (m6A), the methylation targeting the N6 position of adenosine, is the most common internal modification of mRNA in eukaryotes. Considering the roles of m6A in regulating gene expression, the investigation of m6A roles in the biological processes including cell renewal, differentiation, apoptosis, and invasion of cancer cells has become a hot research topic. There are three kinds of protein involved in m6A regulation. The methyltransferases and demethylases cooperatively regulate the m6A levels, while the m6A reading proteins recognize the m6A sites and mediate multiple m6A-dependent biological functions including mRNA splicing, transfer, translation, and degradation. At present, a large number of studies have found that the changes of m6A levels in tumor cells play a very important role in the occurrence and development of tumors, as well as metastasis and invasion of tumor cells. This review summarizes the different roles of m6A modification in the occurrence and development of various cancers, and discusses the possibility of choosing the m6A related proteins as potential therapeutic targets.
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Ohwada K, Yamawo A. Functional roles of ants in a temperate grassland. Naturwissenschaften 2021; 108:56. [PMID: 34665328 DOI: 10.1007/s00114-021-01767-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 10/20/2022]
Abstract
Ants in temperate grasslands are consumers and ecosystem engineers, influencing biodiversity and potentially grassland productivity. However, the effects of ant exclusion or suppression on resource removal and the biological community in temperate grasslands have yet to be fully explored. We conducted ant-suppression experiments and evaluated the effects of ants on ground-dwelling arthropod communities in the field by using pitfall and bait traps. In the laboratory, we evaluated the effects of ants on the ant-attended aphid Aphis rumicis, which is a honeydew resource for ants, and the slug (Deroceras laeve), an aphid predator. Aboveground arthropod communities were not affected by the ant-suppression treatment. However, slugs (D. laeve and Ambigolimax valentianus) visited bait resources more frequently in the ant-suppression treatment area. In the ant-absence condition in the laboratory experiment, there were fewer aphids on the plants compared to the ant-presence condition owing to predation by D. laeve. Our results suggest that ant abundance in temperate grasslands influences the predation activity of slugs toward honeydew sources such as aphids.
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Affiliation(s)
- Kouichi Ohwada
- Department of Biological Sciences, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan
| | - Akira Yamawo
- Department of Biological Sciences, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori, 036-8561, Japan.
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Li S, Wei X, He J, Cao Q, Du D, Zhan X, Zeng Y, Yuan S, Sun L. The comprehensive landscape of miR-34a in cancer research. Cancer Metastasis Rev 2021; 40:925-948. [PMID: 33959850 DOI: 10.1007/s10555-021-09973-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 12/17/2020] [Accepted: 04/29/2021] [Indexed: 12/12/2022]
Abstract
MicroRNA-34 (miR-34) plays central roles in human diseases, especially cancers. Inactivation of miR-34 is detected in cancer cell lines and tumor tissues versus normal controls, implying its potential tumor-suppressive effect. Clinically, miR-34 has been identified as promising prognostic indicators for various cancers. In fact, members of the miR-34 family, especially miR-34a, have been convincingly proved to affect almost the whole cancer progression process. Here, a total of 512 (miR-34a, 10/21), 85 (miR-34b, 10/16), and 114 (miR-34c, 10/14) putative targets of miR-34a/b/c are predicted by at least ten miRNA databases, respectively. These targets are further analyzed in gene ontology (GO), KEGG pathway, and the Reactome pathway dataset. The results suggest their involvement in the regulation of signal transduction, macromolecule metabolism, and protein modification. Also, the targets are implicated in critical signaling pathways, such as MAPK, Notch, Wnt, PI3K/AKT, p53, and Ras, as well as apoptosis, cell cycle, and EMT-related pathways. Moreover, the upstream regulators of miR-34a, mainly including transcription factors (TFs), lncRNAs, and DNA methylation, will be summarized. Meanwhile, the potential TF upstream of miR-34a/b/c will be predicted by PROMO, JASPAR, Animal TFDB 3.0, and GeneCard databases. Notably, miR-34a is an attractive target for certain cancers. In fact, miR-34a-based systemic delivery combined with chemotherapy or radiotherapy can more effectively control tumor progression. Collectively, this review will provide a panorama for miR-34a in cancer research.
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Affiliation(s)
- Sijing Li
- New Drug Screening Center, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiaohui Wei
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Jinyong He
- New Drug Screening Center, China Pharmaceutical University, Nanjing, 210009, China
- China Cell-Gene Therapy Translational Medicine Research Center, Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
- School of Medicine, Sun Yat-sen University, Shenzhen, 518107, China
| | - Quanquan Cao
- MARBEC, Université Montpellier, UM-CNRS-IRD-IFREMER, cc 092, Place E. Bataillon, 34095, Montpellier Cedex 05, France
| | - Danyu Du
- New Drug Screening Center, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiaoman Zhan
- New Drug Screening Center, China Pharmaceutical University, Nanjing, 210009, China
| | - Yuqi Zeng
- New Drug Screening Center, China Pharmaceutical University, Nanjing, 210009, China
| | - Shengtao Yuan
- Jiangsu Center for Pharmacodynamics Research and Evaluation, China Pharmaceutical University, Nanjing, 210009, China.
| | - Li Sun
- New Drug Screening Center, China Pharmaceutical University, Nanjing, 210009, China.
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Aburas H, İspirli H, Taylan O, Yilmaz MT, Dertli E. Structural and physicochemical characterisation and antioxidant activity of an α-D-glucan produced by sourdough isolate Weissella cibaria MED17. Int J Biol Macromol 2020; 161:648-55. [PMID: 32512101 DOI: 10.1016/j.ijbiomac.2020.06.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/26/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022]
Abstract
An exopolysaccharide (EPS) producer slimy-mucoid type colony was isolated from sourdough and identified as Weissella cibaria MED17. The 1H and 13C NMR spectra of EPS MED17 demonstrated that this EPS was a dextran type glucan ((1 → 6)-linked α-D-glucose core structure) containing (1 → 3)-linked α-D-glucose branches and proportion of (1 → 6)-linked α-D-glucose units to (1 → 3)-linked α-D-glucose units was 94.3:5.7%. The FTIR analysis also confirmed the (1 → 6)-linked α-D-glucose linkage. A high level of thermal stability was observed for glucan MED17 as no degradation up to 300 °C was observed by TGA and DSC analysis. The XRD analysis of glucan MED17 showed its semi- crystalline nature and its compact sheet-like morphology was observed by SEM analysis. Finally, antioxidant characteristics of glucan MED17 were determined by ABTS and DPPH radical scavenging activity tests that revealed a moderate antioxidant activity of glucan MED17. These findings show potential techno-functional characteristics of glucan MED17.
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Bellamy AS, Svensson O, van den Brink PJ, Gunnarsson J, Tedengren M. Insect community composition and functional roles along a tropical agricultural production gradient. Environ Sci Pollut Res Int 2018; 25:13426-13438. [PMID: 29603106 PMCID: PMC5978824 DOI: 10.1007/s11356-018-1818-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 11/28/2017] [Accepted: 03/19/2018] [Indexed: 05/12/2023]
Abstract
High intensity agricultural production systems are problematic not only for human health and the surrounding environment, but can threaten the provision of ecosystem services on which farm productivity depends. This research investigates the effects of management practices in Costa Rica on on-farm insect diversity, using three different types of banana farm management systems: high-input conventional system, low-input conventional system, and organic system. Insect sampling was done using pitfall and yellow bowl traps, left for a 24-h period at two locations inside the banana farm, at the edge of the farm, and in adjacent forest. All 39,091 individual insects were classified to family level and then morphospecies. Insect species community composition and diversity were compared using multivariate statistics with ordination analysis and Monte Carlo permutation testing, and revealed that each of the management systems were significantly different from each other for both trap types. Insect diversity decreased as management intensity increased. Reduced insect diversity resulted in fewer functional groups and fewer insect families assuming different functions essential to ecosystem health. Organic farms had similar species composition on the farm compared to adjacent forest sites, whereas species composition increasingly differed between farm and forest sites as management intensity increased. We conclude that while organic production has minimal impact on insect biodiversity, even small reductions in management intensity can have a significantly positive impact on on-farm insect biodiversity and functional roles supported.
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Affiliation(s)
- Angelina Sanderson Bellamy
- Sustainable Places Research Institute and School of Planning and Geography, Cardiff University, 33 Park Place, Cardiff, CF10 3BA, Wales.
| | - Ola Svensson
- Department of Ecology, Environment and Botany, Stockholm University, SE-109 61, Stockholm, Sweden
| | - Paul J van den Brink
- Department of Aquatic Ecology and Water Quality Management, Wageningen University, Wageningen University and Research Centre, P.O. Box 47, 6700 AA, Wageningen, The Netherlands
- Alterra, Centre for Water and Climate, Wageningen University and Research Centre, P.O. Box 47, 6700 AA, Wageningen, The Netherlands
| | - Jonas Gunnarsson
- Department of Ecology, Environment and Botany, Stockholm University, SE-109 61, Stockholm, Sweden
| | - Michael Tedengren
- Department of Ecology, Environment and Botany, Stockholm University, SE-109 61, Stockholm, Sweden
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Mao F, Wang B, Xiao Q, Cheng F, Lei T, Guo D. LRIG proteins in glioma: Functional roles, molecular mechanisms, and potential clinical implications. J Neurol Sci 2017; 383:56-60. [PMID: 29246624 DOI: 10.1016/j.jns.2017.10.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/26/2017] [Accepted: 10/17/2017] [Indexed: 12/26/2022]
Abstract
Gliomas are the most common intracranial tumors of the nervous system. These tumors are characterized by unlimited cell proliferation and excessive invasiveness. Despite the advances in diagnostic imaging, microneurosurgical techniques, radiation therapy, and chemotherapy, significant increases in the progression free survival of glioma patients have not been achieved. Improvements in our understanding of the molecular subtypes of gliomas and the underlying alterations in specific signaling pathways may impact both the diagnosis and the treatment strategies for patients with gliomas. Growth factors and their corresponding receptor tyrosine kinases are associated with oncogenesis and development of tumors in numerous human cancer types, including glioma. Leucine-rich repeats and immunoglobulin-like domains (LRIG) are integral membrane proteins which contain three vertebrate members including LRIG1, LRIG2 and LRIG3. They mainly function as regulators of growth factor signaling. Specifically, LRIG1 has been identified as a tumor suppressor in human cancers. In contrast, LRIG2 appears to function as a tumor promoter, while LRIG3 appears to have a function similar to that of LRIG1. In the present review, we summarize the functional roles, molecular mechanisms, and clinical perspectives of LRIG proteins in gliomas and propose that these proteins may be useful in the future as targets for treatment and prognostication in glioma patients.
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Affiliation(s)
- Feng Mao
- Department of Neurosurgery and Sino-German Neuro-Oncology Molecular Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Baofeng Wang
- Department of Neurosurgery and Sino-German Neuro-Oncology Molecular Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qungen Xiao
- Department of Neurosurgery and Sino-German Neuro-Oncology Molecular Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fangling Cheng
- Department of Neurosurgery and Sino-German Neuro-Oncology Molecular Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ting Lei
- Department of Neurosurgery and Sino-German Neuro-Oncology Molecular Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dongsheng Guo
- Department of Neurosurgery and Sino-German Neuro-Oncology Molecular Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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