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Mathew J, Adhia DB, Smith ML, De Ridder D, Mani R. Closed-Loop Infraslow Brain-Computer Interface can Modulate Cortical Activity and Connectivity in Individuals With Chronic Painful Knee Osteoarthritis: A Secondary Analysis of a Randomized Placebo-Controlled Clinical Trial. Clin EEG Neurosci 2024:15500594241264892. [PMID: 39056313 DOI: 10.1177/15500594241264892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Introduction. Chronic pain is a percept due to an imbalance in the activity between sensory-discriminative, motivational-affective, and descending pain-inhibitory brain regions. Evidence suggests that electroencephalography (EEG) infraslow fluctuation neurofeedback (ISF-NF) training can improve clinical outcomes. It is unknown whether such training can induce EEG activity and functional connectivity (FC) changes. A secondary data analysis of a feasibility clinical trial was conducted to determine whether EEG ISF-NF training can significantly alter EEG activity and FC between the targeted cortical regions in people with chronic painful knee osteoarthritis (OA). Methods. A parallel, two-arm, double-blind, randomized, sham-controlled clinical trial was conducted. People with chronic knee pain associated with OA were randomized to receive sham NF training or source-localized ratio ISF-NF training protocol to down-train ISF bands at the somatosensory (SSC), dorsal anterior cingulate (dACC), and uptrain pregenual anterior cingulate cortices (pgACC). Resting state EEG was recorded at baseline and immediate post-training. Results. The source localization mapping demonstrated a reduction (P = .04) in the ISF band activity at the left dorsolateral prefrontal cortex (LdlPFC) in the active NF group. Region of interest analysis yielded significant differences for ISF (P = .008), slow (P = .007), beta (P = .043), and gamma (P = .012) band activities at LdlPFC, dACC, and bilateral SSC. The FC between pgACC and left SSC in the delta band was negatively correlated with pain bothersomeness in the ISF-NF group. Conclusion. The EEG ISF-NF training can modulate EEG activity and connectivity in individuals with chronic painful knee osteoarthritis, and the observed EEG changes correlate with clinical pain measures.
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Affiliation(s)
- Jerin Mathew
- Centre for Health, Activity, and Rehabilitation Research, School of Physiotherapy, University of Otago, Dunedin, New Zealand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Pain@Otago Research Theme, University of Otago, Dunedin, New Zealand
| | - Divya Bharatkumar Adhia
- Pain@Otago Research Theme, University of Otago, Dunedin, New Zealand
- Division of Neurosurgery, Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | | | - Dirk De Ridder
- Pain@Otago Research Theme, University of Otago, Dunedin, New Zealand
- Division of Neurosurgery, Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Ramakrishnan Mani
- Centre for Health, Activity, and Rehabilitation Research, School of Physiotherapy, University of Otago, Dunedin, New Zealand
- Pain@Otago Research Theme, University of Otago, Dunedin, New Zealand
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2
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Ma Y, Li Q, Tang Y, Zhang Z, Liu R, Luo Q, Wang Y, Hu J, Chen Y, Li Z, Zhao C, Ran Y, Mu Y, Li Y, Xu X, Gong Y, He Z, Ba Y, Guo K, Dong K, Li X, Tan W, Zhu Y, Xiang Z, Xu H. The architecture of silk-secreting organs during the final larval stage of silkworms revealed by single-nucleus and spatial transcriptomics. Cell Rep 2024; 43:114460. [PMID: 38996068 DOI: 10.1016/j.celrep.2024.114460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/26/2024] [Accepted: 06/22/2024] [Indexed: 07/14/2024] Open
Abstract
Natural silks are renewable proteins with impressive mechanical properties and biocompatibility that are useful in various fields. However, the cellular and spatial organization of silk-secreting organs remains unclear. Here, we combined single-nucleus and spatially resolved transcriptomics to systematically map the cellular and spatial composition of the silk glands (SGs) of mulberry silkworms late in larval development. This approach allowed us to profile SG cell types and cell state dynamics and identify regulatory networks and cell-cell communication related to efficient silk protein synthesis; key markers were validated via transgenic approaches. Notably, we demonstrated the indispensable role of the ecdysone receptor (ultraspiracle) in regulating endoreplication in SG cells. Our atlas presents the results of spatiotemporal analysis of silk-secreting organ architecture late in larval development; this atlas provides a valuable reference for elucidating the mechanism of efficient silk protein synthesis and developing sustainable products made from natural silk.
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Affiliation(s)
- Yan Ma
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Qingjun Li
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yiyun Tang
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Zhiyong Zhang
- Beijing SeekGene BioSciences Co., Ltd., Beijing 102206, China
| | - Rongpeng Liu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Qin Luo
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yuting Wang
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Jie Hu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yuqin Chen
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Zhiwei Li
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Chen Zhao
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yiting Ran
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yuanyuan Mu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yinghao Li
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Xiaoqing Xu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yuyan Gong
- Beijing SeekGene BioSciences Co., Ltd., Beijing 102206, China
| | - Zihan He
- Beijing SeekGene BioSciences Co., Ltd., Beijing 102206, China
| | - Yongbing Ba
- Shanghai OE Biotech. Co., Ltd., Shanghai 201212, China
| | - Kaiqi Guo
- Shanghai OE Biotech. Co., Ltd., Shanghai 201212, China
| | - Keshu Dong
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Xiao Li
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Wei Tan
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yumeng Zhu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Zhonghuai Xiang
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Hanfu Xu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, China.
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3
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Li B, Wang W, Zhao L, Wu Y, Li X, Yan D, Gao Q, Yan Y, Zhang J, Feng Y, Zheng J, Shu B, Wang J, Wang H, He L, Zhang Y, Pan M, Wang D, Tang BZ, Liao Y. Photothermal therapy of tuberculosis using targeting pre-activated macrophage membrane-coated nanoparticles. NATURE NANOTECHNOLOGY 2024; 19:834-845. [PMID: 38383890 DOI: 10.1038/s41565-024-01618-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024]
Abstract
Conventional antibiotics used for treating tuberculosis (TB) suffer from drug resistance and multiple complications. Here we propose a lesion-pathogen dual-targeting strategy for the management of TB by coating Mycobacterium-stimulated macrophage membranes onto polymeric cores encapsulated with an aggregation-induced emission photothermal agent that is excitable with a 1,064 nm laser. The coated nanoparticles carry specific receptors for Mycobacterium tuberculosis, which enables them to target tuberculous granulomas and internal M. tuberculosis simultaneously. In a mouse model of TB, intravenously injected nanoparticles image individual granulomas in situ in the lungs via signal emission in the near-infrared region IIb, with an imaging resolution much higher than that of clinical computed tomography. With 1,064 nm laser irradiation from outside the thoracic cavity, the photothermal effect generated by these nanoparticles eradicates the targeted M. tuberculosis and alleviates pathological damage and excessive inflammation in the lungs, resulting in a better therapeutic efficacy compared with a combination of first-line antibiotics. This precise photothermal modality that uses dual-targeted imaging in the near-infrared region IIb demonstrates a theranostic strategy for TB management.
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Affiliation(s)
- Bin Li
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital of Southern Medical University, Guangzhou, China
- School of Inspection, Ningxia Medical University, Yinchuan, China
- Institute of Translational Medicine, Department of Clinical Laboratory & Department of Burn Surgery, The First People's Hospital of Foshan, Foshan, China
| | - Wei Wang
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital of Southern Medical University, Guangzhou, China
| | - Lu Zhao
- Institute of Translational Medicine, Department of Clinical Laboratory & Department of Burn Surgery, The First People's Hospital of Foshan, Foshan, China
| | - Yunxia Wu
- Institute of Translational Medicine, Department of Clinical Laboratory & Department of Burn Surgery, The First People's Hospital of Foshan, Foshan, China
| | - Xiaoxue Li
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital of Southern Medical University, Guangzhou, China
| | - Dingyuan Yan
- Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, China
| | - Qiuxia Gao
- Institute of Translational Medicine, Department of Clinical Laboratory & Department of Burn Surgery, The First People's Hospital of Foshan, Foshan, China
| | - Yan Yan
- Department of Critical Care Medicine, Department of Emergency, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jie Zhang
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, Xizang Minzu University, Xianyang, China
| | - Yi Feng
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital of Southern Medical University, Guangzhou, China
| | - Judun Zheng
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital of Southern Medical University, Guangzhou, China
| | - Bowen Shu
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital of Southern Medical University, Guangzhou, China
| | - Jiamei Wang
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital of Southern Medical University, Guangzhou, China
| | - Huanhuan Wang
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital of Southern Medical University, Guangzhou, China
| | - Lingjie He
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital of Southern Medical University, Guangzhou, China
| | - Yunlong Zhang
- Department of Critical Care Medicine, Department of Emergency, Renmin Hospital of Wuhan University, Wuhan, China
| | - Mingliang Pan
- Department of Critical Care Medicine, Department of Emergency, Renmin Hospital of Wuhan University, Wuhan, China
| | - Dong Wang
- Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, China.
| | - Ben Zhong Tang
- Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, China.
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, China.
| | - Yuhui Liao
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital of Southern Medical University, Guangzhou, China.
- School of Inspection, Ningxia Medical University, Yinchuan, China.
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4
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Xing J, Xu H, Zhu M, Zhang Y, Bai M, Zhou X, Liu H, Wang Y. Gas Chromatography-Mass Spectrometry Metabolite Analysis Combined with Transcriptomics Reveals Genes Involved in Wax Biosynthesis in Allium fistulosum L. Int J Mol Sci 2024; 25:6106. [PMID: 38892292 PMCID: PMC11173144 DOI: 10.3390/ijms25116106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Cuticular waxes are essential for protecting plants from various environmental stresses. Allium fistulosum serves as an excellent model for investigating the regulatory mechanisms underlying cuticular wax synthesis with notable epidermal wax characteristics. A combination of gas chromatography-mass spectrometry (GC-MS) metabolite analysis and transcriptomics was used to investigate variations in metabolites and gene expression patterns between the wild type (WT) and glossy mutant type (gl2) of A. fistulosum. The WT surface had a large number of acicular and lamellar waxy crystals, whereas the leaf surface of gl2 was essentially devoid of waxy crystals. And the results revealed a significant decrease in the content of 16-hentriacontanone, the principal component of cuticular wax, in the gl2 mutant. Transcriptomic analysis revealed 3084 differentially expressed genes (DEGs) between WT and gl2. Moreover, we identified 12 genes related to fatty acid or wax synthesis. Among these, 10 DEGs were associated with positive regulation of wax synthesis, whereas 2 genes exhibited negative regulatory functions. Furthermore, two of these genes were identified as key regulators through weighted gene co-expression network analysis. Notably, the promoter region of AfisC5G01838 (AfCER1-LIKE1) exhibited a 258-bp insertion upstream of the coding region in gl2 and decreased the transcription of the AfCER1-LIKE1 gene. This study provided insights into the molecular mechanisms governing cuticular wax synthesis in A. fistulosum, laying the foundation for future breeding strategies.
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Affiliation(s)
- Jiayi Xing
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences (BAAFS), Beijing 100097, China; (J.X.); (H.X.); (M.Z.); (Y.Z.); (M.B.); (X.Z.)
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Crops, Department of Horticulture, Agricultural College, Shihezi University, Shihezi 832003, China
| | - Huanhuan Xu
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences (BAAFS), Beijing 100097, China; (J.X.); (H.X.); (M.Z.); (Y.Z.); (M.B.); (X.Z.)
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingzhao Zhu
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences (BAAFS), Beijing 100097, China; (J.X.); (H.X.); (M.Z.); (Y.Z.); (M.B.); (X.Z.)
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China
| | - Yuchen Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences (BAAFS), Beijing 100097, China; (J.X.); (H.X.); (M.Z.); (Y.Z.); (M.B.); (X.Z.)
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China
| | - Mifeng Bai
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences (BAAFS), Beijing 100097, China; (J.X.); (H.X.); (M.Z.); (Y.Z.); (M.B.); (X.Z.)
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China
| | - Xuyang Zhou
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences (BAAFS), Beijing 100097, China; (J.X.); (H.X.); (M.Z.); (Y.Z.); (M.B.); (X.Z.)
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China
| | - Huiying Liu
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Crops, Department of Horticulture, Agricultural College, Shihezi University, Shihezi 832003, China
| | - Yongqin Wang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences (BAAFS), Beijing 100097, China; (J.X.); (H.X.); (M.Z.); (Y.Z.); (M.B.); (X.Z.)
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China
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Liu Y, Niu J, Ye F, Solberg T, Lu B, Wang C, Nowacki M, Gao S. Dynamic DNA N 6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus. Genome Res 2024; 34:256-271. [PMID: 38471739 PMCID: PMC10984389 DOI: 10.1101/gr.278796.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
The formation of resting cysts commonly found in unicellular eukaryotes is a complex and highly regulated survival strategy against environmental stress that involves drastic physiological and biochemical changes. Although most studies have focused on the morphology and structure of cysts, little is known about the molecular mechanisms that control this process. Recent studies indicate that DNA N 6-adenine methylation (6mA) could be dynamically changing in response to external stimuli; however, its potential role in the regulation of cyst formation remains unknown. We used the ciliate Pseudocohnilembus persalinus, which can be easily induced to form cysts to investigate the dynamic pattern of 6mA in trophonts and cysts. Single-molecule real-time (SMRT) sequencing reveals high levels of 6mA in trophonts that decrease in cysts, along with a conversion of symmetric 6mA to asymmetric 6mA. Further analysis shows that 6mA, a mark of active transcription, is involved in altering the expression of encystment-related genes through changes in 6mA levels and 6mA symmetric-to-asymmetric conversion. Most importantly, we show that reducing 6mA levels by knocking down the DNA 6mA methyltransferase PpAMT1 accelerates cyst formation. Taken together, we characterize the genome-wide 6mA landscape in P. persalinus and provide insights into the role of 6mA in gene regulation under environmental stress in eukaryotes. We propose that 6mA acts as a mark of active transcription to regulate the encystment process along with symmetric-to-asymmetric conversion, providing important information for understanding the molecular response to environmental cues from the perspective of 6mA modification.
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Affiliation(s)
- Yongqiang Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Junhua Niu
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Fei Ye
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Therese Solberg
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
- Department of Molecular Biology, Keio University School of Medicine, 160-8582 Tokyo, Japan
- Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio University, 108-8345 Tokyo, Japan
| | - Borong Lu
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Chundi Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Shan Gao
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
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6
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Zonneveld KLM, Cox AD, Asaro MM, Hranchuk KS, Alami A, Kelly LD, Frijters JC. Comparing instructor-led, video-model, and no-instruction control tutorials for creating single-subject graphs in Microsoft Excel: A systematic replication and extension. J Appl Behav Anal 2024; 57:502-514. [PMID: 38321637 DOI: 10.1002/jaba.1053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 12/10/2023] [Indexed: 02/08/2024]
Abstract
Visual inspection of single-subject data is the primary method for behavior analysts to interpret the effect of an independent variable on a dependent variable; however, there is no consensus on the most suitable method for teaching graph construction for single-subject designs. We systematically replicated and extended Tyner and Fienup (2015) using a repeated-measures between-subjects design to compare the effects of instructor-led, video-model, and no-instruction control tutorials on the graphing performance of 81 master's students with some reported Microsoft Excel experience. Our mixed-design analysis revealed a statistically significant main effect of pretest, tutorial, and posttest submissions for each tutorial group and a nonsignificant main effect of tutorial group. Tutorial group significantly interacted with submissions, suggesting that both instructor-led and video-model tutorials may be superior to providing graduate students with a written list of graphing conventions (i.e., control condition). Finally, training influenced performance on an untrained graph type (multielement) for all tutorial groups.
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Affiliation(s)
| | - Alison D Cox
- Department of Applied Disability Studies, Brock University, St. Catharines, ON, Canada
| | - Madeline M Asaro
- Department of Applied Disability Studies, Brock University, St. Catharines, ON, Canada
| | - Kieva S Hranchuk
- Department of Applied Disability Studies, Brock University, St. Catharines, ON, Canada
| | - Arezu Alami
- Department of Applied Disability Studies, Brock University, St. Catharines, ON, Canada
| | - Laura D Kelly
- Department of Applied Disability Studies, Brock University, St. Catharines, ON, Canada
| | - Jan C Frijters
- Department of Applied Disability Studies, Brock University, St. Catharines, ON, Canada
- Department of Child and Youth Studies, Brock University, St. Catharines, ON, Canada
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7
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Pan R, Hua T, Ding Y, Bai H, Jiang Y, Wang Z, Hu M, Chen G, Wu X, Chang G. Study on changing disciplinarian of beak colors in ducks and the regulation network based on transcriptome sequencing. Poult Sci 2024; 103:103266. [PMID: 38039827 PMCID: PMC10698678 DOI: 10.1016/j.psj.2023.103266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023] Open
Abstract
Beak color in ducks is a primary characteristic of local breeds and genetic resources. Among them, black beaks, a rare packaging trait of high-quality duck products, have attracted much attention. In this study, Runzhou White Created ducks (black beak) and white-feathered Putian black ducks (yellow beak) were used to construct the F2 generation resource population to study the changing discipline of beak color combined with the beak color statistics of gray-beaked ducklings of Runzhou White Created ducks. Subsequently, transcriptome sequencing was performed to identify genetic markers related to beak color. To explore the rules of beak color change and its regulatory network, trends, and trend analysis and weighted gene co-expression network analysis(WGCNA)were performed. The screening results were verified by real-time quantitative polymerase chain reaction. A large difference was observed between the beak colors of birds from the F1 generation at 0 and 42 d of age. The F2 generation results show that nearly half of the black-beaked ducklings become green-beaked; the proportion of black spots for gray- and patterned-beaked ducklings increases with age, with most becoming green-beaked. Moreover, the beak color darkened from the first day, and the gray color value decreased significantly from the second day. Transcriptome sequencing indicated that TYR was differentially expressed between black and yellow beaks at 4 to 6 wk of age, and trend and WGCNA analyses showed that EDNRB signaling pathway genes and MITF were highly expressed in the first week, and TYR, TYRP1, and DCT were highly expressed at 4 to 6 wk of age. Therefore, there is melanin synthesis and deposition after hatching for gray- and patterned-beaked ducklings, while the yellow pigment might be deposited in the epidermis of beaks for black-beaked ducklings. The EDNRB signaling pathway is probably involved in early melanosome maturation and melanin formation in duck beaks, and genes such as TYR can maintain the black-beak phenotype.
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Affiliation(s)
- Rui Pan
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Tian Hua
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yifan Ding
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Yong Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Min Hu
- Zhenjiang Tiancheng Agricultural Science and Technology Co., Ltd., Zhenjiang 212000, China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.
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Song BN, Liu CK, Zhao AQ, Tian RM, Xie DF, Xiao YL, Chen H, Zhou SD, He XJ. Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses. BMC PLANT BIOLOGY 2024; 24:70. [PMID: 38263006 PMCID: PMC10807117 DOI: 10.1186/s12870-024-04750-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/12/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND The genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on Sanicula provided us with a good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, the evolutionary history of this genus also remains inadequately understood. The plastid genomes possessing highly conserved structure and limited evolutionary rate have proved to be an effective tool for studying plant phylogeny and evolution. RESULTS In the current study, we newly sequenced and assembled fifteen Sanicula complete plastomes. Combined with two previously reported plastomes, we performed comprehensively plastid phylogenomics analyses to gain novel insights into the evolutionary history of this genus. The comparative results indicated that the seventeen plastomes exhibited a high degree of conservation and similarity in terms of their structure, size, GC content, gene order, IR borders, codon bias patterns and SSRs profiles. Such as all of them displayed a typical quadripartite structure, including a large single copy region (LSC: 85,074-86,197 bp), a small single copy region (SSC: 17,047-17,132 bp) separated by a pair of inverted repeat regions (IRs: 26,176-26,334 bp). And the seventeen plastomes had similar IR boundaries and the adjacent genes were identical. The rps19 gene was located at the junction of the LSC/IRa, the IRa/SSC junction region was located between the trnN gene and ndhF gene, the ycf1 gene appeared in the SSC/IRb junction and the IRb/LSC boundary was located between rpl12 gene and trnH gene. Twelve specific mutation hotspots (atpF, cemA, accD, rpl22, rbcL, matK, ycf1, trnH-psbA, ycf4-cemA, rbcL-accD, trnE-trnT and trnG-trnR) were identified that can serve as potential DNA barcodes for species identification within the genus Sanicula. Furthermore, the plastomes data and Internal Transcribed Spacer (ITS) sequences were performed to reconstruct the phylogeny of Sanicula. Although the tree topologies of them were incongruent, both provided strong evidence supporting the monophyly of Saniculoideae and Apioideae. In addition, the sister groups between Saniculoideae and Apioideae were strongly suggested. The Sanicula species involved in this study were clustered into a clade, and the Eryngium species were also clustered together. However, it was clearly observed that the sections of Sanicula involved in the current study were not respectively recovered as monophyletic group. Molecular dating analysis explored that the origin of this genus was occurred during the late Eocene period, approximately 37.84 Ma (95% HPD: 20.33-52.21 Ma) years ago and the diversification of the genus was occurred in early Miocene 18.38 Ma (95% HPD: 10.68-25.28 Ma). CONCLUSION The plastome-based tree and ITS-based tree generated incongruences, which may be attributed to the event of hybridization/introgression, incomplete lineage sorting (ILS) and chloroplast capture. Our study highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions, and to efficiently explore the evolutionary history of this genus. Molecular dating analysis explored that the diversification of the genus occurred in the early Miocene, which was largely influenced by the prevalence of the East Asian monsoon and the uplift of the Hengduan Mountains (HDM). In summary, our study provides novel insights into the plastome evolution, phylogenetic relationships, taxonomic framework and evolution of genus Sanicula.
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Affiliation(s)
- Bo-Ni Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chang-Kun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - An-Qi Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Rong-Ming Tian
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yu-Lin Xiao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Huai Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Zhang Y, Fan X, Zang H, Liu X, Feng P, Ye D, Zhu L, Wu Y, Jiang H, Chen D, Guo R. Novel Insights into the circRNA-Modulated Developmental Mechanism of Western Honey Bee Larval Guts. INSECTS 2023; 14:897. [PMID: 37999096 PMCID: PMC10671861 DOI: 10.3390/insects14110897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/10/2023] [Accepted: 11/18/2023] [Indexed: 11/25/2023]
Abstract
Circular RNAs (circRNAs) are a class of novel non-coding RNAs (ncRNAs) that play essential roles in the development and growth of vertebrates through multiple manners. However, the mechanism by which circRNAs modulate the honey bee gut development is currently poorly understood. Utilizing the transcriptome data we obtained earlier, the highly expressed circRNAs in the Apis mellifera worker 4-, 5-, and 6-day-old larval guts were analyzed, which was followed by an in-depth investigation of the expression pattern of circRNAs during the process of larval guts development and the potential regulatory roles of differentially expressed circRNAs (DEcircRNAs). In total, 1728 expressed circRNAs were detected in the A. mellifera larval guts. Among the most highly expressed 10 circRNAs, seven (novel_circ_000069, novel_circ_000027, novel_circ_000438, etc.) were shared by the 4-, 5-, and 6-day-old larval guts. In addition, 21 (46) up-regulated and 22 (27) down-regulated circRNAs were, respectively, screened in the Am4 vs. Am5 (Am5 vs. Am6) comparison groups. Additionally, nine DEcircRNAs, such as novel_circ_000340, novel_circ_000758 and novel_circ_001116, were shared by these two comparison groups. These DEcircRNAs were predicted to be transcribed from 14 and 29 parental genes; these were respectively annotated to 15 and 22 GO terms such as biological regulation and catalytic activity as well as 16 and 21 KEGG pathways such as dorsoventral axis formation and apoptosis. Moreover, a complicated competing endogenous RNA (ceRNA) network was observed; novel_circ_000838 in the Am4 vs. Am5 comparison group potentially targeted ame-miR-6000a-3p, further targeting 518 mRNAs engaged in several developmental signaling pathways (e.g., TGF-beta, hedgehog, and wnt signaling pathway) and immune pathways (e.g., phagosome, lysosome, and MAPK signaling pathway). The results demonstrated that the novel_circ_000838-ame-miR-6000a-3p axis may plays a critical regulatory part in the larval gut development and immunity. Furthermore, back-splicing sites of six randomly selected DEcircRNAs were amplified and verified by PCR; an RT-qPCR assay of these six DEcircRNAs confirmed the reliability of the used high-throughput sequencing data. Our findings provide a novel insight into the honey bee gut development and pave a way for illustration of the circRNA-modulated developmental mechanisms underlying the A. mellifera worker larval guts.
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Affiliation(s)
- Yiqiong Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - He Zang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Xiaoyu Liu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
| | - Peilin Feng
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
| | - Daoyou Ye
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
| | - Leran Zhu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
| | - Ying Wu
- Jilin Institute of Apicultural Research, Jilin 132013, China; (Y.W.); (H.J.)
| | - Haibin Jiang
- Jilin Institute of Apicultural Research, Jilin 132013, China; (Y.W.); (H.J.)
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
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Wang W, Zhang X, Xu X, Xu X, Fu L, Chen H. Systematic identification of reference genes for qRT-PCR of Ardisia kteniophylla A. DC under different experimental conditions and for anthocyanin-related genes studies. FRONTIERS IN PLANT SCIENCE 2023; 14:1284007. [PMID: 38023897 PMCID: PMC10656778 DOI: 10.3389/fpls.2023.1284007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
Ardisia kteniophylla A. DC, widely known as folk medicinal herb and ornamental plant, has been extensively investigated due to its unique leaf color, anti-cancer and other pharmacological activities. The quantitative real-time PCR (qRT-PCR) was an excellent tool for the analysis of gene expression with its high sensitivity and quantitative properties. Normalizing gene expression with stable reference genes was essential for qRT-PCR accuracy. In addition, no studies have yet been performed on the selection, verification and stability of internal reference genes suitable for A. kteniophylla, which has greatly hindered the biomolecular researches of this species. In this study, 29 candidate genes were successfully screened according to stable expression patterns of large-scale RNA seq data that from a variety of tissues and the roots of different growth stages in A. kteniophylla. The candidates were then further determined via qRT-PCR in various experimental samples, including MeJA, ABA, SA, NaCl, CuSO4, AgNO3, MnSO4, CoCl2, drought, low temperature, heat, waterlogging, wounding and oxidative stress. To assess the stability of the candidates, five commonly used strategies were employed: delta-CT, geNorm, BestKeeper, NormFinder, and the comprehensive tool RefFinder. In summary, UBC2 and UBA1 were found to be effective in accurately normalizing target gene expression in A. kteniophella regardless of experimental conditions, while PP2A-2 had the lowest stability. Additionally, to verify the reliability of the recommended reference genes under different colored leaf samples, we examined the expression patterns of six genes associated with anthocyanin synthesis and regulation. Our findings suggested that PAP1 and ANS3 may be involved in leaf color change in A. kteniphella. This study successfully identified the ideal reference gene for qRT-PCR analysis in A. kteniphella, providing a foundation for future research on gene function, particularly in the biosynthesis of anthocyanins.
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Affiliation(s)
- Wentao Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Modern Agricultural Sciences, University of Chinese Acadamy of Science, Beijing, China
| | - Xiaohang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Modern Agricultural Sciences, University of Chinese Acadamy of Science, Beijing, China
| | - Xiaoxia Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Modern Agricultural Sciences, University of Chinese Acadamy of Science, Beijing, China
| | - Xingchou Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Life Science, Gannan Normal University, Ganzhou, China
| | - Lin Fu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hongfeng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Abstract
Practitioners frequently use single-case data for decision-making related to behavioral programming and progress monitoring. Visual analysis is an important and primary tool for reporting results of graphed single-case data because it provides immediate, contextualized information. Criticisms exist concerning the objectivity and reliability of the visual analysis process. When practitioners are equipped with knowledge about single-case designs, including threats and safeguards to internal validity, they can make technically accurate conclusions and reliable data-based decisions with relative ease. This paper summarizes single-case experimental design and considerations for professionals to improve the accuracy and reliability of judgments made from single-case data. This paper can also help practitioners to appropriately incorporate single-case research design applications in their practice.
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Wu Z, Han Y, Li X, Zhang Q, Deng R, Ren H, He W, Wu X, Guo H, Zhu D. Design, synthesis and anticancer evaluation of polymethoxy aurones as potential cell cycle inhibitors. Heliyon 2023; 9:e21054. [PMID: 37886750 PMCID: PMC10597867 DOI: 10.1016/j.heliyon.2023.e21054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
Background Cancer is the most fatal disease in humans and the aberrant activity of various cell cycle proteins results in uncontrolled tumor cell proliferation, thus, regulating the cell cycle is an attractive target in cancer therapy. Objectives Aurone is a naturally occurring active compound with a wide range of biological activities, of which 3, 4, 5-trimethoxyphenyl (TMP) is an important microtubule targeting pharmacophore. Based on the pharmacophore combination principle, we incorporate the TMP pharmacophore into the aurone structure and design a novel polymethoxy derivative that is expected to inhibit tumor cell proliferation through regulating the cell cycle. Methods By introducing different substituents on C-4' and C-3', a series of new 4, 5, 6-trimethoxy aurone derivatives have been designed and synthesized. DU145, MCF-7 and H1299 cell lines were selected to evaluate their anticancer activity. The compound with the best cytotoxicity was then selected and the anticancer mechanisms were investigated by network pharmacology, flow cytometry, Western blot, and cell heat transfer assay. ADMET prediction evaluated the draggability of aurone derivatives. Results Aurones 1b and 1c have selective anti-proliferative activity against DU145 cells. Among them, the compound 1c have better cytotoxicity against DU145. Compound 1c could bind the active cavity of CyclinB1/CDK1/CKS complex protein and induced G2/M phase arrest of DU145 cells by regulating the expression of CyclinB1 and p21. Compound 1c satisfies the Lipinski rule, is suitable for the absorption and metabolism index, and has a lower risk of cardiac toxicity. Conclusions Polymethoxy aurones 1c might function as a CyclinB1/CDK1 inhibitor that deserved to be further developed for the treatment of prostate cancer.
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Affiliation(s)
- Zheng Wu
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & Guangxi Health Commission Key Laboratory of Basic Research on Antigeriatric Drugs, College of Pharmacy, Guangxi Medical University, Nanning, 530021, China
| | - Yaoyao Han
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & Guangxi Health Commission Key Laboratory of Basic Research on Antigeriatric Drugs, College of Pharmacy, Guangxi Medical University, Nanning, 530021, China
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education & Center for Translational Medicine, Guangxi Medical University, Nanning, 530021, China
| | - Xiaolan Li
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & Guangxi Health Commission Key Laboratory of Basic Research on Antigeriatric Drugs, College of Pharmacy, Guangxi Medical University, Nanning, 530021, China
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education & Center for Translational Medicine, Guangxi Medical University, Nanning, 530021, China
| | - Qiuping Zhang
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education & Center for Translational Medicine, Guangxi Medical University, Nanning, 530021, China
| | - Renjin Deng
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & Guangxi Health Commission Key Laboratory of Basic Research on Antigeriatric Drugs, College of Pharmacy, Guangxi Medical University, Nanning, 530021, China
| | - Hong Ren
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & Guangxi Health Commission Key Laboratory of Basic Research on Antigeriatric Drugs, College of Pharmacy, Guangxi Medical University, Nanning, 530021, China
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education & Center for Translational Medicine, Guangxi Medical University, Nanning, 530021, China
| | - Wenjing He
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & Guangxi Health Commission Key Laboratory of Basic Research on Antigeriatric Drugs, College of Pharmacy, Guangxi Medical University, Nanning, 530021, China
| | - Xinduo Wu
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & Guangxi Health Commission Key Laboratory of Basic Research on Antigeriatric Drugs, College of Pharmacy, Guangxi Medical University, Nanning, 530021, China
| | - Hongwei Guo
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & Guangxi Health Commission Key Laboratory of Basic Research on Antigeriatric Drugs, College of Pharmacy, Guangxi Medical University, Nanning, 530021, China
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education & Center for Translational Medicine, Guangxi Medical University, Nanning, 530021, China
| | - Dan Zhu
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & Guangxi Health Commission Key Laboratory of Basic Research on Antigeriatric Drugs, College of Pharmacy, Guangxi Medical University, Nanning, 530021, China
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Pan R, Hua T, Guo Q, Bai H, Jiang Y, Wang Z, Bi Y, Chen G, Wu X, Chang G. Identification of SNPs in MITF associated with beak color of duck. Front Genet 2023; 14:1161396. [PMID: 37671042 PMCID: PMC10475569 DOI: 10.3389/fgene.2023.1161396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/27/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction: Beak color-a pigment-related trait-is an important feature of duck breeds. Recently, little research has addressed genetic mechanism of the beak colors in poultry, whereas the process and the regulation factors of melanin deposition have been well described. Methods: To investigate the genetic mechanism of beak colors, we conducted an integrated analysis of genomic selection signatures to identify a candidate site associated with beak color. For this, we used black-billed (Yiyang I meat duck synthetic line H1, H2, H3&HF) and yellow-billed ducks (Cherry Valley ducks and white feather Putian black duck). Quantitative real-time PCR and genotyping approaches were used to verify the function of the candidate site. Results: We identified 3,895 windows containing 509 genes. After GO and KEGG enrichment analysis, nine genes were selected. Ultimately, MITF was selected by comparing the genomic differentiation (FST). After loci information selection, 41 extreme significantly different loci were selected, which are all located in intron regions of MITF and are in almost complete linkage disequilibrium. Subsequently, the site ASM874695v1:10:g.17814522T > A in MITF was selected as the marker site. Furthermore, we found that MITF expression is significantly higher in black-beaked ducks than in yellow-beaked ducks of the F2 generation (p < 0.01). After genotyping, most yellow-billed individuals are found with homozygous variant; at the same time, there are no birds with homozygous variant in black-billed populations, while the birds with homozygous and heterozygous variant share the same proportion. Conclusion: MITF plays a very critical role in the melanogenesis and melanin deposition of duck beaks, which can effectively affect the beak color. The MITF site, ASM874695v1:10:g.17814522T > A could be selected as a marker site for the duck beak color phenotype.
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Affiliation(s)
- Rui Pan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tian Hua
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qixin Guo
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hao Bai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yong Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yulin Bi
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xinsheng Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
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Zhao X, Jiang X, Li Z, Song Q, Xu C, Luo K. Jasmonic acid regulates lignin deposition in poplar through JAZ5-MYB/NAC interaction. FRONTIERS IN PLANT SCIENCE 2023; 14:1232880. [PMID: 37546258 PMCID: PMC10401599 DOI: 10.3389/fpls.2023.1232880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023]
Abstract
Jasmonic acid (JA) is a phytohormone involved in plant defense, growth, and development, etc. However, the regulatory mechanisms underlying JA-mediated lignin deposition and secondary cell wall (SCW) formation remain poorly understood. In this study, we found that JA can inhibit lignin deposition and SCW thickening in poplar trees through exogenous MeJA treatment and observation of the phenotypes of a JA synthesis mutant, opdat1. Hence, we identified a JA signal inhibitor PtoJAZ5, belonging to the TIFY gene family, which is involved in the regulation of secondary vascular development of Populus tomentosa. RT-qPCR and GUS staining revealed that PtoJAZ5 was highly expressed in poplar stems, particularly in developing xylem. Overexpression of PtoJAZ5 inhibited SCW thickening and down-regulated the expression of SCW biosynthesis-related genes. Further biochemical analysis showed that PtoJAZ5 interacted with multiple SCW switches NAC/MYB transcription factors, including MYB3 and WND6A, through yeast two-hybrid and bimolecular fluorescent complementation experiments. Transcriptional activation assays demonstrated that MYB3-PtoJAZ5 and WND6A-PtoJAZ5 complexes regulated the expression of lignin synthetic genes. Our results suggest that PtoJAZ5 plays a negative role in JA-induced lignin deposition and SCW thickening in poplar and provide new insights into the molecular mechanisms underlying JA-mediated regulation of SCW formation.
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Affiliation(s)
- Xin Zhao
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
- Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xuemei Jiang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Zeyu Li
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Qin Song
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Changzhen Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
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15
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Zhang J, Feng D, Cheng J, Wüthrich K. Adenosine A 2A Receptor (A 2AAR) Ligand Screening Using the 19F-NMR Probe FPPA. J Am Chem Soc 2023. [PMID: 37276462 DOI: 10.1021/jacs.3c04218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The binding affinity of G protein-coupled receptor (GPCR) ligands is customarily measured by radio-ligand competition experiments. As an alternative approach, 19F nuclear magnetic resonance spectroscopy (19F-NMR) is used for the screening of small-molecule lead compounds in drug discovery; the two methods are complementary in that the measurements are performed with widely different experimental conditions. Here, we used the structure of the A2A adenosine receptor (A2AAR) complex with V-2006 (3-(4-amino-3-methylbenzyl)-7-(furan-2-yl)-3H-[1,2,3]triazolo[4,5-d]pyrimidin-5-amine) as the basis for the design of a fluorine-containing probe molecule, FPPA (4-(furan-2-yl)-7-(4-(trifluoromethyl)benzyl)-7H-pyrrolo[2,3-d]pyramidin-2-amine), for binding studies with A2AAR. A protocol of experimental conditions for drug screening and measurements of drug binding affinities using 1D 19F-NMR observation of FPPA is validated with studies of known A2AAR ligands. 19F-NMR with FPPA is thus found to be a robust approach for the discovery of ligands with new core structures, which will expand the libraries of A2AAR-targeting drug candidates.
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Affiliation(s)
- Jinfeng Zhang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Dandan Feng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Kurt Wüthrich
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- Department of Integrated Structural and Computational Biology, Scripps Research, La Jolla, California 92037, United States
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
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16
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Jia J, Liu Q, Wu C. Microplastic and antibiotic proliferated the colonization of specific bacteria and antibiotic resistance genes in the phycosphere of Chlorella pyrenoidosa. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131618. [PMID: 37201280 DOI: 10.1016/j.jhazmat.2023.131618] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023]
Abstract
Despite that the phycosphere was an important niche for the proliferation of various bacteria and antibiotic resistance genes (ARGs), the factors that affect the colonization of bacteria and ARGs in the phycosphere are still poorly understood. In this study, sterile C. pyrenoidosa co-cultured with bacteria from different sources and provided with polylactic acid microplastic (PLA MPs) and florfenicol (FF) was examined. Results showed that bacteria promoted the growth of C. pyrenoidosa and increased its chlorophyll contents. PLA MPs and FF also showed positive effects on C. pyrenoidosa due to the "Hormesis effect". The occurrence of bacteria in the phycosphere was significantly affected by their sources and the addition of PLA MPs and FF. However, the core microbiota of the phycosphere in each group was similar. Additionally, PLA MPs and FF proliferated the abundance of phenicol-related ARGs (especially floR) and mobile genetic elements in the phycosphere. Notably, PLA MPs and FF enhanced the abundance of Flavobacterium, a potential host of ARGs. Our results highlighted the important roles of bacteria in microalgae and demonstrated exogenous pollutants could promote the spread of ARGs between surrounding environments and the phycosphere, which provide new insights into the occurrence and spread of ARGs in the phycosphere.
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Affiliation(s)
- Jia Jia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Qian Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chenxi Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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17
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Liang RN, Yan DQ, Zhang XP, Chen X, Zhang WH, Jia HL. Kidney Mesenchymal stem cells alleviate cisplatin-induced kidney injury and apoptosis in rats. Tissue Cell 2023; 80:101998. [PMID: 36529038 DOI: 10.1016/j.tice.2022.101998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE This experiment was designed to demonstrate Mesenchymal stem cells (MSCs) derived from kidney can alleviate cisplatin-induced kidney injury and renal cell apoptosis through paracrine pathway. METHODS Firstly, MSCs were isolated from kidney of young rats, and their surface-specific markers were identified by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and immunofluorescence staining. Self-renewal ability of Kidney Mesenchymal Stem Cells (KMSCs) was observed by cell counting and 5-Bromo-2'-deoxyuridine (BrdU) fluorescence staining. KMSCs at logarithmic growth stage were traced and injected into rat through tail vein. RESULTS The results showed that KMSCs homed in the kidney tissues, decreased the secretion of inflammatory factors (CRP, TNFα, IL-1β, IL-6), and alleviated renal function. Hematoxylin and Eosin (H&E), Masson and Periodic Acid-silver Methenamine (PASM) staining showed that KMSCs could alleviate pathological damage in rats. Terminal Deoxynucleotidyl Transferase mediated dUTP Nick-End Labeling (TUNEL) assay showed that KMSCs could reduce the apoptosis of rat kidney cells induced by cisplatin. Finally, Immunohistochemistry (IHC) results showed that cisplatin could induce higher expression of the pro-apoptotic protein Bax and lower expression of anti-apoptotic Bcl-2 in kidney tissues. However, KMSCs could reverse the pro-apoptotic effect of cisplatin on kidney cells and improve the survival rate of rats. CONCLUSIONS In conclusion, KMSCs were successfully isolated from kidney tissues, and KMSCs have therapeutic effects on rat kidney injury induced by cisplatin.
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Affiliation(s)
- Rui-Ning Liang
- Fourth Clinical Medical College of Xinjiang Medical University, Urumqi, Xinjiang 830099, PR China; Affiliated Hospital of Traditional Chinese Medicine of Xinjiang Medical University, Urumqi, Xinjiang 830000, PR China.
| | - De-Qi Yan
- Fourth Clinical Medical College of Xinjiang Medical University, Urumqi, Xinjiang 830099, PR China; Affiliated Hospital of Traditional Chinese Medicine of Xinjiang Medical University, Urumqi, Xinjiang 830000, PR China
| | - Xing-Ping Zhang
- Fourth Clinical Medical College of Xinjiang Medical University, Urumqi, Xinjiang 830099, PR China; Affiliated Hospital of Traditional Chinese Medicine of Xinjiang Medical University, Urumqi, Xinjiang 830000, PR China.
| | - Xu Chen
- Fourth Clinical Medical College of Xinjiang Medical University, Urumqi, Xinjiang 830099, PR China; Affiliated Hospital of Traditional Chinese Medicine of Xinjiang Medical University, Urumqi, Xinjiang 830000, PR China
| | - Wen-Hui Zhang
- Fourth Clinical Medical College of Xinjiang Medical University, Urumqi, Xinjiang 830099, PR China; Affiliated Hospital of Traditional Chinese Medicine of Xinjiang Medical University, Urumqi, Xinjiang 830000, PR China
| | - Hong-Lin Jia
- Fourth Clinical Medical College of Xinjiang Medical University, Urumqi, Xinjiang 830099, PR China; Affiliated Hospital of Traditional Chinese Medicine of Xinjiang Medical University, Urumqi, Xinjiang 830000, PR China
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18
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Lanovaz MJ, Primiani R. Waiting for baseline stability in single-case designs: Is it worth the time and effort? Behav Res Methods 2023; 55:843-854. [PMID: 35469087 PMCID: PMC10027773 DOI: 10.3758/s13428-022-01858-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2022] [Indexed: 11/08/2022]
Abstract
Researchers and practitioners often use single-case designs (SCDs), or n-of-1 trials, to develop and validate novel treatments. Standards and guidelines have been published to provide guidance as to how to implement SCDs, but many of their recommendations are not derived from the research literature. For example, one of these recommendations suggests that researchers and practitioners should wait for baseline stability prior to introducing an independent variable. However, this recommendation is not strongly supported by empirical evidence. To address this issue, we used Monte Carlo simulations to generate graphs with fixed, response-guided, and random baseline lengths while manipulating trend and variability. Then, our analyses compared the type I error rate and power produced by two methods of analysis: the conservative dual-criteria method (a structured visual aid) and a support vector classifier (a model derived from machine learning). The conservative dual-criteria method produced fewer errors when using response-guided decision-making (i.e., waiting for stability) and random baseline lengths. In contrast, waiting for stability did not reduce decision-making errors with the support vector classifier. Our findings question the necessity of waiting for baseline stability when using SCDs with machine learning, but the study must be replicated with other designs and graph parameters that change over time to support our results.
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Affiliation(s)
- Marc J Lanovaz
- École de psychoéducation, Université de Montréal, C.P. 6128, succursale Centre-Ville, Montreal, QC, H3C 3J7, Canada.
- Centre de recherche de l'Institut universitaire en santé mentale de Montréal, Montreal, Canada.
| | - Rachel Primiani
- École de psychoéducation, Université de Montréal, C.P. 6128, succursale Centre-Ville, Montreal, QC, H3C 3J7, Canada
- Centre de recherche de l'Institut universitaire en santé mentale de Montréal, Montreal, Canada
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19
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Repeated Superovulation Accelerates Primordial Follicle Activation and Atresia. Cells 2022; 12:cells12010092. [PMID: 36611886 PMCID: PMC9818786 DOI: 10.3390/cells12010092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
For humans, ARTs (assisted reproductive technologies) have become the most effective method to treat subfertility/infertility in clinic. To obtain enough oocytes during ART, ovarian stimulation is performed by exogenous hormones, and some patients undergo several ovarian stimulation cycles. Although some adverse effects of ARTs on women and offspring are reported, few studies are focused on the effects of multiple superovulation on ovarian reserve. In the present study, we found that repeated superovulation significantly reduced primordial follicle number and the serum AMH. Compared to the decreased antral follicle number, the expression of genes related to primordial follicle activation, such as Foxo3, Akt, and Rptor, and the atretic follicle number in ovaries were increased by superovulation times. We further found that repeated superovulation reduced the plasma level of FSH, LH, and estradiol, and increased the expression of genes related to apoptosis (Bax, Casp3 (caspase-3), Casp8, and Casp9) in granulosa cells, providing evidence that repeated superovulation disrupted the balance between survival and death in granulosa cells. In summary, our results suggest that repeated superovulation has adverse effects on folliculogenesis.
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20
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Identification and Analysis of Stress-Associated Proteins (SAPs) Protein Family and Drought Tolerance of ZmSAP8 in Transgenic Arabidopsis. Int J Mol Sci 2022; 23:ijms232214109. [PMID: 36430587 PMCID: PMC9696418 DOI: 10.3390/ijms232214109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Stress-associated proteins (SAPs), a class of A20/AN1 zinc finger proteins, play vital roles in plant stress response. However, investigation of SAPs in maize has been very limited. Herein, to better trace the evolutionary history of SAPs in maize and plants, 415 SAPs were identified in 33 plant species and four species of other kingdoms. Moreover, gene duplication mode exploration showed whole genome duplication contributed largely to SAP gene expansion in angiosperms. Phylogeny reconstruction was performed with all identified SAPs by the maximum likelihood (ML) method and the SAPs were divided into five clades. SAPs within the same clades showed conserved domain composition. Focusing on maize, nine ZmSAPs were identified. Further promoter cis-elements and stress-induced expression pattern analysis of ZmSAPs indicated that ZmSAP8 was a promising candidate in response to drought stress, which was the only AN1-AN1-C2H2-C2H2 type SAP in maize and belonged to clade I. Additionally, ZmSAP8 was located in the nucleus and had no transactivation activity in yeast. Overexpressing ZmSAP8 enhanced the tolerance to drought stress in Arabidopsis thaliana, with higher seed germination and longer root length. Our results should benefit the further functional characterization of ZmSAPs.
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21
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Cui F, Li X, Wu W, Luo W, Wu Y, Brosché M, Overmyer K. Ectopic expression of BOTRYTIS SUSCEPTIBLE1 reveals its function as a positive regulator of wound-induced cell death and plant susceptibility to Botrytis. THE PLANT CELL 2022; 34:4105-4116. [PMID: 35946779 PMCID: PMC9516177 DOI: 10.1093/plcell/koac206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/31/2022] [Indexed: 06/01/2023]
Abstract
Programmed cell death (PCD) is integral to plant life and required for stress responses, immunity, and development. Our understanding of the regulation of PCD is incomplete, especially concerning regulators involved in multiple divergent processes. The botrytis-susceptible (bos1) mutant of Arabidopsis is highly susceptible to fungal infection by Botrytis cinerea (Botrytis). BOS1 (also known as MYB108) regulates cell death propagation during plant responses to wounding. The bos1-1 allele contains a T-DNA insertion in the 5'-untranslated region upstream of the start codon. This insertion results in elevated expression of BOS1/MYB108. We used clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated nuclease 9 (Cas9) system (CRISPR/Cas9) to create new bos1 alleles with disrupted exons, and found that these lines lacked the typical bos1-1 wounding and Botrytis phenotypes. They did exhibit reduced fertility, as was previously observed in other bos1 alleles. Resequencing of the bos1-1 genome confirmed the presence of a mannopine synthase (MAS) promoter at the T-DNA left border. Expression of the BOS1 gene under control of the MAS promoter in wild-type plants conferred the characteristic phenotypes of bos1-1: Botrytis sensitivity and response to wounding. Multiple overexpression lines demonstrated that BOS1 was involved in regulation of cell death propagation in a dosage-dependent manner. Our data indicate that bos1-1 is a gain-of-function mutant and that BOS1 function in regulation of fertility and Botrytis response can both be understood as misregulated cell death.
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Affiliation(s)
| | | | | | - Wenbo Luo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Ying Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Mikael Brosché
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Program, Viikki Plant Science Centre, University of Helsinki, Helsinki FI-00014, Finland
| | - Kirk Overmyer
- Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Program, Viikki Plant Science Centre, University of Helsinki, Helsinki FI-00014, Finland
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22
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Wu J, Meng J, Li H. WeChat-platform-based education and care program as a candidate approach to relieve anxiety, depression, and post-traumatic stress disorder in parents of pediatric and adolescent patients with osteosarcoma. Front Psychol 2022; 13:913940. [PMID: 36092098 PMCID: PMC9453747 DOI: 10.3389/fpsyg.2022.913940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
Background WeChat is the main social platform in China, characterized by its versatility and ease of communication. This study aimed to explore the effect of a WeChat-platform-based education and care (WBEC) program on relieving anxiety, depression, and post-traumatic stress disorder (PTSD) in parents of pediatric and adolescent patients with osteosarcoma. Methods In total, 48 patients and 86 parents were enrolled in this randomized, controlled study and then assigned to the WBEC program (24 patients and 45 parents) and the usual education and care (UEC) program (22 patients and 41 parents) for 6 months as a 1:1 ratio. Results Parents in the WBEC group had lower Hospital Anxiety and Depression Scale (HADS) for anxiety (HADS-A) scores at M3 (7.8 ± 2.2 vs. 9.1 ± 2.5; p = 0.010) and M6 (7.7 ± 2.5 vs. 8.9 ± 2.4; p = 0.027) when compared to the UEC group, while anxiety rate was only decreased at M3 (43.2% vs. 63.4%; p = 0.049) in the WBEC group. Meanwhile, parental HADS for depression (HADS-D) scores were reduced at M3 (7.0 ± 2.0 vs. 8.0 ± 2.1; p = 0.047) and M6 (7.1 ± 1.9 vs. 8.0 ± 2.4; p = 0.045) in the WBEC group when compared with the UEC group; while depression rate remained the same. Parental Impact of Event Scale-Revised (IES-R) scores were slightly reduced among the WBEC group at M6 when compared with the UEC group [12.0 (interquartile range (IQR): 10.0–20.8] vs. 15.0 (IQR: 9.5–25.0; p = 0.077)], but not statistically significant. Conclusion WeChat-platform-based education and care is considered a feasible intervention to reduce anxiety and depression in parents of pediatric and adolescent patients with osteosarcoma, while also providing mild relief from PTSD.
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23
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Kranak MP, Mitteer DR. A concise review of recent advancements in the graphical training of behavior analysts. J Appl Behav Anal 2022; 55:1349-1354. [PMID: 35766363 DOI: 10.1002/jaba.943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/02/2022] [Indexed: 11/08/2022]
Abstract
This Concise Review is an appraisal of contemporary research on teaching single-case experimental design (SCED) graphical creation published between 2017-2021. Recent work on SCED graphical creation is summarized and areas for future research are highlighted.
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Affiliation(s)
| | - Daniel R Mitteer
- Children's Specialized Hospital-Rutgers University Center for Autism Research, Education and Services (CSH-RUCARES).,Rutgers Robert Wood Johnson Medical School
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24
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Yin Y, Xie Z, Chen D, Guo H, Han M, Zhu Z, Bi J. Integrated investigation of DNA methylation, gene expression and immune cell population revealed immune cell infiltration associated with atherosclerotic plaque formation. BMC Med Genomics 2022; 15:108. [PMID: 35534881 PMCID: PMC9082837 DOI: 10.1186/s12920-022-01259-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/03/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The clinical consequences of atherosclerosis are significant source of morbidity and mortality throughout the world, while the molecular mechanisms of the pathogenesis of atherosclerosis are largely unknown. METHODS In this study, we integrated the DNA methylation and gene expression data in atherosclerotic plaque samples to decipher the underlying association between epigenetic and transcriptional regulation. Immune cell classification was performed on the basis of the expression pattern of detected genes. Finally, we selected ten genes with dysregulated methylation and expression levels for RT-qPCR validation. RESULTS Global DNA methylation profile showed obvious changes between normal aortic and atherosclerotic lesion tissues. We found that differentially methylated genes (DMGs) and differentially expressed genes (DEGs) were highly associated with atherosclerosis by being enriched in atherosclerotic plaque formation-related pathways, including cell adhesion and extracellular matrix organization. Immune cell fraction analysis revealed that a large number of immune cells, especially macrophages, activated mast cells, NK cells, and Tfh cells, were specifically enriched in the plaque. DEGs associated with immune cell fraction change showed that they were mainly related to the level of macrophages, monocytes, resting NK cells, activated CD4 memory T cells, and gamma delta T cells. These genes were highly enriched in multiple pathways of atherosclerotic plaque formation, including blood vessel remodeling, collagen fiber organization, cell adhesion, collagen catalogic process, extractable matrix assembly, and platelet activation. We also validated the expression alteration of ten genes associated with infiltrating immune cells in atherosclerosis. CONCLUSIONS In conclusion, these findings provide new evidence for understanding the mechanisms of atherosclerotic plaque formation, and provide a new and valuable research direction based on immune cell infiltration.
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Affiliation(s)
- Yihong Yin
- Department of Neural Medicine, The Second Hospital of Shandong University, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 17 Lujiang Road, Hefei, 230001, China
| | - Zhaohong Xie
- Department of Neural Medicine, The Second Hospital of Shandong University, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China
| | - Dong Chen
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co. Ltd, Wuhan, 430075, China
| | - Hao Guo
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co. Ltd, Wuhan, 430075, China
| | - Min Han
- Department of Neural Medicine, The Second Hospital of Shandong University, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China
| | - Zhengyu Zhu
- Department of Neural Medicine, The Second Hospital of Shandong University, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China.
| | - Jianzhong Bi
- Department of Neural Medicine, The Second Hospital of Shandong University, Shandong University, No. 247 Beiyuan Street, Jinan, 250033, China.
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25
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Manolov R, Tanious R, Fernández-Castilla B. A proposal for the assessment of replication of effects in single-case experimental designs. J Appl Behav Anal 2022; 55:997-1024. [PMID: 35467023 PMCID: PMC9324994 DOI: 10.1002/jaba.923] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 11/23/2022]
Abstract
In science in general and in the context of single‐case experimental designs, replication of the effects of the intervention within and/or across participants or experiments is crucial for establishing causality and for assessing the generality of the intervention effect. Specific developments and proposals for assessing whether an effect has been replicated or not (or to what extent) are scarce, in the general context of behavioral sciences, and practically null in the single‐case experimental designs context. We propose an extension of the modified Brinley plot for assessing how many of the effects replicate. To make this assessment possible, a definition of replication is suggested, on the basis of expert judgment, rather than on statistical criteria. The definition of replication and its graphical representation are justified, presenting their strengths and limitations, and illustrated with real data. A user‐friendly software is made available for obtaining automatically the graphical representation.
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Affiliation(s)
- Rumen Manolov
- Department of Social Psychology and Quantitative Psychology, University of Barcelona
| | - René Tanious
- Psychology and Educational Sciences, Methodology of Educational Sciences Research Group, KU Leuven - University of Leuven, Leuven, Belgium
| | - Belén Fernández-Castilla
- Psychology and Educational Sciences, Methodology of Educational Sciences Research Group, KU Leuven - University of Leuven, Leuven, Belgium
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26
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Yu S, Ma J. Spindle and Kinetochore-Associated Complex is Associated With Poor Prognosis in Adrenocortical Carcinoma. J Surg Res 2022; 277:50-59. [PMID: 35460921 DOI: 10.1016/j.jss.2022.03.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 02/15/2022] [Accepted: 03/19/2022] [Indexed: 01/22/2023]
Abstract
INTRODUCTION The spindle and kinetochore-associated (SKA) complex, composed of three subunits (SKA1, SKA2, and SKA3), stabilizes spindle microtubule attachment to the kinetochore (KT) in the middle stage of mitosis. High expression of this complex is associated with poor prognosis for several tumors. However, the potential role of SKA complex overexpression in rare malignant diseases, such as adrenocortical carcinoma (ACC), has not been well investigated. MATERIALS AND METHODS In this study, we used several databases to explore the relationship between SKA subunit expression and prognosis in ACC patients. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) databases were used to analyze enriched pathways in ACC. RESULTS The results suggest that each of the three SKA subunits are overexpressed in ACC and that high expression is correlated with poor patient prognosis. Overexpression of the SKA complex is associated with the expression of organelle fission, nuclear division, and chromosome segregation pathways. Furthermore, differential expression of hub genes for proteins that interact physically or functionally with the SKA complex (CCNB2, UBE2C, BUB1B, TPX2, CCNA2, CDCA8, CCNB1, MELK, TOP2A, and KIF2C) revealed additional potential biomarkers for ACC. CONCLUSIONS Our findings provide additional understanding of the mechanisms of ACC and suggest an approach for biomarker discovery using publicly available resources.
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Affiliation(s)
- Shoukai Yu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jun Ma
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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27
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Zeng X, Zheng W, Sheng Y, Ma H. UBE2B promotes ovarian cancer growth via promoting RAD18 mediated ZMYM2 monoubiquitination and stabilization. Bioengineered 2022; 13:8000-8012. [PMID: 35313791 PMCID: PMC9161992 DOI: 10.1080/21655979.2022.2048991] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Ubiquitin-conjugating enzyme E2 B (UBE2B) can form a heterodimer with ubiquitin E3 ligase RAD18. In this study, we aimed to explore new substrates of the UBE2B/RAD18 complex and their regulatory effects in ovarian cancer. Protein physical interactions were predicted using GeneMANIA. Serial sections of commercial ovarian cancer tissue arrays were used to check the protein expression of UBE2B, RAD18, and ZMYM2. Immunofluorescence staining and co-immunoprecipitation assays were performed to check their location and interactions. Cycloheximide chase assay was applied to explore the influence of UBE2B and RAD18 on ZMYM2 degradation. Xenograft tumor models were constructed to assess the influence of the UBE2B-ZMYM2 axis on in vivo tumor growth. A strong positive correlation between UBE2B and ZMYM2 and a moderate positive correlation between RAD18 and ZMYM2 were observed in 23 ovarian cancer cases. In CAOV4 and OVCAR3 cells, myc-ZMYM2 interacted with UBE2B and RAD18. UBE2B and ZMYM2 could be detected in the samples immunoprecipitated by anti-RAD18. UBE2B overexpression or knockdown did not alter ZMYM2 mRNA expression. UBE2B overexpression increased ZMYM2 monoubiquitination but reduced its polyubiquitination. RAD18 knockdown impaired UBE2B-induced ZMYM2 monoubiquitination. UBE2B overexpression significantly enhanced the stability of ZMYM2 protein, the effect of which was weakened by RAD18 knockdown. UBE2B overexpression significantly enhanced the growth of xenograft tumors derived from CAOV4 cells. ZMYM2 knockdown remarkedly suppressed tumor growth and impaired the growth-promoting effect of UBE2B overexpression. In conclusion, this study revealed a novel regulatory effect of the UBE2B/RAD18 complex on ZMYM2 monoubiquitination and stability in ovarian cancer.
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Affiliation(s)
- Xi Zeng
- Department of Obstetrics & Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wen Zheng
- Laboratory of Clinical Proteomics and Metabolomics, Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuting Sheng
- Department of Obstetrics & Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hongwei Ma
- Department of Obstetrics & Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
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28
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Bi Y, Liu J, Ma M, Tao L, Peng Y, Dai X, Ji Z, Bai R, Jian M, Chen T, Luo L, Wang F, Ding Z, Liu A, Bao F. Comparative proteomics profiling revealed the involvement of GRB2-ROCK2 axis in Lyme neuroborreliosis caused by Borrelia Burgdorferi. J Cell Mol Med 2022; 26:2312-2321. [PMID: 35212166 PMCID: PMC8995463 DOI: 10.1111/jcmm.17253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/23/2022] [Accepted: 02/11/2022] [Indexed: 11/28/2022] Open
Abstract
The zoonotic Lyme neuroborreliosis (LNB) disease is caused by Borrelia burgdorferi, with wide distribution, rapid dissemination and high disability rate. However, the molecular mechanism underlying B. burgdorferi mediated neuroborreliosis remains largely unknown. Here, the frontal cortex from rhesus brains was incubated with B. burgdorferi, and proteomics profiling was evaluated by isobaric tag for relative and absolute quantitation. Proteins were identified and quantified, and differentially expressed proteins (DEPs) were isolated by comparing co-cultured samples and control samples. A total of 43, 164 and 368 DEPs were significantly altered after 6, 12 and 24 h treatment with B. burgdorferi respectively. Gene ontology and KEGG pathway analyses revealed that chemokine biological process was significantly enriched. Two genes in chemokine pathway including GRB2 and ROCK2 were significantly up-regulated after B. burgdorferi co-culturing. By in vitro assay, we confirmed that the expression of GRB2 and ROCK2 was increased after B. burgdorferi infection. In conclusion, our study revealed the involvement of chemokine pathway in the pathogenesis of LNB. GRB2 and ROCK2 may be novel biomarkers and therapeutic targets for LNB.
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Affiliation(s)
- Yunfeng Bi
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Dermatology, the Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jianjun Liu
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Biomedical Engineering Research Center, Kunming Medical University, Kunming, China
| | - Mingbiao Ma
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Lvyan Tao
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Yun Peng
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Xiting Dai
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Zhenhua Ji
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Ruolan Bai
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Miaomiao Jian
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Taigui Chen
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Lisha Luo
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Feng Wang
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Zhe Ding
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Aihua Liu
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Fukai Bao
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
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Yu S. Overexpression of SKA Complex Is Associated With Poor Prognosis in Gliomas. Front Neurol 2022; 12:755681. [PMID: 35095717 PMCID: PMC8791909 DOI: 10.3389/fneur.2021.755681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
The spindle and kinetochore-associated complex is composed of three members: SKA1, SKA2, and SKA3. It is necessary for stabilizing spindle microtubules attaching to kinetochore (KT) in the middle stage of mitosis. The SKA complex is associated with poor prognosis in several human cancers. However, the role of SKA complex in rare malignant diseases, such as gliomas, has not been fully investigated. We investigated several databases, including Oncomine, UALCAN, and cBioPortal to explore the expression profile and prognostic significance of SKA complex in patients with gliomas. Gene ontology and Kyoto Encyclopedia of Genes and Genome pathways were used to analyze the potential enriched pathways. The genes co-expressed with SKA complex were identified and used for developing a protein-protein interaction (PPI) network using the STRING database. We found a significant overexpression of the mRNA levels of SKA1, SKA2, and SKA3 in patients with glioma patients. Higher expression of SKA1 and SKA3, but not SKA2, was significantly correlated with shorter overall survival of patients with glioma. In glioma, SKA complex was found to be involved in nuclear division, chromosome segregation, and DNA replication. The results of PPI network identified 10 hub genes (CCNB2, UBE2C, BUB1B, TPX2, CCNA2, CCNB1, MELK, TOP2A, PBK, and KIF11), all of which were overexpressed and negatively associated with prognosis of patients with glioma. In conclusion, our study sheds new insights into the biological role and prognostic significance of SKA complex in glioma.
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Affiliation(s)
- Shoukai Yu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital and Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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30
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Zhu Y, Zhang Z, Song J, Qian W, Gu X, Yang C, Shen N, Xue F, Tang Y. SARS-CoV-2-Encoded MiRNAs Inhibit Host Type I Interferon Pathway and Mediate Allelic Differential Expression of Susceptible Gene. Front Immunol 2022; 12:767726. [PMID: 35003084 PMCID: PMC8733928 DOI: 10.3389/fimmu.2021.767726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022] Open
Abstract
Infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the rapid spread of coronavirus disease 2019 (COVID-19), has generated a public health crisis worldwide. The molecular mechanisms of SARS-CoV-2 infection and virus–host interactions are still unclear. In this study, we identified four unique microRNA-like small RNAs encoded by SARS-CoV-2. SCV2-miR-ORF1ab-1-3p and SCV2-miR-ORF1ab-2-5p play an important role in evasion of type I interferon response through targeting several genes in type I interferon signaling pathway. Particularly worth mentioning is that highly expressed SCV2-miR-ORF1ab-2-5p inhibits some key genes in the host innate immune response, such as IRF7, IRF9, STAT2, OAS1, and OAS2. SCV2-miR-ORF1ab-2-5p has also been found to mediate allelic differential expression of COVID-19-susceptible gene OAS1. In conclusion, these results suggest that SARS-CoV-2 uses its miRNAs to evade the type I interferon response and links the functional viral sequence to the susceptible genetic background of the host.
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Affiliation(s)
- Youwei Zhu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaoyang Zhang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weizhou Qian
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangqian Gu
- Department of Hepatobiliary Surgery, Wuxi People's Hospital Affiliated Nanjing Medical University, Wuxi, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Nan Shen
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai, China.,Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Feng Xue
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai, China
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31
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Using GraphPad Prism's Heat Maps for Efficient, Fine-Grained Analyses of Single-Case Data. Behav Anal Pract 2022; 15:505-514. [PMID: 35692516 PMCID: PMC9120324 DOI: 10.1007/s40617-021-00664-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2021] [Indexed: 01/05/2023] Open
Abstract
Behavior analysts sometimes consider various forms of data analysis when making clinical decisions and when attempting to illuminate interesting relations in existing datasets. For example, an ongoing plot of when problem behavior occurs across days and times can yield useful information regarding the function(s) of problem behavior. In a post-hoc analysis, a plot of within-session error patterns can reveal which variables may be contributing to faulty stimulus control. Such analyses can be burdensome to conduct manually (e.g., changing the color of individual data points based on error type), and more efficient methods (e.g., using conditional formatting in Microsoft Excel data tables) might not be conducive for producing publication-quality figures. In the present article, we provide an overview of how behavior analysts can use GraphPad Prism's heat-map feature to efficiently populate fine-grained graphs of behavior with data points that are coded automatically (e.g., with categorical colors or gradients). Implications for clinical utility and research production are discussed.
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32
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Das T, Rana EA, Dutta A, Bostami MB, Rahman M, Deb P, Nath C, Barua H, Biswas PK. Antimicrobial resistance profiling and burden of resistance genes in zoonotic Salmonella isolated from broiler chicken. Vet Med Sci 2022; 8:237-244. [PMID: 34599790 PMCID: PMC8788989 DOI: 10.1002/vms3.648] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Salmonella is frequently found in poultry of which only motile serovars have zoonotic significance due to their potential to induce human gastrointestinal infections. Antimicrobial resistance, being a public health concern, the emergence of multidrug-resistant (MDR) Salmonella serotypes affecting food chain has greater impact worldwide. AIM Information on circulation of zoonotic Salmonella strains in commercial poultry farm level is limited in many parts of the world. This cross-sectional study was aimed to investigate the zoonotic Salmonella strains circulating in the broiler farm environment with their detailed antimicrobial resistance profiling. METHODS Pooled faecal samples were collected randomly from commercial broiler farms of Chattogram district, Bangladesh. Standard bacteriological procedure was followed to isolate Salmonella, and identification was confirmed by genus specific polymerase chain reaction (PCR). After phenotypic characterisation of resistance profile against eight antimicrobials by disc diffusion technique, all strains were screened by PCR for some selected resistance genes. RESULTS: Out of the 350 samples, Salmonella was isolated and identified from 86 samples. In antimicrobial sensitivity testing, more than 98.8% isolates showed resistance to ampicillin and 94.2% to tetracycline followed by enrofloxacin (56%) and ciprofloxacin (50%). Notably, 94% isolates were found to be MDR. The results of PCR assays revealed that 81.4% of the isolates were carrying the tetA gene, 19.8% the tetB and 10.47% the tetC gene. The prevalence of the isolates bearing the blaTEM , blaCTX-M and Sul-I gene were 95.4%, 7.0 % and 37.2 %, respectively. CONCLUSION There is a great risk to secure healthy poultry products due to the circulation of these MDR zoonotic Salmonella.
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Affiliation(s)
- Tridip Das
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram, Bangladesh
- Poultry Research and Training Centre, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram, Bangladesh
| | - Eaftekhar Ahmed Rana
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram, Bangladesh
| | - Avijit Dutta
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram, Bangladesh
| | - Md Bayazid Bostami
- Teaching and Training Pet Hospital and Research Centre, Chattogram Veterinary and Animal Sciences University, Bangladesh
| | - Mizanur Rahman
- Teaching and Training Pet Hospital and Research Centre, Chattogram Veterinary and Animal Sciences University, Bangladesh
| | - Probir Deb
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram, Bangladesh
| | - Chandan Nath
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram, Bangladesh
| | - Himel Barua
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram, Bangladesh
| | - Paritosh Kumar Biswas
- Department of Microbiology and Veterinary Public Health, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram, Bangladesh
- Poultry Research and Training Centre, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram, Bangladesh
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33
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Cihon JH, Ferguson JL, Milne CM, Leaf JB. Teaching behavior analysts to create multiple baseline graphs using SigmaPlot. BEHAVIORAL INTERVENTIONS 2021. [DOI: 10.1002/bin.1833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Joseph H. Cihon
- Autism Partnership Foundation Seal Beach California USA
- Institute for Behavioral Studies Endicott College Beverly Massachusetts USA
| | - Julia L. Ferguson
- Autism Partnership Foundation Seal Beach California USA
- Institute for Behavioral Studies Endicott College Beverly Massachusetts USA
| | - Christine M. Milne
- Autism Partnership Foundation Seal Beach California USA
- Institute for Behavioral Studies Endicott College Beverly Massachusetts USA
| | - Justin B. Leaf
- Autism Partnership Foundation Seal Beach California USA
- Institute for Behavioral Studies Endicott College Beverly Massachusetts USA
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34
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Sánchez-Ceinos J, Guzmán-Ruiz R, Rangel-Zúñiga OA, López-Alcalá J, Moreno-Caño E, Del Río-Moreno M, Romero-Cabrera JL, Pérez-Martínez P, Maymo-Masip E, Vendrell J, Fernández-Veledo S, Fernández-Real JM, Laurencikiene J, Rydén M, Membrives A, Luque RM, López-Miranda J, Malagón MM. Impaired mRNA splicing and proteostasis in preadipocytes in obesity-related metabolic disease. eLife 2021; 10:65996. [PMID: 34545810 PMCID: PMC8545398 DOI: 10.7554/elife.65996] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 09/20/2021] [Indexed: 12/17/2022] Open
Abstract
Preadipocytes are crucial for healthy adipose tissue expansion. Preadipocyte differentiation is altered in obese individuals, which has been proposed to contribute to obesity-associated metabolic disturbances. Here, we aimed at identifying the pathogenic processes underlying impaired adipocyte differentiation in obese individuals with insulin resistance (IR)/type 2 diabetes (T2D). We report that down-regulation of a key member of the major spliceosome, PRFP8/PRP8, as observed in IR/T2D preadipocytes from subcutaneous (SC) fat, prevented adipogenesis by altering both the expression and splicing patterns of adipogenic transcription factors and lipid droplet-related proteins, while adipocyte differentiation was restored upon recovery of PRFP8/PRP8 normal levels. Adipocyte differentiation was also compromised under conditions of endoplasmic reticulum (ER)-associated protein degradation (ERAD) hyperactivation, as occurs in SC and omental (OM) preadipocytes in IR/T2D obesity. Thus, targeting mRNA splicing and ER proteostasis in preadipocytes could improve adipose tissue function and thus contribute to metabolic health in obese individuals.
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Affiliation(s)
- Julia Sánchez-Ceinos
- Department of Cell Biology, Physiology, and Immunology, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Rocío Guzmán-Ruiz
- Department of Cell Biology, Physiology, and Immunology, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Oriol Alberto Rangel-Zúñiga
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain.,Lipids and Atherosclerosis Unit, Department of Internal Medicine, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Jaime López-Alcalá
- Department of Cell Biology, Physiology, and Immunology, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Elena Moreno-Caño
- Department of Cell Biology, Physiology, and Immunology, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Mercedes Del Río-Moreno
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain.,OncObesity and Metabolism Group. Department of Cell Biology, Physiology and Immunology, IMIBIC/University of Córdoba/Reina Sofía University Hospital, Córdoba, Spain
| | - Juan Luis Romero-Cabrera
- Lipids and Atherosclerosis Unit, Department of Internal Medicine, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Pablo Pérez-Martínez
- Lipids and Atherosclerosis Unit, Department of Internal Medicine, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Elsa Maymo-Masip
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERdem), Instituto de Salud Carlos III, Madrid, Spain.,Hospital Universitari de Tarragona Joan XXIII, Institut d´Investigació Sanitària Pere Virgili Universitat Rovira i Virgil, Tarragona, Spain
| | - Joan Vendrell
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERdem), Instituto de Salud Carlos III, Madrid, Spain.,Hospital Universitari de Tarragona Joan XXIII, Institut d´Investigació Sanitària Pere Virgili Universitat Rovira i Virgil, Tarragona, Spain
| | - Sonia Fernández-Veledo
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERdem), Instituto de Salud Carlos III, Madrid, Spain.,Hospital Universitari de Tarragona Joan XXIII, Institut d´Investigació Sanitària Pere Virgili Universitat Rovira i Virgil, Tarragona, Spain
| | - José Manuel Fernández-Real
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain.,Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, and Eumetabolism and Health Group, Girona Biomedical Research Institute (IdibGi), Girona, Spain
| | - Jurga Laurencikiene
- Lipid Laboratory. Department of Medicine Huddinge/Karolinska Institute (KI)/Karolinska University Hospital, Stockholm, Sweden
| | - Mikael Rydén
- Lipid Laboratory. Department of Medicine Huddinge/Karolinska Institute (KI)/Karolinska University Hospital, Stockholm, Sweden
| | - Antonio Membrives
- Unidad de Gestión Clínica de Cirugía General y Digestivo, Sección de Obesidad, Reina Sofia University Hospital, Córdoba, Spain
| | - Raul M Luque
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain.,OncObesity and Metabolism Group. Department of Cell Biology, Physiology and Immunology, IMIBIC/University of Córdoba/Reina Sofía University Hospital, Córdoba, Spain
| | - José López-Miranda
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain.,Lipids and Atherosclerosis Unit, Department of Internal Medicine, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - María M Malagón
- Department of Cell Biology, Physiology, and Immunology, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
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35
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Cheng Y, Cao X, Zhang J, Chen D, Zhu J, Xu L, Qin L. Dysregulated lncRNAs are Involved in the Progress of Sepsis by Constructing Regulatory Networks in Whole Blood Cells. Front Pharmacol 2021; 12:678256. [PMID: 34483898 PMCID: PMC8416166 DOI: 10.3389/fphar.2021.678256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/05/2021] [Indexed: 12/13/2022] Open
Abstract
Sepsis is a highly heterogeneous syndrome that is caused by an unbalanced host response to an infection. Long noncoding RNAs (lncRNAs) have been reported to exert regulatory roles in a variety of biological processes, and became potential biomarkers and therapeutic targets for diverse diseases. However, current understanding on the roles of lncRNAs in sepsis is extremely limited. Herein, to decipher the underlying functions of lncRNAs, we reexplored the 83 transcriptome datasets from specimens with sepsis, no_sepsis by final diagnosis, and control. The results of differentially expressed genes (DEGs), differentially expressed lncRNA (DElncRNA) analysis, and co-expression analysis of lncRNA–mRNA pairs were obtained. We found that the expression pattern of lncRNAs was significantly activated in sepsis specimens, which was clearly distinguished in sepsis from no_sepsis and control specimens. By performing co-expression analysis, we found DElncRNAs were closely related to T-cell activation and immune response–related terms in sepsis by regulating mRNA expression in the trans manner. The lncRNA–mRNA network and the qRT-PCR test revealed that lncRNAs LINC00861, RP11-284N8.3, and CTB-61M7.2 were significantly correlated with the pathogenesis of sepsis. In addition, weighted gene co-expression analysis (WGCNA) and cis-regulation analysis also revealed sepsis-specific lncRNAs were highly associated with important biological processes correlated with sepsis. In summary, the systematic dysregulation of lncRNAs is tightly involved in the remodeling of gene expression regulatory network in sepsis, and the lncRNA–mRNA expression network may be used to refine biomarker predictions for developing novel therapeutic approaches in sepsis.
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Affiliation(s)
- Yanwei Cheng
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Xue Cao
- Department of Rheumatology and Immunology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Jiange Zhang
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Dong Chen
- ABLife BioBigData Institute, Wuhan, China
| | - Juan Zhu
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Lijun Xu
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Lijie Qin
- Department of Emergency, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
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36
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Jia J, Gomes-Silva G, Plath M, Pereira BB, UeiraVieira C, Wang Z. Shifts in bacterial communities and antibiotic resistance genes in surface water and gut microbiota of guppies (Poecilia reticulata) in the upper Rio Uberabinha, Brazil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 211:111955. [PMID: 33497859 DOI: 10.1016/j.ecoenv.2021.111955] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Anthropogenic activities especially water pollution can affect the diversity and composition of microbial communities and promote the spread of antibiotic resistance genes (ARGs). In this study, water samples and guppies (Poecilia reticulata) were sampled from six sampling sites along the Uberabinha River in southeastern Brazil, both microbial communities and ARGs of surface waters and intestinal microbiota of guppies (Poecilia reticulata) were detected. According to the results of 16S rRNA amplicon sequencing, Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria were dominant phyla in both water and intestinal microbiota, but the abundance of putative pathogens was higher at heavily polluted sites. Up to 83% of bacteria in intestinal microbiota originated from water microbiota; this proportion was relatively higher in less polluted compared to polluted environments. ARGs providing resistance of tetracyclines and quinolones were dominant in both water and gut microbiota. The relative abundances of class I integrons and ARGs were as high as 1.74 × 10-1/16S rRNA copies and 3.61 × 10-1/16S rRNA copies, respectively, at heavily polluted sites. Correlation analysis suggests that integrons and bacteria play key roles in explaining the widespread occurrence of ARGs in the surface, but not in intestinal microbiota. We could rule out the class I integrons a potential intermediary bridge for ARGs between both types of microbiomes. Our results highlight the tight link in microbial communities and ARGs between ambient microbiota of stream ecosystems and intestinal microbiota of fish. Our study could have far-reaching consequences for fisheries and consumer safety and calls for investigations of gut microbiota of target species of both commercial fisheries and recreational (hobby) angling.
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Affiliation(s)
- Jia Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Guilherme Gomes-Silva
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Martin Plath
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Boscolli Barbosa Pereira
- Institute of Geography, Department of Environmental Health, Federal University of Uberlândia, Santa Mônica Campus, Uberlândia, Minas Gerais 34.408-100, Brazil; Institute of Biotechnology, Department of Genetics and Biochemistry, Federal University of Uberlândia, Umuarama Campus, Uberlândia, Minas Gerais 34.408-100, Brazil
| | - Carlos UeiraVieira
- Institute of Geography, Department of Environmental Health, Federal University of Uberlândia, Santa Mônica Campus, Uberlândia, Minas Gerais 34.408-100, Brazil
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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37
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Lehardy RK, Luczynski KC, Hood SA, McKeown CA. Remote teaching of publication-quality, single-case graphs in Microsoft Excel. J Appl Behav Anal 2021; 54:1265-1280. [PMID: 33527372 DOI: 10.1002/jaba.805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 11/09/2022]
Abstract
Microsoft Excel is ubiquitous, cost-effective, and can be used to create publication-quality single-case design graphs. We systematically replicated the GraphPad Prism video tutorial by Mitteer et al. (2018) to teach 24 master's students to create multiple-baseline graphs using Excel 2016. Students' mean accuracy on the multiple-baseline graph was 25% in pretraining, 86% with the video tutorial, and 96% with the review checklist. Next, students used the same video tutorial to create multielement and reversal graphs. Students' mean accuracy on the multielement graph was 93% with video tutorial and 94% with review checklist, and accuracy on the reversal graph was 82% with video tutorial and 94% with review checklist. Students reported moderate to high satisfaction with both training components. The results support scientist-practitioners using the video tutorial and review checklists to create three common graphs using Excel 2016, Excel 2019, and Excel Office 365.
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Yang Y, Shen L, Gao H, Ran J, Li X, Jiang H, Li X, Cao Z, Huang Y, Zhao S, Song C, Pan H. Comparison of cecal microbiota composition in hybrid pigs from two separate three-way crosses. Anim Biosci 2020; 34:1202-1209. [PMID: 33332946 PMCID: PMC8255879 DOI: 10.5713/ab.20.0681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/26/2020] [Indexed: 11/27/2022] Open
Abstract
Objective The intestinal microbiota plays an important role in host physiology, metabolism, immunity, and behavior. And host genetics could influence the gut microbiota of hybrid animals. The three-way cross model is commonly utilized in commercial pig production; however, the use of this model to analyse the gut microbial composition is rarely reported. Methods Two three-way hybrid pigs were selected, with Saba pigs as the starting maternal pig: Duroc× (Berkshire×Saba) (DBS) pig, Berkshire×(Duroc×Saba) (BDS) pig. One hundred pigs of each model were reared from 35 days (d) to 210 d. The body weight or feed consumption of all pigs were recorded and their feed/gain (F/G) ratio was calculated. On day 210, 10 pigs from each three-way cross were selected for slaughter, and cecal chyme samples were collected for 16S rRNA gene sequencing. Results The final body weight (FBW) and average daily gain (ADG) of DBS pigs were significantly higher than those of BDS pigs (p<0.05), while the F/G ratios of DBS pigs were significantly lower than those of BDS pigs (p<0.05). The dominant phyla in DBS and BDS pigs were Bacteroidetes (55.23% vs 59%, respectively) and Firmicutes (36.65% vs 34.86%, respectively) (p>0.05). At the genus level, the abundance of Prevotella, Roseburia, and Anaerovibrio in DBS pigs was significantly lower than in BDS pigs (p<0.01). The abundance of Eubacterium, Clostridium XI, Bacteroides, Methanomassiliicoccus, and Parabacteroides in DBS pigs was significantly higher than in BDS pigs (p<0.05). The FBWs and ADGs were positively correlated with Bacteroides, ClostridiumXI, and Parabacteroides but negatively correlated with the Prevotella, Prevotella/Bacteroides (P/B) ratio, Roseburia, and Anaerovibrio. Conclusion These results indicated that host genetics affect the cecal microbiota composition and the porcine gut microbiota is associated with growth performance, thereby suggesting that gut microbiota composition may be a useful biomarker in porcine genetics and breeding.
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Affiliation(s)
- Yuting Yang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Liyan Shen
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Huan Gao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jinming Ran
- Dazhou Vocational and Technical College, Dazhou 635000, China
| | - Xian Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Hengxin Jiang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Xueyan Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Zhenhui Cao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Ying Huang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Sumei Zhao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Chunlian Song
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.,Collge of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Hongbin Pan
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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Li Y, Xu H, Cai D, Zhu S, Liu X, Zhao Y, Zhang Z, Bian Y, Xue M, Zhang L. Integration of transcriptomic, proteomic and metabolomic data to reveal the biological mechanisms of AAI injury in renal epithelial cells. Toxicol In Vitro 2020; 70:105054. [PMID: 33212167 DOI: 10.1016/j.tiv.2020.105054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/06/2020] [Accepted: 11/14/2020] [Indexed: 10/23/2022]
Abstract
Overexposure to aristolochic acid I (AAI) can induce aristolochic acid nephropathy (AAN). However, the comprehensive mechanisms of AAI-induced nephrotoxicity have not been entirely explicated. To investigate the toxicological mechanisms by which AAI induces renal injury, human kidney cells (HK-2 cells) were subjected to comprehensive transcriptomic, proteomic and metabolomic analyses. The transcriptomic analysis identified a total of 7749 differentially expressed genes (DEGs) after AAI treatment, while the proteomic analysis found 598 differentially expressed proteins (DEPs) after AAI treatment. The metabolomic analysis revealed 49 and 42 differentially expressed metabolites (DEMs) in the positive and negative ion modes, respectively. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed on these DEGs, DEPs and DEMs. The results of the comprehensive analyses of transcripts, proteins, and metabolites indicated that the DEGs, DEPs, and DEMs were jointly regulated in three ways. These genes, proteins and metabolites and their related dysregulated pathways may be promising targets for research on the mechanisms of AAI injury in human renal epithelial cells. This study provides large-scale omics data that can be used to formulate new strategies for the prevention, rapid diagnosis, and treatment of AAI injury.
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Affiliation(s)
- Yu Li
- School of Pharmacy, Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, PR China
| | - Houxi Xu
- Key Laboratory of Acupuncture and Medicine Research of the Ministry of Education, Nanjing University of Chinese Medicine, Nanjing 210046, China
| | - Danhong Cai
- School of Pharmacy, Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, PR China
| | - Sirui Zhu
- School of Pharmacy, Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, PR China
| | - Xiaoli Liu
- School of Pharmacy, Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, PR China
| | - Ye Zhao
- School of Pharmacy, Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, PR China
| | - Zhaofeng Zhang
- School of Pharmacy, Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, PR China
| | - Yaoyao Bian
- School of Pharmacy, Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, PR China
| | - Mei Xue
- College of Basic Medical Sciences, Institute of TCM-related Comorbid Depression, Nanjing University of Chinese Medicine, Nanjing 210023, PR China.
| | - Liang Zhang
- School of Pharmacy, Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, PR China.
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González V, Vargas-Straube MJ, Beys-da-Silva WO, Santi L, Valencia P, Beltrametti F, Cámara B. Enzyme Bioprospection of Marine-Derived Actinobacteria from the Chilean Coast and New Insight in the Mechanism of Keratin Degradation in Streptomyces sp. G11C. Mar Drugs 2020; 18:E537. [PMID: 33126528 PMCID: PMC7693968 DOI: 10.3390/md18110537] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/13/2020] [Accepted: 10/17/2020] [Indexed: 01/10/2023] Open
Abstract
Marine actinobacteria are viewed as a promising source of enzymes with potential technological applications. They contribute to the turnover of complex biopolymers, such as pectin, lignocellulose, chitin, and keratin, being able to secrete a wide variety of extracellular enzymes. Among these, keratinases are a valuable alternative for recycling keratin-rich waste, which is generated in large quantities by the poultry industry. In this work, we explored the biocatalytic potential of 75 marine-derived actinobacterial strains, focusing mainly on the search for keratinases. A major part of the strains secreted industrially important enzymes, such as proteases, lipases, cellulases, amylases, and keratinases. Among these, we identified two streptomycete strains that presented great potential for recycling keratin wastes-Streptomyces sp. CHA1 and Streptomyces sp. G11C. Substrate concentration, incubation temperature, and, to a lesser extent, inoculum size were found to be important parameters that influenced the production of keratinolytic enzymes in both strains. In addition, proteomic analysis of culture broths from Streptomyces sp. G11C on turkey feathers showed a high abundance and diversity of peptidases, belonging mainly to the serine and metallo-superfamilies. Two proteases from families S08 and M06 were highly expressed. These results contributed to elucidate the mechanism of keratin degradation mediated by streptomycetes.
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Affiliation(s)
- Valentina González
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química y Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile; (V.G.); (M.J.V.-S.)
| | - María José Vargas-Straube
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química y Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile; (V.G.); (M.J.V.-S.)
| | - Walter O. Beys-da-Silva
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 90610-000, Brazil; (W.O.B.-d.-S.); (L.S.)
| | - Lucélia Santi
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 90610-000, Brazil; (W.O.B.-d.-S.); (L.S.)
| | - Pedro Valencia
- Laboratorio de Biocatálisis y Procesamiento de Alimentos, Departamento de Ingeniería Química y Ambiental, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile;
| | | | - Beatriz Cámara
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química y Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile; (V.G.); (M.J.V.-S.)
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Liang C, Wang X, Zhang Z, Xiao F, Feng H, Ma Q, Huang J, Qiang G, Zhong D, Liu D. ACOT11 promotes cell proliferation, migration and invasion in lung adenocarcinoma. Transl Lung Cancer Res 2020; 9:1885-1903. [PMID: 33209610 PMCID: PMC7653140 DOI: 10.21037/tlcr-19-509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background Lung cancer is one of the most common cancers in the word. However, the underlying mechanism remains largely unknown. ACOT11 encodes enzymes hydrolyzing the fatty acyl-CoA esters into free fatty acids and CoA. Besides from its role in fatty acid metabolism, the other aspects regarding its function in the progression of lung cancer have not been revealed. Methods We first explored the clinical profile of ACOT11 in tumor samples. Next, we combined gene knockdown in vitro and in vivo and microarray gene profiling analysis to decipher the unknown regulatory role of ACOT11 in lung cancer carcinoma. Furthermore, we explored the potential molecular mechanisms of ACOT11 with immunoprecipitation. Results We found high expression of ACOT11 in tumor samples. High expression of ACOT11 showed significantly poor prognosis in lung squamous carcinoma (LUSC) patients. Knocking down of ACOT11 inhibited the cell proliferation, migration as well as invasion in vitro and in vivo. It also promoted the cell apoptosis and cell cycle arrest via multiple signaling pathways. Additionally, ACOT11 could bind with CSE1L, which was proved to be an oncogene in lung cancer and speculated to be a potential target of ACOT11. Conclusions The results revealed that ACOT11 regulates proliferation, migration and invasion of lung cancer carcinoma via multiple signaling pathways, indicating its potential value in molecular therapy.
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Affiliation(s)
- Chaoyang Liang
- Department of Thoracic Surgery, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Xiaowei Wang
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Zhenrong Zhang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Fei Xiao
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Hongxiang Feng
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Qianli Ma
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Jingjing Huang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Guangliang Qiang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Dingrong Zhong
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Deruo Liu
- Department of Thoracic Surgery, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
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Marano KE, Vladescu JC, Reeve KF, Sidener TM, Cox DJ. A review of the literature on staff training strategies that minimize trainer involvement. BEHAVIORAL INTERVENTIONS 2020. [DOI: 10.1002/bin.1727] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kathleen E. Marano
- Department of Applied Behavior Analysis Caldwell University Caldwell New Jersey USA
| | - Jason C. Vladescu
- Department of Applied Behavior Analysis Caldwell University Caldwell New Jersey USA
| | - Kenneth F. Reeve
- Department of Applied Behavior Analysis Caldwell University Caldwell New Jersey USA
| | - Tina M. Sidener
- Department of Applied Behavior Analysis Caldwell University Caldwell New Jersey USA
| | - David J. Cox
- The Johns Hopkins University School of Medicine Baltimore Maryland USA
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Okozide OE, Adebusoye SA, Obayori OS. Aerobic degradation of 2,4-dinitrotoluene: Effect of raw organic wastes and nitrogen fortification. JOURNAL OF ENVIRONMENTAL QUALITY 2020; 49:835-846. [PMID: 33016493 DOI: 10.1002/jeq2.20088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
2,4-Dinitrotoluene (2,4-DNT), a principal derivative generated in the synthesis of 2,4,6-trinitrotoluene, is widely used as a waterproofer, plasticizer, and gelatinizer in propellants and explosives. This compound has been documented as a priority pollutant because of its toxicity. Therefore, its removal from contaminated systems is a major focus of research and environmental attention. The presence of 2,4-DNT bacterial-degrading strains that could utilize 2,4-DNT as growth substrate in polluted sites in Ibadan, Nigeria, was determined using continual enrichment techniques on nitroaromatic mixtures. Proteus sp. strain OSES2 isolated in this study was characterized by phenotypic typing and 16S ribosomal RNA gene sequencing. Growth of the strain on 2,4-DNT resulted in an exponential increase in biomass and complete substrate utilization within 72 h, accompanied by NO3 - elimination. Degradation competence was enhanced in the presence of corn steep liquor, molasses, and Tween 80 compared with incubation without amendment. Conversely, amendment with nitrogen sources yielded no significant improvement in degradation. Use of these organic wastes as candidates in a bioremediation strategy should be exploited. This would provide a less-expensive organic source supplement for cleanup purposes, with the ultimate aim of reducing the cost of bioremediation while reducing wastes intended for landfill.
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Affiliation(s)
- Osekokhune E Okozide
- Dep. of Microbiology, Faculty of Science, Univ. of Lagos, Akoka, Lagos, 100213, Nigeria
| | - Sunday A Adebusoye
- Dep. of Microbiology, Faculty of Science, Univ. of Lagos, Akoka, Lagos, 100213, Nigeria
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Shi J, Huang Y, Wen C, He S, Wu L, Zhou H. Genome-wide identification and characterization of long non-coding RNAs involved in acquired resistance to gefitinib in non-small-cell lung cancer. Comput Biol Chem 2020; 87:107288. [PMID: 32521497 DOI: 10.1016/j.compbiolchem.2020.107288] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/28/2022]
Abstract
Acquired resistance is a major obstacle to the therapeutic efficacy of gefitinib in non-small-cell lung cancer (NSCLC). Current knowledge about the role of long non-coding RNAs (lncRNAs) in this phenomenon is insufficient. In this study, we searched RNA sequencing data for lncRNAs associated with acquired resistance to gefitinib in NSCLC, and constructed a functional lncRNA-mRNA co-expression network and protein-protein interaction (PPI) network to analyze their putative target genes and biological functions. The expression levels of 14 outstanding dysregulated lncRNAs and mRNA were verified using real-time PCR. Changes in the expression levels of 39 lncRNAs and 121 mRNAs showed common patterns in our two pairs of gefitinib-sensitive and gefitinib-resistant NSCLC cell lines. The co-expression network included 1235 connections among these common differentially expressed lncRNAs and mRNAs. The significantly enriched signaling pathways based on dysregulated mRNAs were mainly involved in the Hippo signaling pathway; proteoglycans in cancer; and valine, leucine, and isoleucine biosynthesis. The results show that LncRNAs play an important part in acquired gefitinib resistance in NSCLC by regulating mRNA expression and function, and may represent potential new molecular biomarkers and therapeutic targets for gefitinib-resistant NSCLC.
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Affiliation(s)
- Jingjing Shi
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yutang Huang
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Chunjie Wen
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Shuai He
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Lanxiang Wu
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China.
| | - Honghao Zhou
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China; Pharmacogenetics Research Institute, Institute of Clinical Pharmacology, Central South University, Changsha 410078, China
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Zou Y, Chen G, Jin J, Wang Y, Xu M, Peng J, Ding Y. Small RNA and Transcriptome Sequencing Reveals miRNA Regulation of Floral Thermogenesis in Nelumbo nucifera. Int J Mol Sci 2020; 21:E3324. [PMID: 32397143 PMCID: PMC7246644 DOI: 10.3390/ijms21093324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 11/24/2022] Open
Abstract
The sacred lotus (Nelumbo nucifera Gaertn.) can produce heat autonomously and maintain a relatively stable floral chamber temperature for several days when blooming. Floral thermogenesis is critical for flower organ development and reproductive success. However, the regulatory role of microRNA (miRNA) underlying floral thermogenesis in N. nucifera remains unclear. To comprehensively understand the miRNA regulatory mechanism of thermogenesis, we performed small RNA sequencing and transcriptome sequencing on receptacles from five different developmental stages. In the present study, a total of 172 known miRNAs belonging to 39 miRNA families and 126 novel miRNAs were identified. Twenty-nine thermogenesis-related miRNAs and 3024 thermogenesis-related mRNAs were screened based on their expression patterns. Of those, seventeen differentially expressed miRNAs (DEMs) and 1765 differentially expressed genes (DEGs) had higher expression during thermogenic stages. The upregulated genes in the thermogenic stages were mainly associated with mitochondrial function, oxidoreductase activity, and the energy metabolism process. Further analysis showed that miR156_2, miR395a_5, miR481d, and miR319p may play an important role in heat-producing activity by regulating cellular respiration-related genes. This study provides comprehensive miRNA and mRNA expression profile of receptacle during thermogenesis in N. nucifera, which advances our understanding on the regulation of floral thermogenesis mediated by miRNA.
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Affiliation(s)
- Yu Zou
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (G.C.); (J.J.); (Y.W.); (M.X.)
| | - Guanglong Chen
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (G.C.); (J.J.); (Y.W.); (M.X.)
| | - Jing Jin
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (G.C.); (J.J.); (Y.W.); (M.X.)
| | - Ying Wang
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (G.C.); (J.J.); (Y.W.); (M.X.)
| | - Meiling Xu
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (G.C.); (J.J.); (Y.W.); (M.X.)
| | - Jing Peng
- Institute of Vegetable, Wuhan Academy of Agricultural Science, Wuhan 430065, China;
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (G.C.); (J.J.); (Y.W.); (M.X.)
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Mitteer DR, Greer BD, Randall KR, Briggs AM. Further Evaluation of Teaching Behavior Technicians to Input Data and Graph Using GraphPad Prism. BEHAVIOR ANALYSIS (WASHINGTON, D.C.) 2020; 20:81-93. [PMID: 33244483 DOI: 10.1037/bar0000172] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We replicated and extended Mitteer, Greer, Fisher, and Cohrs (2018) by examining the effects of a video model on inputting data into GraphPad Prism, which is a necessary skill for graph construction. We used a concurrent multiple-probe-across-behavior design with two behavior technicians to assess data-input and graphing skills separately prior to and during access to relevant video models. We evaluated the generality of the training procedures by assessing both skills during data-input-plus-graphing sessions without access to the video models. The video models resulted in mastery of data-input and graphing skills when assessed individually. We observed training effects generalize to data-input-plus-graphing sessions once behavior technicians experienced all relevant video models. These results suggest that individuals should view both data-input and graphing video models prior to depicting single-case design data in Prism but that these skills can maintain at high levels of accuracy without continued access to the training materials.
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Affiliation(s)
| | - Brian D Greer
- University of Nebraska Medical Center's Munroe-Meyer Institute
| | - Kayla R Randall
- University of Nebraska Medical Center's Munroe-Meyer Institute
| | - Adam M Briggs
- University of Nebraska Medical Center's Munroe-Meyer Institute
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The pan-cancer landscape of netrin family reveals potential oncogenic biomarkers. Sci Rep 2020; 10:5224. [PMID: 32251318 PMCID: PMC7090012 DOI: 10.1038/s41598-020-62117-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 03/09/2020] [Indexed: 02/02/2023] Open
Abstract
Recent cancer studies have found that the netrin family of proteins plays vital roles in the development of some cancers. However, the functions of the many variants of these proteins in cancer remain incompletely understood. In this work, we used the most comprehensive database available, including more than 10000 samples across more than 30 tumor types, to analyze the six members of the netrin family. We performed comprehensive analysis of genetic change and expression of the netrin genes and analyzed epigenetic and pathway relationships, as well as the correlation of expression of these proteins with drug sensitivity. Although the mutation rate of the netrin family is low in pan-cancer, among the tumor patients with netrin mutations, the highest number are Uterine Corpus Endometrial Carcinoma patients, accounting for 13.6% of cases (54 of 397). Interestingly, the highest mutation rate of a netrin family member is 38% for NTNG1 (152 of 397). Netrin proteins may participate in the development of endocrine-related tumors and sex hormone-targeting organ tumors. Additionally, the participation of NTNG1 and NTNG2 in various cancers shows their potential for use as new tumor markers and therapeutic targets. This analysis provides a broad molecular perspective of this protein family and suggests some new directions for the treatment of cancer.
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Yang X, Zhang Z, Zhang L, Zhou L. MicroRNA hsa-mir-3923 serves as a diagnostic and prognostic biomarker for gastric carcinoma. Sci Rep 2020; 10:4672. [PMID: 32170105 PMCID: PMC7070044 DOI: 10.1038/s41598-020-61633-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/01/2020] [Indexed: 12/12/2022] Open
Abstract
Gastric carcinoma (GC) refers to a common digestive system disease that exhibits a very high incidence. MicroRNA hsa-mir-3923 belongs to a type of miRNA, of which the function has been merely investigated in breast, pancreatic cancers and pre-neoplasic stages of gastric cancer. It has not been studied or reported in gastric carcinoma, so the relationship between gastric hsa-mir-3923 expression and the clinics feature and pathology of GC cases was examined. This study employed data mining for analyzing gastric carcinoma data in The Cancer Genome Atlas database. A Chi squared test was performed for assessing the relations of hsa-mir-3923 expression with clinics-related and pathology-regulated variables. This study conducted the assessment of the role of hsa-mir-3923 in prognostic process using Kaplan-Meier curves, Receiver operating characteristic (ROC) analysis and proportional hazards model (Cox) study. With the use of Gene Expression Omnibus, this study carried out gene set enrichment analysis (GSEA). In the meantime, the common miRNA database was compared to predict potential target genes; as revealed by co-expression analysis, a regulatory network probably existed, containing hsa-mir-3923. For the analysis of the most tightly associated cytological behavior and pathway in GC, this study adopted the databases for Annotation, Visualization and Integrated Discovery (David) and KO-Based Annotation System (KOBAS). Cytoscape, R and STRING were employed for mapping probable regulatory networks displaying relations to hsa-mir-3923. Lastly, we obtained 69 genes most tightly associated with hsa-mir-3923 and described their relationship with Circos plot. As revealed from the results, hsa-mir-3923 displayed up-regulation in gastric carcinoma, and it displayed associations with vital status, N stage and histologic grade when being expressed. The predicted results of miRNA target genes suggested that there may be a close relationship between 66 genes and hsa-mir-3923 in gastric cancer. As indicated from co-expression data, a small regulating network of 4 genes probably existed. Our results elucidated that hsa-mir-3923 high-expression reveals poor prognosis of GC patients.
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Affiliation(s)
- Xiaohui Yang
- Department of Obstetrics & Gynecology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Ze Zhang
- Department of General Surgery, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Lichao Zhang
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Li Zhou
- Department of Obstetrics & Gynecology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China.
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Liu T, Wei WY, Wang KY, Yang Q, Wang EL. Pathological and immunological analyses of Thelohanellus kitauei (Myxozoa:Myxosporea) infection in the scattered mirror carp, Cyprinus carpio. Sci Rep 2019; 9:20014. [PMID: 31882981 PMCID: PMC6934683 DOI: 10.1038/s41598-019-56752-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/04/2019] [Indexed: 11/09/2022] Open
Abstract
Thelohanellus kitauei is a spore-forming myxosporean parasite prevalent in scattered mirror carp (Cyprinus carpio) that generates numerous cysts in the intestine and causes mass mortality in fish. To investigate the infection and mortality induced by T. kitauei in pond-reared farms in Luo-Jiang (104°51’N, 31°31’E), southwest China, morphological and molecular analyses of infected fish were conducted. Natural and specific immune indicators were further evaluated to determine the immunological effects of response to parasitic infection. The infectious parasite was identified as Thelohanellus kitauei based on morphological, 18S rDNA and infectious characteristics. Scattered mirror carp was determined as the specific intermediate host of the parasite. However, T. kitauei still caused considerable damage to the fish, in particular, injury and blockage of the intestines, resulting in malnutrition and even death. The mature spores of T. kitauei colonize the intestinal submucosa of carp and form cysts of various sizes that block the intestinal tract and release spores into the enteric cavity upon rupture, leading to the next phase of T. kitauei growth. Moreover, T. kitauei-infected carp showed weaker innate immunity. IgM is involved in the fight against parasitic infection while cytokines, such as IL-6, IL-1β and TNF-α, had an impact on infection processes. To our knowledge, this is the first report to show that T. kitauei infects and causes death in scattered mirror carp. Our collective findings from systematic pathology, morphology and immunology experiments provide a foundation for further research on infections by this type of parasite and development of effective treatment strategies.
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Affiliation(s)
- Tao Liu
- Department of Basic Veterinary, Veterinary Medicine College, Sichuan Agricultural University, Cheng'du, 611134, Sichuan, P.R. China
| | - Wen-Yan Wei
- China Institute of fisheries of chengdu agriculture and forestry academy, Cheng du, 610000, China
| | - Kai-Yu Wang
- Department of Basic Veterinary, Veterinary Medicine College, Sichuan Agricultural University, Cheng'du, 611134, Sichuan, P.R. China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Cheng'du, 611134, Sichuan, P.R. China.
| | - Qian Yang
- Department of Basic Veterinary, Veterinary Medicine College, Sichuan Agricultural University, Cheng'du, 611134, Sichuan, P.R. China
| | - Er-Long Wang
- Department of Basic Veterinary, Veterinary Medicine College, Sichuan Agricultural University, Cheng'du, 611134, Sichuan, P.R. China
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Zhang Z, Wang S, Yang F, Meng Z, Liu Y. LncRNA ROR1‑AS1 high expression and its prognostic significance in liver cancer. Oncol Rep 2019; 43:55-74. [PMID: 31746401 PMCID: PMC6908930 DOI: 10.3892/or.2019.7398] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/27/2019] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a common disease of the digestive system with no curative treatments. Long noncoding RNA tyrosine protein kinase transmembrane receptor 1 antisense RNA 1 (lncRNA ROR1-AS1) is an lncRNA whose functions have been predicted in human diseases; however, its important role in cancer has been probed only in mantle cell lymphoma, not in HCC. Therefore, the present study aimed to elucidate the prognostic significance of lncRNA ROR1-AS1 in HCC. The Cancer Genome Atlas Liver Hepatocellular Carcinoma was used to analyze the expression of ROR1-AS1 in liver cancer. χ2 tests were performed to evaluate associations between clinical characteristics and ROR1-AS1 expression. The role of ROR1-AS1 in HCC prognosis was assessed using Kaplan-Meier curves and proportional hazards model (Cox) analysis. Gene set enrichment analysis was performed by using a Gene Expression Omnibus dataset. At the same time, Multi Experiment Matrix was used to predict genes that may be co-expressed with ROR1-AS1. The Database for Annotation, Visualization and Integrated Discovery and KO-Based Annotation System were used to analyze the most closely associated cytological behaviors and pathways in HCC. Then, the genes in the three databases were integrated to screen mRNAs, microRNAs and lncRNAs that had co-expression relationships with ROR1-AS1. Cytoscape, Search Tool for the Retrieval of Interacting Genes/Proteins and Molecular Evolutionary Genetics Analysis were used to map potential regulatory networks and developmental relationships associated with ROR1-AS1. Finally, 12 genes most closely associated with ROR1-AS1 were identified, and their relationship was described using a Circos plot. The results showed that ROR1-AS1 was upregulated in HCC, and its expression was related to clinical stage, T stage and N stage. Furthermore, Kaplan-Meier curves and Cox analysis indicated that high expression of ROR1-AS1 was associated with poor prognosis, and that ROR1-AS1 was an independent risk factor for HCC. Co-expression data suggested that there may be a large regulatory network of 45 genes with indirect associations with ROR1-AS1, a small regulatory network of 15 genes with direct or indirect regulatory relationships, and a special regulatory network containing 12 genes directly associated with ROR1-AS1. The present findings indicated that high expression of ROR1-AS1 suggests poor prognosis in patients with HCC.
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Affiliation(s)
- Ze Zhang
- Department of Hepatobiliary‑Pancreatic Surgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Shouqian Wang
- Department of General Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Fan Yang
- Department of General Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Zihui Meng
- Department of Hepatobiliary‑Pancreatic Surgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Yahui Liu
- Department of General Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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