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Li L, Duo H, Zhang X, Gong H, Li B, Hao Y. Comparative Transcriptomic Analysis Revealing the Potential Mechanisms of Erythritol-Caused Mortality and Oviposition Inhibition in Drosophila melanogaster. Int J Mol Sci 2024; 25:3738. [PMID: 38612549 PMCID: PMC11011834 DOI: 10.3390/ijms25073738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Erythritol has shown excellent insecticidal performance against a wide range of insect species, but the molecular mechanism by which it causes insect mortality and sterility is not fully understood. The mortality and sterility of Drosophila melanogaster were assessed after feeding with 1M erythritol for 72 h and 96 h, and gene expression profiles were further compared through RNA sequencing. Enrichment analysis of GO and KEGG revealed that expressions of the adipokinetic hormone gene (Akh), amylase gene (Amyrel), α-glucosidase gene (Mal-B1/2, Mal-A1-4, Mal-A7/8), and triglyceride lipase gene (Bmm) were significantly up-regulated, while insulin-like peptide genes (Dilp2, Dilp3 and Dilp5) were dramatically down-regulated. Seventeen genes associated with eggshell assembly, including Dec-1 (down 315-fold), Vm26Ab (down 2014-fold) and Vm34Ca (down 6034-fold), were significantly down-regulated or even showed no expression. However, there were no significant differences in the expression of three diuretic hormone genes (DH44, DH31, CAPA) and eight aquaporin genes (Drip, Big brain, AQP, Eglp1, Eglp2, Eglp3, Eglp4 and Prip) involved in osmolality regulation (all p value > 0.05). We concluded that erythritol, a competitive inhibitor of α-glucosidase, severely reduced substrates and enzyme binding, inhibiting effective carbohydrate hydrolysis in the midgut and eventually causing death due to energy deprivation. It was clear that Drosophila melanogaster did not die from the osmolality of the hemolymph. Our findings elucidate the molecular mechanism underlying the mortality and sterility in Drosophila melanogaster induced by erythritol feeding. It also provides an important theoretical basis for the application of erythritol as an environmentally friendly pesticide.
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Affiliation(s)
| | | | | | | | - Bo Li
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (L.L.)
| | - Youjin Hao
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (L.L.)
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Nie X, Qin D, Zhou X, Duo H, Hao Y, Li B, Liang G. Clustering ensemble in scRNA-seq data analysis: Methods, applications and challenges. Comput Biol Med 2023; 159:106939. [PMID: 37075602 DOI: 10.1016/j.compbiomed.2023.106939] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/31/2023] [Accepted: 04/14/2023] [Indexed: 04/21/2023]
Abstract
With the rapid development of single-cell RNA-sequencing techniques, various computational methods and tools were proposed to analyze these high-throughput data, which led to an accelerated reveal of potential biological information. As one of the core steps of single-cell transcriptome data analysis, clustering plays a crucial role in identifying cell types and interpreting cellular heterogeneity. However, the results generated by different clustering methods showed distinguishing, and those unstable partitions can affect the accuracy of the analysis to a certain extent. To overcome this challenge and obtain more accurate results, currently clustering ensemble is frequently applied to cluster analysis of single-cell transcriptome datasets, and the results generated by all clustering ensembles are nearly more reliable than those from most of the single clustering partitions. In this review, we summarize applications and challenges of the clustering ensemble method in single-cell transcriptome data analysis, and provide constructive thoughts and references for researchers in this field.
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Affiliation(s)
- Xiner Nie
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, China; College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Dan Qin
- Department of Biology, College of Science, Northeastern University, Boston, MA, 02115, USA
| | - Xinyi Zhou
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Hongrui Duo
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Youjin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China.
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, China.
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He H, Duo H, Hao Y, Zhang X, Zhou X, Zeng Y, Li Y, Li B. Computational drug repurposing by exploiting large-scale gene expression data: Strategy, methods and applications. Comput Biol Med 2023; 155:106671. [PMID: 36805225 DOI: 10.1016/j.compbiomed.2023.106671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023]
Abstract
De novo drug development is an extremely complex, time-consuming and costly task. Urgent needs for therapies of various diseases have greatly accelerated searches for more effective drug development methods. Luckily, drug repurposing provides a new and effective perspective on disease treatment. Rapidly increased large-scale transcriptome data paints a detailed prospect of gene expression during disease onset and thus has received wide attention in the field of computational drug repurposing. However, how to efficiently mine transcriptome data and identify new indications for old drugs remains a critical challenge. This review discussed the irreplaceable role of transcriptome data in computational drug repurposing and summarized some representative databases, tools and strategies. More importantly, it proposed a practical guideline through establishing the correspondence between three gene expression data types and five strategies, which would facilitate researchers to adopt appropriate strategies to deeply mine large-scale transcriptome data and discover more effective therapies.
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Affiliation(s)
- Hao He
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China; State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, PR China
| | - Hongrui Duo
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Youjin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Xiaoxi Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Xinyi Zhou
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Yujie Zeng
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China
| | - Yinghong Li
- The Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing, 400044, PR China.
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Zhang XY, Jian YN, Guo ZH, Duo H, Wei YM. [Establishment and preliminary application of a recombinase-aided isothermal amplification assay-based multiplex nucleic acid assay for detection of three Echinococcus species]. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi 2021; 33:339-345. [PMID: 34505439 DOI: 10.16250/j.32.1374.2021094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To establish a multiplex nucleic acid assay for rapid detection of Echinococcus multilocularis, E. granulosus and E. shiquicus based on the recombinase-aided isothermal amplification assay (RAA) and to preliminarily assess its diagnostic efficiency. METHODS The mitochondrial genomic sequences of E. multilocularis (GenBank accession number: NC_000928), E. granulosus (GenBank accession number: NC_044548) and E. shiquicus (GenBank accession number: NC_009460) were used as target sequences, and three pairs of primers were designed based on the RAA primer design principle and synthesized for the subsequent multiple RAA amplification. The genomic DNA of E. multilocularis, E. granulosus and E. shiquicus at different concentrations and the recombinant plasmids containing the target gene at various concentrations were amplified to evaluate the diagnostic sensitivity of the multiplex RAA assay, and the genomic DNA of E. multilocularis, E. granulosus, E. shiquicus, Taenia multiceps, T. saginata, T. asiatica, Dipylidium caninum, T. hydatigena, Toxocara canis, Fasciola hepatica, T. pisiformis, Mesocestoides lineatus and Cryptosporidiumn canis was detected using the multiplex RAA assay to evaluate its specificity. In addition, the reaction condition of the multiplex RAA assay was optimized, and was then employed to detect the tissues with echinococcosis lesions, simulated canine fecal samples and field captured fox fecal samples to examine its application values. RESULTS The multiplex RAA assay was effective to specifically amplify the mitochondrial gene fragments of E. multilocularis, E. granulosus and E. shiquicus within 40 min at 39 °C, with sequence lengths of 540, 430 bp and 200 bp, respectively. This multiplex RAA assay showed the minimum detection limits of 2.0, 2.5 pg/μL and 3.1 pg/μL for detection of the genomic DNA of E. multilocularis, E. granulosus and E. shiquicus, and presented the minimum detection limit of 200 copies/μL for detection of the recombinant plasmids containing E. multilocularis, E. granulosus and E. shiquicus target genes. This multiplex RAA assay was effective to simultaneously detect single and multiple infections with E. multilocularis, E. granulosus and E. shiquicus, but failed to amplify the genomic DNA of T. multiceps, T. saginata, T. asiatica, D. caninum, T. hydatigena, T. canis, F. hepatica, T. pisiformis, M. lineatus and C. canis. In addition, the optimized multiplex RAA assay was effective to detect all positive samples from the tissue samples with echinococcosis lesions, simulated canine fecal samples and field captured fox fecal samples, which was fully consistent with the detection of the single PCR assay. CONCLUSIONS A sensitive and specific multiplex nucleic acid assay for rapid detection of E. multilocularis, E. granulosus and E. shiquicus has been successfully established.
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Affiliation(s)
- X Y Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China.,Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, China
| | - Y N Jian
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China.,Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, China
| | - Z H Guo
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, China
| | - H Duo
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, China
| | - Y M Wei
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
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Dang Z, Fu Y, Duo H, Fan H, Qiao Z, Guo Z, Feng K, Chui W, Shen X, Geng Qiu J, Ni M, He S, Zhao H, Peng M, Xiao N, Nonaka N, Nasu T, Huang F, Oku Y, Hayashimoto N, Hu W, Li W. An epidemiological survey of echinococcosis in intermediate and definitive hosts in Qinghai Province, China. Trop Biomed 2017; 34:483-490. [PMID: 33593033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In order to understand the epidemiological status of alveolar and cystic echinococcosis in intermediate and definitive hosts in Qinghai Province, China, during the period 2007-2011, we investigated the infection in humans and animals, including yaks, Tibetan sheep, Tibetan dogs, and wild foxes distributed in different counties around the province. Sera from local residents were examined using a rapid serodiagnostic kit to detect specific antibodies against Echinococcus. Seropositive samples were confirmed with B-scan ultrasonography and X-ray examinations. Yaks and Tibetan sheep were checked at slaughterhouses, and cysts and suspicious lesions were collected for analysis. A rapid diagnostic strip was used to detect Echinococcus adults in Tibetan dogs. Positive dogs were dewormed and the parasites collected. Wild foxes were trapped and necropsies performed with particular attention to the intestine. Forty-eight of 735 (6.4%) humans tested were positive and 475 of 854 (55.6%) Tibetan sheep and 85 of 352 (24.15%) yaks were infected with Echinococcus. Across different counties, 214 of 948 (22.57%) Tibetan dogs were positive, and five of 36 (13.9%) wild foxes were infected with Echinococcus. Molecular studies showed that all the infections detected in humans, domestic yaks, and Tibetan sheep were the G1 genotype (E. granulosus), whereas the parasites from Tibetan foxes and Tibetan dogs were E. shiquicus and E. multilocularis, respectively. In conclusion, Echinococcosis is hyperendemic in Qinghai Province in both its intermediate and definitive hosts and the G1 genotype of cystic Echinococcus is the dominant strain.
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Affiliation(s)
- Z Dang
- Key Laboratory on Biology of Parasite and Vector, Ministry of Health, Shanghai, China; National Center for International Research on Tropical Diseases, Shanghai, China; WHO Collaborating Center for Tropical Diseases, Shanghai, China; National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai 200025, China
| | - Y Fu
- Academy of Animal and Veterinary Medicine, Qinghai University of Animal and Veterinary Sciences, Xining 810016, China
| | - H Duo
- Academy of Animal and Veterinary Medicine, Qinghai University of Animal and Veterinary Sciences, Xining 810016, China
| | - H Fan
- Affiliated Hospital of Qinghai University, Xining 810016, China
| | - Z Qiao
- Academy of Animal and Veterinary Medicine, Qinghai University of Animal and Veterinary Sciences, Xining 810016, China
| | - Z Guo
- Key Laboratory on Biology of Parasite and Vector, Ministry of Health, Shanghai, China; National Center for International Research on Tropical Diseases, Shanghai, China; WHO Collaborating Center for Tropical Diseases, Shanghai, China; National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai 200025, China
- Affiliated Hospital of Qinghai University, Xining 810016, China
| | - K Feng
- Academy of Animal and Veterinary Medicine, Qinghai University of Animal and Veterinary Sciences, Xining 810016, China
- Laboratory of Veterinary Parasitic Diseases, Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - W Chui
- Academy of Animal and Veterinary Medicine, Qinghai University of Animal and Veterinary Sciences, Xining 810016, China
| | - X Shen
- Academy of Animal and Veterinary Medicine, Qinghai University of Animal and Veterinary Sciences, Xining 810016, China
| | - J Geng Qiu
- Zhen Qin Township Veterinary Station, Chengduo 815100, China
| | - M Ni
- Haiyan Veterinary Stations, Haiyan 812200, China
| | - S He
- Haiyan Veterinary Stations, Haiyan 812200, China
| | - H Zhao
- Medical College of Qinghai University, Xining 810016, China
| | - M Peng
- Academy of Animal and Veterinary Medicine, Qinghai University of Animal and Veterinary Sciences, Xining 810016, China
| | - N Xiao
- Key Laboratory on Biology of Parasite and Vector, Ministry of Health, Shanghai, China; National Center for International Research on Tropical Diseases, Shanghai, China; WHO Collaborating Center for Tropical Diseases, Shanghai, China; National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai 200025, China
| | - N Nonaka
- Laboratory of Veterinary Parasitic Diseases, Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - T Nasu
- Laboratory of Veterinary Parasitic Diseases, Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - F Huang
- Parasitology Laboratory, School of Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
| | - Y Oku
- Parasitology Laboratory, School of Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
| | - N Hayashimoto
- ICLAS Monitoring Center, Central Institute for Experimental Animals, 3-25-12 Tonomachi, Kawasaki, Kanagawa 210-0821, Japan
| | - W Hu
- Key Laboratory on Biology of Parasite and Vector, Ministry of Health, Shanghai, China; National Center for International Research on Tropical Diseases, Shanghai, China; WHO Collaborating Center for Tropical Diseases, Shanghai, China; National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai 200025, China
| | - W Li
- Academy of Animal and Veterinary Medicine, Qinghai University of Animal and Veterinary Sciences, Xining 810016, China
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