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Guan P, Fan S, Dong W, Wang X, Li Z, Song M, Suo B. Comparative genomic analysis and multilocus sequence typing of Staphylococcus aureus reveals candidate genes for low-temperature tolerance. Sci Total Environ 2024; 923:171331. [PMID: 38428609 DOI: 10.1016/j.scitotenv.2024.171331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
Staphylococcus aureus is one of the most frequently detected foodborne pathogens in cold chain foods. Worryingly, small colony variants (SCVs) can survive in cold environments for a long time and can revert to rapidly growing cells in suitable environments, causing serious food safety issues. This study investigated the underlying mechanism of SCV formation at low temperature (4 °C) via comparative genomics. Multilocus sequence typing (MLST) of 105 strains of S. aureus was divided into 9 sequence types. The ST352 strains exhibited the greatest tolerance to low temperature, with a mean reduction in survival rate of 10.34 % (p < 0.05). Comparative genomics revealed a total of 1941 core genes in the three S. aureus strains, and BB-1 had 468 specific genes, which were enriched mainly in translation, DNA recombination, DNA repair, metabolic pathways, two-component systems, and quorum sensing. Molecular docking analysis revealed that the binding of the RsbW protein to the SigB protein of BB-1 decreased due to base mutations in rsbW, while the binding to the RsbV protein was enhanced. In addition, the results of real-time quantitative PCR showed that the RsbV-RsbW/SigB system of BB-1 may play a role in the low-temperature survival of S. aureus and the formation of SCVs. These results suggest that genes specific to BB-1 may contribute to the mechanism of adaptation to low temperature and the formation of SCVs. This study helps elucidate the causes of SCV formation by S. aureus at low temperature at the molecular level and provides a basis for exploring the safety control of cold chain food environments.
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Affiliation(s)
- Peng Guan
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Shijia Fan
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Wenjing Dong
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Xiaojie Wang
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China
| | - Zhen Li
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China
| | - Miao Song
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China
| | - Biao Suo
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China.
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Zhang N, Zhang L, Peng Y, Fu F, Wang L, Mei Q, Wei Y. Yak IGFBP3 promotes hepatocyte proliferation through PI3K-Akt signaling pathway. Gene 2024; 917:148460. [PMID: 38604506 DOI: 10.1016/j.gene.2024.148460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/19/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
IGFBP3 (Insulin-like growth factor binding protein 3) constitutes a crucial constituent of the insulin-like growth factor (IGF), which are intimately associated with the organism's growth and development processes. Despite its significance, the precise function of IGFBP3 in yak liver development remains largely unexplored. In the present study, we systematically examined the expression profile of IGFBP3 in the liver tissues of yaks across various growth stages, elucidated its influence on the activity of yak hepatocytes, and probed its effects on murine liver development. A comparative analysis revealed that the expression of IGFBP3 was significantly higher in the liver tissue of 5-year-old yaks compared to their 15-month-old and 1-day-old counterparts (P < 0.01). To further validate its biological function, pET-28a-BgIGFBP3 prokaryotic expression vector was constructed. Upon exposing yak hepatocytes to varying concentrations of Bos grunniens (Bg) IGFBP3 protein, we observed augmented cellular activities and elevated colony formation rates. Moreover, our investigation revealed the upregulation of key genes within the PI3K-Akt signaling pathway, including ERBB2, IRS1, PIK3R1, AKT1, RAF1, MAP2K2, and MAPK3, in both yak hepatocyte cultures and murine models. These findings collectively indicate that BgIGFBP3 promotes the proliferation of yak hepatocytes and enhances murine liver development by modulating the PI3K-Akt signaling pathway. The functional relevance of BgIGFBP3 was substantiated through in vivo and in vitro experiments, thereby underscoring its potential as a regulatory factor in liver development processes.
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Affiliation(s)
- Nanchi Zhang
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Ling Zhang
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Ying Peng
- School of Computer Science and Engineering, Southwest Minzu University, Chengdu 610041, China
| | - Fang Fu
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Li Wang
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China.
| | - Qundi Mei
- Key Laboratory of Animal Science of National Ethnic Affairs Commission of China, Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu 610041, China
| | - Yong Wei
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Sciences Academy, Chengdu 610066, China.
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Chen X, Wang F, Fu Y, Huang L, Li F, Zhao H, Guan X, Li Q, Li Q, Wang Y, Guo Y, Xie Z. Development and evaluation of a multiplex digital PCR method for sensitive and accurate detection of respiratory pathogens in children. Virology 2024; 590:109948. [PMID: 38064870 DOI: 10.1016/j.virol.2023.109948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/09/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024]
Abstract
The emergence of multiplex digital polymerase chain reaction (dPCR) and other detection technologies for respiratory pathogens in recent years has facilitated greater understanding of respiratory virus epidemics. In this study, a multiplex dPCR method was developed and evaluated as a means of detecting five respiratory pathogens in children with acute lower respiratory tract infection (ALRTI). With 139 nasopharyngeal swabs collected from children with ALRTI, pathogens were detected using dPCR and quantitative real-time PCR (qPCR) methods. Of those specimens, dPCR detected 86 positive cases, while qPCR identified 84. Moreover, dPCR exhibited higher sensitivity than qPCR, and displayed no cross-reactivity with common respiratory pathogens. These findings suggest that dPCR-based method could become one of the most promising options for acute respiratory pathogen detection.
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Affiliation(s)
- Xiangpeng Chen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Fang Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Yiliang Fu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Luci Huang
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Fei Li
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Hongwei Zhao
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiaolei Guan
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Qiuping Li
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Qi Li
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yilu Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China.
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
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Gu M, Han Y, Dai X, Ma X, Ge W, Wei W, Yang S. RNA-seq transcriptome analysis provides new insights into the negative effects of tannic acid on the intestinal function of Brandt's voles (Lasiopodomys brandtii). Gene 2024; 893:147944. [PMID: 38381510 DOI: 10.1016/j.gene.2023.147944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/05/2023] [Accepted: 10/27/2023] [Indexed: 02/22/2024]
Abstract
Tannic acid (TA), a significant plant secondary metabolite, is contained in the daily food of Brandt's voles. Its adverse effect on gut function has been shown in earlier research, but the underlying molecular mechanisms remain uncertain. In this study, male Brandt's vole (13 weeks old) were divided into two groups and given 0 (control) or 1,200 (TA-treated) mg•kg-1 TA for 18 days. Then RNA sequencing was used to conduct a thorough transcriptome analysis on the duodenum, jejunum, and ileum of Brandt's voles. Results showed that TA significantly increased serum total cholesterol concentration (P < 0.05) and decreased the nutrient digestibility (P < 0.05) of Brandt's voles. Furthermore, there were 174 differentially expressed genes (DEGs) in the duodenum, 96 DEGs in the jejunum, and 88 DEGs in the ileum between the control and TA-treated groups. Enrichment analysis revealed that many genes associated with bile secretion, fat digestion and absorption, innate immune response, and tight junction such as ABCG2, ABCG8, PEAK1, and IFR2, etc. were altered after TA treatment, which were verified by quantitative real-time PCR. These findings suggested that TA can change the expression of intestinal genes, thereby, altering nutrition metabolism and immunological function, eventually hindering the growth of Brandt's voles. The results of this study provide a theoretical basis for explaining how TA affects the gut function of Brandt's voles at the molecular level.
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Affiliation(s)
- Minghui Gu
- Department of College of Biological Science and Technology, Yangzhou University, China.
| | - Yuxuan Han
- Department of College of Biological Science and Technology, Yangzhou University, China.
| | - Xin Dai
- Department of College of Biological Science and Technology, Yangzhou University, China.
| | - Xuwei Ma
- Department of College of Biological Science and Technology, Yangzhou University, China.
| | - Weiwei Ge
- Department of College of Biological Science and Technology, Yangzhou University, China.
| | - Wanhong Wei
- Department of College of Biological Science and Technology, Yangzhou University, China.
| | - Shengmei Yang
- Department of College of Biological Science and Technology, Yangzhou University, China.
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Pereira IDS, Cruz ABD, Maia MM, Carneiro FM, Gava R, Spegiorin LCJF, Brandão CC, Truzzi IGDC, Junior GMDF, de Mattos LC, Pereira-Chioccola VL, Meira-Strejevitch CS. Identification and validation of reference genes of circulating microRNAs for use as control in gestational toxoplasmosis. Mol Biochem Parasitol 2023; 256:111592. [PMID: 37666471 DOI: 10.1016/j.molbiopara.2023.111592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 08/21/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
Toxoplasmosis causes serious harm to the fetus, as tachyzoite dissemination, during pregnancy in women developing the primo-infection. The microRNAs (miRNAs) are small non-coding RNAs, which have regulatory roles in cells by silencing messenger RNA. Circulating miRNA are promising biomarkers for diagnosis and prognosis of numerous diseases. The miRNAs levels are estimated by quantitative real-time PCR (qPCR), however, the relative quantification of each miRNA expression requires proper normalization methods using endogenous miRNAs as control. This study analyzed the expression of three endogenous miRNAs (miR-484, miR -423-3p and miR-26b-5p) for use as normalizers in future studies of target miRNAs for gestational toxoplasmosis (GT). A total of 32 plasma samples were used in all assays divided in 21 from women with GT and 11 from healthy women. The stability of each endogenous miRNA was evaluated by the algorithm methods RefFinder that included GeNorm, Normfinder, BestKeeper and comparative delta-CT programs. The miR-484 was the most stably gene, and equivalently expressed in GT and NC groups. These results contribute to future studies of target miRNAs in clinical samples of women with gestational toxoplasmosis.
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Affiliation(s)
- Ingrid de Siqueira Pereira
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo, Brazil; Programa de Pós-Graduação em Ciências da Coordenadoria de Controle de Doenças da Secretaria de Estado da Saúde de São Paulo, Brazil
| | - Allecineia Bispo da Cruz
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo, Brazil; Programa de Pós-Graduação em Ciências da Coordenadoria de Controle de Doenças da Secretaria de Estado da Saúde de São Paulo, Brazil
| | - Marta Marques Maia
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo, Brazil; Programa de Pós-Graduação em Ciências da Coordenadoria de Controle de Doenças da Secretaria de Estado da Saúde de São Paulo, Brazil
| | - Francieli Marinho Carneiro
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo, Brazil; Programa de Pós-Graduação em Ciências da Coordenadoria de Controle de Doenças da Secretaria de Estado da Saúde de São Paulo, Brazil
| | - Ricardo Gava
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo, Brazil
| | | | | | | | | | | | - Vera Lucia Pereira-Chioccola
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo, Brazil; Programa de Pós-Graduação em Ciências da Coordenadoria de Controle de Doenças da Secretaria de Estado da Saúde de São Paulo, Brazil
| | - Cristina Silva Meira-Strejevitch
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, Sao Paulo, Brazil; Programa de Pós-Graduação em Ciências da Coordenadoria de Controle de Doenças da Secretaria de Estado da Saúde de São Paulo, Brazil.
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Nusair SD, Abandah B, Al-Share QY, Abu-Qatouseh L, Ahmad MIA. Toxicity induced by orellanine from the mushroom Cortinarius orellanus in primary renal tubular proximal epithelial cells (RPTEC): Novel mechanisms of action. Toxicon 2023; 235:107312. [PMID: 37806454 DOI: 10.1016/j.toxicon.2023.107312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/30/2023] [Accepted: 10/01/2023] [Indexed: 10/10/2023]
Abstract
The toxicity of Orellanine (OR), a significant factor in mushroom poisoning, has severe effects on the kidneys, particularly the proximal tubules. This study investigated the acute toxicity of OR from the Cortinarius orellanus mushroom in human Primary Renal Tubular Proximal Epithelial Cells (RPTEC). Additionally, the half maximal inhibitory concentration (IC50) of OR in MCF-7 cells was established. RPTEC were subjected to a 6.25 μg/ml dose of orellanine for 24 h, while Control cells were exposed to 0.05% DMSO (vehicle). The RT2 Profiler™ PCR Array Human Nephrotoxicity was utilized to identify genes that were upregulated or downregulated. Western blotting confirmed the protein product of some significantly regulated genes compared to control cells. The IC50 of OR was found to be 319.2 μg/ml. The mechanism of OR toxicity involved several pathways including apoptosis, metal ion binding, cell proliferation, tissue remodeling, xenobiotic metabolism, transporters, extracellular matrix molecules, and cytoskeleton pathways. Other genes from non-specific pathways were also identified. These findings enhance our understanding of OR nephrotoxicity and pave the way for future research into potential treatments or antidotes for natural mushroom poisoning.
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Affiliation(s)
- Shreen D Nusair
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Jordan.
| | - Bayan Abandah
- Department of Legal Medicine, Toxicology and Forensic Science, Faculty of Medicine, Jordan University of Science and Technology, Jordan
| | - Qusai Y Al-Share
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Jordan
| | - Luay Abu-Qatouseh
- Department of Pharmacology and Biomedical Sciences, Faculty of Pharmacy, University of Petra, Jordan
| | - Mohammad I A Ahmad
- University of Petra Pharmaceutical Center (UPPC), Faculty of Pharmacy & Medical Sciences, University of Petra, Jordan; Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Portugal
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Strand DA, Jinnerot T, Aspán A, Viljamaa-Dirks S, Heinikainen S, Rolén E, Vrålstad T. Molecular detection of Aphanomyces astaci - An improved species specific qPCR assay. J Invertebr Pathol 2023; 201:108008. [PMID: 37863282 DOI: 10.1016/j.jip.2023.108008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
The parasitic oomycete Aphanomyces astaci is the causative agent of crayfish plague, a devastating disease for European freshwater crayfish. Species specific quantitative real-time PCR (qPCR) can offer rapid detection of the pathogen. However, the well established A. astaci qPCR assay recommended by the World Organization for Animal Health (WOAH) amplifies the recently described Aphanomyces fennicus. Consequently, false-positive results may occur. This calls for the improvement of the established species specific A. astaci qPCR assay in order to avoid amplifying A. fennicus while screening for A. astaci. We developed an improved species specific A. astaci qPCR assay and validated the assay across three laboratories, using established procedures including different qPCR master mixes for each respective laboratory. Genomic DNA from A. astaci, A. fennicus and closely related Aphanomyces spp. was analysed and compared with both the improved and established assay. Additionally, DNA from crayfish tissue and environmental samples were analysed with both assays. The improved assay showed similar sensitivity with the established assay for all sample types, while proving highly specific for A. astaci avoiding amplification of A. fennicus and the other tested Aphanomyces spp. Environmental DNA (eDNA) samples collected at River Lierelva in Norway amplified with the established assay, but not with the improved assay indicating false positive. We were able to sequence a 530 bp fragment of the ITS region from these eDNA samples and the consensus sequence showed 99.9-100 % pairwise identity with A. fennicus and 97.2-98 % pairwise identity with A. astaci, suggesting that the occurrence of A. fennicus is not limited to Finland, where it was first discovered.
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Affiliation(s)
| | | | - Anna Aspán
- National Veterinary Institute, Uppsala, Sweden
| | | | | | - Elin Rolén
- Norwegian Veterinary Institute, Oslo, Norway
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Liu A, Phillips K, Jia J, Deng P, Zhang D, Chang S, Lu SE. Development of a qPCR detection approach for pathogenic Burkholderia cenocepacia associated with fresh vegetables. Food Microbiol 2023; 115:104333. [PMID: 37567623 DOI: 10.1016/j.fm.2023.104333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 08/13/2023]
Abstract
Natural environment serves as a reservoir for Burkholderia cepacia complex organisms, including the highly transmissible opportunistic human pathogen B. cenocepacia. Currently, there is a lack of an effective and quantitative method for B. cenocepacia detection in fresh food and other environmental niches. A quantitative real-time PCR (qPCR) detection method for B. cenocepacia bacteria was established in this study and validated using artificially inoculated fresh vegetable samples. Genome-wide comparative methods were applied to identify target regions for the design of species-specific primers. Assay specificity was measured with 12 strains of closely related Burkholderia bacteria and demonstrated the primer pair BCF6/R6 were 100% specific for detection of B. cenocepacia. The described qPCR assay evaluated B. cenocepacia with a 2 pg μl-1 limit of detection and appropriate linearity (R2 = 0.999). In 50 samples of experimentally infected produce (lettuce, onion, and celery), the assay could detect B. cenocepacia as low as 2.6 × 102 cells in each sample equal to 1 g. The established qPCR method quantitatively detects B. cenocepacia with high sensitivity and specificity, making it a promising technique for B. cenocepacia detection and epidemiological research on B. cepacia complex organisms from fresh vegetables.
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Affiliation(s)
- Aixin Liu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA; College of Plant Protection, Shandong Agricultural University, Shandong, 271018, China
| | - Kate Phillips
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Jiayuan Jia
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Peng Deng
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Dunhua Zhang
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Sam Chang
- Coastal Research and Extension Center, Seafood Processing Laboratory, Department of Food Science, Nutrition and Health Promotion, Mississippi State University, Pascagoula, MS, 39567, USA
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA.
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Ren S, Zeng G, Yi Y, Liu L, Tu H, Chai T, Hu L. Combinations of plasma cfDNA concentration, integrity and tumor markers are promising biomarkers for early diagnosis of non-small cell lung cancer. Heliyon 2023; 9:e20851. [PMID: 37860559 PMCID: PMC10582504 DOI: 10.1016/j.heliyon.2023.e20851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023] Open
Abstract
Background Circulating cell-free DNA (cfDNA) concentration and integrity as noninvasive biomarkers play an important role in cancer diagnosis, prognosis and therapy monitoring. However, few studies have been conducted on the combination of plasma cfDNA concentration, integrity and tumor markers (CEA, CA125, NSE and CYFRA21-1) for cancer detection. Thus, the purpose of this study was to investigate the diagnostic value of combining plasma cfDNA concentration, integrity and tumor markers in early detection of non-small cell lung cancer (NSCLC). Methods Plasma cfDNA concentration from 50 healthy controls and 84 NSCLC patients were assessed by quantitative real-time PCR of ALU repeated sequence. Plasma cfDNA integrity was calculated as the ratio of long to short fragments (ALU115/60). Results Plasma cfDNA concentration (ALU60 and ALU115) and integrity ALU115/60 were significantly higher in NSCLC patients with stage III/IV than in healthy controls (p = 0.0002, p < 0.0001, and p = 0.0093, respectively). The receiver operating characteristic (ROC) curve for discriminating NSCLC patients from healthy controls had an area under the curve (AUC) of 0.936 (95 % CI, 0.939-0.996). Moreover, the combination of plasma cfDNA concentration, integrity and tumor markers (CEA, CA125, NSE and CYFRA21-1) had higher diagnostic performance than either plasma cfDNA concentration alone, integrity alone or tumor markers alone, with sensitivity, specificity and AUC value of 94.05%, 90.00% and 0.968, respectively. These results demonstrated that the combination of plasma cfDNA concentration, integrity and tumor markers could significantly improve the diagnostic accuracy of NSCLC. Conclusion Combination of plasma cfDNA concentration, integrity and tumor markers is a promising biomarker for early diagnosis of NSCLC.
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Affiliation(s)
- Sai Ren
- Department of Laboratory Medicine, The People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Guichuan Zeng
- Department of Ultrasound, Jian She Hospital, Chongqing, China
| | - Yuling Yi
- Department of Laboratory Medicine, The People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Ling Liu
- Department of Laboratory Medicine, The People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Hongmei Tu
- Department of Laboratory Medicine, The People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Tingjia Chai
- Endocrine Laboratory, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Liyi Hu
- Department of Laboratory Medicine, The People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
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10
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Society of Tumor Pathology of Chinese Anti-Cancer Association,, Society of Gene Diagnosis of Tumor of Chinese Anti-Cancer Association,, Society of Ultrastructural and Molecular Pathology of Chinese Research Hospital Association,, Beijing Quality Control and Quality Improvement Center of Pathology. [Chinese expert consensus on clinical practice of quantitative real-time polymerase chain reaction techniques in molecular pathological diagnostics of tumor(2023 edition)]. Zhonghua Zhong Liu Za Zhi 2023; 45:763-72. [PMID: 37805440 DOI: 10.3760/cma.j.cn112152-20221231-00868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 10/09/2023]
Abstract
Quantitative real-time polymerase chain reaction (qPCR) is one of the most widely used molecular pathological diagnostic techniques in China due to its advantages of the simple operation, short turnaround time, high sensitivity, and standardizable result analysis. However, in clinical practice, there is not yet an expert consensus to guide molecular pathological diagnostics of tumor using qPCR techniques in terms of validation and verification of method performance, quality management and interpretation of complex results. Therefore, this expert consensus aims to provide standardized opinions on the practical application of qPCR techniques, and suggestions on how to deal with common problems and abnormal results, and reach a Chinese expert consensus on the clinical practice of qPCR techniques in molecular pathological diagnostics of tumor, in order to standardize the testing process, improve the accuracy of results, and promote the clinical applications of qPCR techniques.
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11
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Ray A, Pradhan D, Arora R, Siraj F, Rastogi S. Microarray profiling of serum micro-RNAs in women with Chlamydia trachomatis-associated recurrent spontaneous abortion: A case control study. Microb Pathog 2023; 182:106273. [PMID: 37507027 DOI: 10.1016/j.micpath.2023.106273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Chlamydia trachomatis infection is a major cause of sexually transmitted diseases and adverse pregnancy outcomes such as recurrent spontaneous abortion (RSA). Micro-RNAs (miRNAs) have been known to be upregulated/downregulated in various reproductive-associated diseases such as ectopic pregnancy, preterm birth and pre-eclampsia. However, there is paucity of literature on miRNA profile in C. trachomatis-infected RSA. The present study aimed to determine the profile of serum miRNAs followed by their validation in C. trachomatis-infected RSA and to find target genes involved in biological pathways. Non-heparinized blood and first void urine were collected from 30 non-pregnant women with RSA and 30 non-pregnant women with ≥2 successful deliveries (controls) attending Department of Obstetrics and Gynaecology, Safdarjung hospital, New Delhi, India. C. trachomatis detection was done in urine by PCR and chlamydial load was determined by quantitative real-time PCR (qRT-PCR). miRNA expression was studied by microarray analysis followed by in vitro validation by qRT-PCR. Analysis of target genes/pathways was characterized in silico. 06 RSA patients were infected with C. trachomatis, while chlamydial load was found to be 6000-12,000 copies/ml. 110 circulating miRNAs were expressed differentially in infected RSA patients compared with controls. Of these, 16 were overexpressed and 94 downregulated. 06 differentially expressed circulating miRNAs were selected to validate the microarray results. qRT-PCR data confirmed the reliability of the microarray results: miR-4443, -5100, -7975 showed statistically significant upregulation, while miR-6808-5p, -3148, -6727-5p were significantly downregulated in infected RSA patients versus controls. Chlamydial load was positively correlated with these upregulated miRNAs. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that target genes of miRNAs in RSA are involved in AMPK, Akt and mTOR signaling pathways. Overall results indicate that differentially expressed circulating miRNAs are involved in pathogenesis of C. trachomatis-associated RSA and have the potential to be used as biomarkers for predicting RSA.
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Affiliation(s)
- Ankita Ray
- Molecular Microbiology Laboratory, ICMR-National Institute of Pathology, Sriramachari Bhawan, Safdarjung Hospital Campus, Post Box No. 4909, New Delhi, 110029, India.
| | - Dibyabhaba Pradhan
- ICMR-AIIMS Computational Genomics Centre, Room No. 5001, Convergence Block, AIIMS, New Delhi, 110029, India.
| | - Renu Arora
- Department of Obstetrics and Gynecology, Vardhman Mahavir Medical College (VMMC) and Safdarjung Hospital, New Delhi, 110029, India.
| | - Fouzia Siraj
- Pathology Laboratory, ICMR-National Institute of Pathology, Sriramachari Bhawan, Safdarjung Hospital Campus, Post Box No. 4909, New Delhi, 110029, India.
| | - Sangita Rastogi
- Molecular Microbiology Laboratory, ICMR-National Institute of Pathology, Sriramachari Bhawan, Safdarjung Hospital Campus, Post Box No. 4909, New Delhi, 110029, India.
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Pospíšilová K, Van't Hof AE, Yoshido A, Kružíková R, Visser S, Zrzavá M, Bobryshava K, Dalíková M, Marec F. Masculinizer gene controls male sex determination in the codling moth, Cydia pomonella. Insect Biochem Mol Biol 2023; 160:103991. [PMID: 37536576 DOI: 10.1016/j.ibmb.2023.103991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/13/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
The molecular mechanisms of sex determination in moths and butterflies (Lepidoptera) with female heterogamety (WZ/ZZ) are poorly understood, except in the silkworm Bombyx mori. However, the Masculinizer (Masc) gene that controls male development and dosage compensation in B. mori, appears to be conserved in Lepidoptera, as its masculinizing function was recently confirmed in several moth species. In this work, we investigated the role of the Masc gene in sex determination of the codling moth Cydia pomonella (Tortricidae), a globally important pest of pome fruits and walnuts. The gene structure of the C. pomonella Masc ortholog, CpMasc, is similar to B. mori Masc. However, unlike B. mori, we identified 14 splice variants of CpMasc in the available transcriptomes. Subsequent screening for sex specificity and genetic variation using publicly available data and RT-PCR revealed three male-specific splice variants. Then qPCR analysis of these variants revealed sex-biased expression showing a peak only in early male embryos. Knockdown of CpMasc by RNAi during early embryogenesis resulted in a shift from male-to female-specific splicing of the C. pomonella doublesex (Cpdsx) gene, its downstream effector, in ZZ embryos, leading to a strongly female-biased sex ratio. These data clearly demonstrate that CpMasc functions as a masculinizing gene in the sex-determining cascade of C. pomonella. Our study also showed that CpMasc transcripts are provided maternally, as they were detected in unfertilized eggs after oviposition and in mature eggs dissected from virgin females. This finding is unique, as maternal provision of mRNA has rarely been studied in Lepidoptera.
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Affiliation(s)
- Kristýna Pospíšilová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Arjen E Van't Hof
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic.
| | - Atsuo Yoshido
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic.
| | - Renata Kružíková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Sander Visser
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic; School of Science and Engineering, University of Groningen, 9700 CC, Groningen, the Netherlands.
| | - Magda Zrzavá
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Kseniya Bobryshava
- Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA.
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, České Budějovice, Czech Republic.
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Al-Bayati L, Fasaei BN, Merat S, Bahonar A, Ghoddusi A. Quantitative analysis of the three gut microbiota in UC and non-UC patients using real-time PCR. Microb Pathog 2023:106198. [PMID: 37295481 DOI: 10.1016/j.micpath.2023.106198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND and study aims: Gastrointestinal microbiota are closely related to the pathogenesis of ulcerative colitis (UC). This study aimed at quantification of F. prausnitzii, Provetella, and Peptostreptococcus in UC and non-UC patients using Real-Time PCR and a new set of primers were also validated for this purpose. MATERIALS AND METHODS In this study, the relative abundance of microbial populations between the UC and non-UC subjects were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR). DNA extraction from biopsies and polymerase chain reaction (PCR) amplification of bacterial 16S rRNA gene-targeted species-specific primers was performed to detect the anaerobic bacterial species. The qRT-PCR was used to show the relative change in the bacterial populations of F. prausnitzii, Provetella, and Peptostreptococcus in the UC and non-UC subjects. RESULTS Our data for detection of the anaerobic intestinal flora showed Faecalibacterium prausnitzii, Provetella and Peptostreptococcus were the predominant microflora in the controls and showed significant differences (p = 0.002, 0.025 and 0.039, respectively). The qRT-PCR analyses of F. prausnitzii, Provetella and Peptostreptococcus were 8.69-, 9.38- and 5.77-higher, respectively, in the control group than in the UC group. CONCLUSION The results of this study showed decreased abundance of F. prausnitzii, Provetella and Peptostreptococcus in the intestine of UC patients in comparison to non-UC patients. Quantitative RT-PCR, as a progressive and sensitive method, could be useful for evaluation of bacterial populations in patients with inflammatory bowel diseases to attain appropriate therapeutic strategies.
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Affiliation(s)
- Luma Al-Bayati
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran; Department of Microbiology, Faculty of Medicine, University of Wassit, Iraq
| | - Bahar Nayeri Fasaei
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Shahin Merat
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Liver and Pancreatobiliary Diseases Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Bahonar
- Department of Food Hygiene, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Arefeh Ghoddusi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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Zhang H, Tong Y, Liu H, Guo L, Jin W, Li X, Meng Q, Yu X, Fang F, Qin Q, Yang M. Establishment of a rapid detection method for plutella xylostella granulovirus based on qPCR. Heliyon 2023; 9:e15170. [PMID: 37095984 PMCID: PMC10122022 DOI: 10.1016/j.heliyon.2023.e15170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 03/22/2023] [Accepted: 03/28/2023] [Indexed: 04/26/2023] Open
Abstract
Plutella xylostella granulovirus (PlxyGV) biopesticide is an effective tool to control the long-term damage of Plutella xylostella (Linnaeus) to cruciferous vegetables. In China, PlxyGV can be produced on a large scale using host insects, and its products have been registered in 2008. In experiments and biopesticide production, the routine enumeration method of PlxyGV virus particles is to use the Petroff-Hausser counting chamber in dark field microscope. However, the accuracy and repeatability of granulovirus (GV) counting are affected due to the small particle size of GV occlusion bodies (OBs), the limitations of optical microscope, the judgment of different operators, host impurities, the addition of biological products. This limits the convenience of its production, product quality, trading and field application. Here we use PlxyGV as an example, the method based on Real-time fluorescence quantitative PCR (qPCR) was optimized from two aspects of sample treatment and specific primers design, which improved the repeatability and accuracy of absolute quantitative OBs of GV. This study provides basic information for accurate quantitative PlxyGV by qPCR method.
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Affiliation(s)
- Huan Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Corresponding author. State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beichenxilu 1-5, Beijing, PR China.
| | - Yan Tong
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huifang Liu
- Hebei Professional College of Political Science and Law, Shijiazhuang, China
| | - Lin Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenyi Jin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xuan Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qian Meng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xupeng Yu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fenfen Fang
- Henan Jiyuan Baiyun Industrial Co. LTD, Jiyuan, China
| | - Qilian Qin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Miaomiao Yang
- School of Life Science and Food Engineering, Shaanxi Preschool Normal University, Xian, China
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Yang H, Tu K, Zhao Y, Sun L, Zhao J, Zhang G. Development of SYBR green RT-qPCR assay for titrating bivalent live infectious bronchitis vaccines. J Virol Methods 2023; 313:114675. [PMID: 36592741 DOI: 10.1016/j.jviromet.2022.114675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/20/2022] [Accepted: 12/30/2022] [Indexed: 01/01/2023]
Abstract
Infectious bronchitis (IB) is a highly contagious viral disease of chickens caused by IB virus (IBV) that can cause substantial economic losses in the poultry industry. IBV variant infections have been continuously reported since the initial description in the 1930s. QX-like IBVs are the predominant circulating genotype globally. A homologous QX vaccine has superior protection efficacy compared with that of other available vaccines, and the combination of Massachusetts (Mass)-like and QX-like strains is being used to combat QX-like IBV infections. Inoculation of embryonated chicken eggs is the standard method for the titration of IBV, and the titer is expressed as 50% egg infectious dose (EID50). However, this method cannot effectively distinguish or quantify different genotypic strains in a mixture of different viruses, especially in the absence of neutralizing monoclonal antibodies. In this study, quantitative real-time PCR (RT-qPCR) was applied using specific primers for the QX- and Mass-like strains to quantitate IBV infection and for comparison with the conventional virus titration quantitative method. A strong positive correlation was observed between RT-qPCR cycle threshold values and the different EID50 concentrations. This method was further used to titrate bivalent IB vaccines, and the amount of individual genotype virus was determined based on specific primers. Thus, this RT-qPCR assay may be used as a highly specific, sensitive, and rapid alternative to the EID50 assay for titering IBVs.
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Affiliation(s)
- Huiming Yang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Kaihang Tu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Ye Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Lu Sun
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jing Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| | - Guozhong Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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Shayeghpour A, Forghani-Ramandi MM, Solouki S, Hosseini A, Hosseini P, Khodayar S, Hasani M, Aghajanian S, Siami Z, Zarei Ghobadi M, Mozhgani SH. Identification of novel miRNAs potentially involved in the pathogenesis of adult T-cell leukemia/lymphoma using WGCNA followed by RT-qPCR test of hub genes. Infect Agent Cancer 2023; 18:12. [PMID: 36841815 PMCID: PMC9968414 DOI: 10.1186/s13027-023-00492-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 02/17/2023] [Indexed: 02/27/2023] Open
Abstract
BACKGROUND Adult T-cell Lymphoma/Leukemia (ATLL) is characterized by the malignant proliferation of T-cells in Human T-Lymphotropic Virus Type 1 and a high mortality rate. Considering the emerging roles of microRNAs (miRNAs) in various malignancies, the analysis of high-throughput miRNA data employing computational algorithms helps to identify potential biomarkers. METHODS Weighted gene co-expression network analysis was utilized to analyze miRNA microarray data from ATLL and healthy uninfected samples. To identify miRNAs involved in the progression of ATLL, module preservation analysis was used. Subsequently, based on the target genes of the identified miRNAs, the STRING database was employed to construct protein-protein interaction networks (PPIN). Real-time quantitative PCR was also performed to validate the expression of identified hub genes in the PPIN network. RESULTS After constructing co-expression modules and then performing module preservation analysis, four out of 15 modules were determined as ATLL-specific modules. Next, the hub miRNA including hsa-miR-18a-3p, has-miR-187-5p, hsa-miR-196a-3p, and hsa-miR-346 were found as hub miRNAs. The protein-protein interaction networks were constructed for the target genes of each hub miRNA and hub genes were identified. Among them, UBB, RPS15A, and KMT2D were validated by Reverse-transcriptase PCR in ATLL patients. CONCLUSION The results of the network analysis of miRNAs and their target genes revealed the major players in the pathogenesis of ATLL. Further studies are required to confirm the role of these molecular factors and to discover their potential benefits as treatment targets and diagnostic biomarkers.
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Affiliation(s)
- Ali Shayeghpour
- grid.411705.60000 0001 0166 0922School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | | | - Setayesh Solouki
- grid.411705.60000 0001 0166 0922School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Amin Hosseini
- Department of Computer, Faculty of Engineering, Raja University, Qazvin, Iran
| | - Parastoo Hosseini
- grid.411705.60000 0001 0166 0922Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran ,grid.411705.60000 0001 0166 0922Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Sara Khodayar
- grid.411705.60000 0001 0166 0922Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mahsa Hasani
- grid.411705.60000 0001 0166 0922School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Sepehr Aghajanian
- grid.411705.60000 0001 0166 0922School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Zeinab Siami
- grid.411705.60000 0001 0166 0922Department of Infectious Diseases, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | | | - Sayed-Hamidreza Mozhgani
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran. .,Non-Communicable Disease Research Center, Alborz University of Medical Sciences, Karaj, Iran.
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Zhang X, Zhao T, Liu W, Xi J, Yao D, Cao Y, You X, Wu J, Gao Z, Lei Y, Zhou C, Zhang X, Zheng J, Luan Y. Quinoline is more genotoxic than 4-methylquinoline in hiHeps cells and rodent liver. Mutat Res Genet Toxicol Environ Mutagen 2023; 886:503582. [PMID: 36868699 DOI: 10.1016/j.mrgentox.2022.503582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
Environmental pollutants, such as quinoline (QN) and 4-methylquinoline (4-MeQ), may be genotoxic and carcinogenic. Earlier studies, including in vitro genotoxicity tests, indicated that 4-MeQ is more mutagenic than QN. However, we hypothesized that the methyl group of 4-MeQ favors detoxication over bioactivation, and this factor may be overlooked in in vitro tests that do not incorporate supplementation with cofactors for enzymes that catalyze conjugation reactions. We used human induced hepatocyte cells (hiHeps), which express such enzymes, and compared the genotoxicity of 4-MeQ and QN. We also carried out an in vivo micronucleus (MN) test in rat liver, since 4-MeQ is not genotoxic in rodent bone marrow. In the Ames test and the Tk gene mutation assay, with rat S9 activation, 4-MeQ was more mutagenic than QN. However, QN induced significantly higher MN frequencies in hiHeps and rat liver than did 4-MeQ. Furthermore, QN upregulated genotoxicity marker genes much more than did 4-MeQ. We also investigated the roles of two important detoxication enzymes, UDP-glucuronosyltransferases (UGTs) and cytosolic sulfotransferases (SULTs). When hiHeps were preincubated with hesperetin (UGT inhibitor) and 2,6-dichloro-4-nitrophenol (SULT inhibitor), MN frequencies were elevated approximately 1.5-fold for 4-MeQ, whereas no significant effects were seen for QN. This study shows that QN is more genotoxic than 4-MeQ, when the roles of SULTs and UGTs in detoxication are considered and our results may improve understanding the structure-activity relationships of quinoline derivatives.
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Knapp J, Lallemand S, Monnien F, Felix S, Courquet S, Umhang G, Millon L. Real-time multiplex PCR for human echinococcosis and differential diagnosis. Parasite 2023; 30:3. [PMID: 36700708 PMCID: PMC9886084 DOI: 10.1051/parasite/2023003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/06/2023] [Indexed: 01/27/2023] Open
Abstract
Molecular identification of rare human infectious pathogens appears to be one of the most relevant current methods for rapid diagnosis and management of patients. PCR techniques, in particular real-time quantitative PCR, are best suited for the detection of DNA from the pathogens, even at low concentrations. Echinococcosis infections are due to helminths of the Echinococcus genus, with closely related species involved in parasitic lesions affecting animals and, accidentally, humans. We developed a multiplex qPCR (MLX qPCR) assay allowing for the detection of four Echinococcus species involved in Europe in alveolar echinococcosis (AE) and cystic echinococcosis (CE) (Echinococcus multilocularis, E. granulosus sensu stricto, E. ortleppi, and E. canadensis), based on short mitochondrial targets. A collection of 81 fresh and formalin-fixed paraffin-embedded tissues (FFPE) of AE and CE lesions was assembled. The qPCR assays were performed in triplex for Echinococcus spp. detection, associated with a qPCR inhibitor control. A duplex qPCR was also designed to enable diagnosis of two other dead-end helminthiases (cysticercosis (Taenia solium), and toxocariasis (Toxocara cati and T. canis)). The sensitivity of the qPCR was assessed and ranged from 1 to 5 × 10-4 ng/μL (seven PCR assays positive), corresponding to 37-42 cycles for quantifiable DNA. The specificity was 100% for all the targets. This multiplex qPCR, adapted to low amounts of DNA can be implemented in the laboratory for the rapid molecular diagnosis of Echinococcosis species.
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Affiliation(s)
- Jenny Knapp
- Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon 25030 Besançon France,UMR CNRS 6249 Laboratoire Chrono-environnement, University of Franche-Comté 16 Route de Gray 25030 Besançon France,Corresponding author:
| | - Séverine Lallemand
- UMR CNRS 6249 Laboratoire Chrono-environnement, University of Franche-Comté 16 Route de Gray 25030 Besançon France
| | - Franck Monnien
- Department of Pathology, University Hospital of Besançon 25030 Besançon France
| | - Sophie Felix
- Department of Pathology, University Hospital of Besançon 25030 Besançon France
| | - Sandra Courquet
- Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon 25030 Besançon France,UMR CNRS 6249 Laboratoire Chrono-environnement, University of Franche-Comté 16 Route de Gray 25030 Besançon France
| | - Gérald Umhang
- ANSES Nancy laboratory for Rabies and Wildlife, National Reference Laboratory for Echinococcus spp., Wildlife Surveillance and Eco-epidemiology Unit, Technopole Agricole et Vétérinaire 54220 Malzéville France
| | - Laurence Millon
- Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon 25030 Besançon France,UMR CNRS 6249 Laboratoire Chrono-environnement, University of Franche-Comté 16 Route de Gray 25030 Besançon France
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Knight KL, Mauriello A, Williams G. Quantitation of DNA Using the Applied Biosystems Quantifiler ® Trio DNA Quantification Kit. Methods Mol Biol 2023; 2685:175-188. [PMID: 37439982 DOI: 10.1007/978-1-0716-3295-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Following the isolation of deoxyribonucleic acid (DNA) from biological samples, the quantitation of amplifiable human DNA is a critical next step in the process of DNA analysis. The Quantifiler® Trio kit provides a simple way to accurately estimate the quantity of human and male DNA with concentrations as low as 5 pg/μL or less. Not only can the Quantifiler® Trio kit determine the quantity of human DNA present, but it can also give an indication of the quality of the sample, which is essential information to have in the decision-making process regarding any downstream testing being done. In this chapter, we describe how to prepare and process quantitation reactions using the Quantifiler® Trio kit. We also provide basic information on how to interpret the results.
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Affiliation(s)
- Kelly L Knight
- Forensic Science Program, George Mason University, Fairfax, VA, USA.
| | | | - Georgia Williams
- Forensic Science Program, George Mason University, Fairfax, VA, USA
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Salarieh N, Emami Meibodi A, Alipour S, Azimirad M, Looha MA, Asadzadeh Aghdaei H, Yadegar A, Shahrokh S, Zali MR. Characterization of the mucosal microbiota in patients with nodular lymphoid hyperplasia with concurrent irritable bowel syndrome compared to healthy controls. Mol Biol Rep 2023; 50:145-155. [PMID: 36315327 DOI: 10.1007/s11033-022-07974-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/21/2022] [Indexed: 01/29/2023]
Abstract
BACKGROUND Nodular lymphoid hyperplasia (NLH) is known as a lymphoproliferative lesion in which multiple small nodules appear on the intestinal wall. It has been documented that patients who struggle with irritable bowel syndrome (IBS) are at greater risk of developing NLH. Here, we aimed to investigate the previously reported pathogens and the abundance of a selection of mucosal microbiota in IBS + NLH patients compared to IBS, and healthy controls. METHODS AND RESULTS Terminal ileum biopsies were collected from 37 IBS + NLH, 37 IBS, and 29 healthy controls. Bacterial culture and PCR was performed to detect the presence of pathogens in biopsies. A qPCR assay was applied to assess the abundance of a selection of bacterial taxa. Totally, five bacterial isolates including two enteropathogenic and one enteroaggregative Escherichia coli (EPEC, EAEC), one enterotoxigenic Staphylococcus aureus (SEA), and one Yersinia enterocolitica strains were detected among the IBS + NLH cases. The relative abundance of Bacteroidetes and Streptococcus spp. in IBS + NLH patients was significantly less than IBS and healthy controls. Firmicutes, Pseudomonas spp., Haemophilus spp., and Campylobacter spp. were notably more abundant in IBS + NLH than in IBS patients. The abundance of Verrucomicrobia was higher in NLH + IBS than in healthy controls. Actinobacteria was also significantly more abundant among NLH + IBS patients than the controls. CONCLUSION Our results demonstrated that mucosal microbiota composition in NLH + IBS patients slightly differs from that of IBS patients and healthy controls. Further research using large-scale cohorts are needed to enhance current understanding of the contribution of the mucosal microbiota to NLH pathogenesis with concurrent IBS.
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Affiliation(s)
- Naghmeh Salarieh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Armitasadat Emami Meibodi
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Alipour
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Azizmohammad Looha
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Pan H, Sun Y, Qiao M, Qi H. Beta-galactosidase gene family genome-wide identification and expression analysis of members related to fruit softening in melon (Cucumis melo L.). BMC Genomics 2022; 23:795. [PMID: 36460944 PMCID: PMC9716742 DOI: 10.1186/s12864-022-09006-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/10/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Texture quality is impotent for melon (Cucumis melo L.) fruit. β-galactosidase (β-Gal, EC 3.2.1.23) is an important cell wall glycosyl hydrolase involved in fruit softening, However, the β-Gal gene (BGALs) family hasn't been identified genome-wide in melon. Thus, it's necessary to conduct an in-depth bioinformatic analysis on melon BGALs family and to seek out the key members who participated in melon fruit softening. RESULTS A total of 21 BGALs members designated as CmBGAL1-CmBGAL21 were identified genome-wide in melon, clustered into A-G seven clades. Among them, three duplications CmBGAL1:CmBGAL3, CmBGAL19:CmBGAL21, and CmBGAL20:CmBGAL21 happened. For conserved domains, besides the Glyco_hydro_35 domain (PF01301), all the members also contained the GHD domain (PF17834) except for CmBGAL12, and the Gal_Lectin (PF02140) domain existed in most CmBGALs at the C-termini. Motifs, protein secondary and tertiary structure analysis showed that the CmBGAL12 is a unique member. Moreover, protein-protein association network analysis showed that the CmBGAL12 is the only node protein. Furthermore, spatiotemporal expression pattern analysis by quantitative real-time PCR (qRT-PCR) suggested that most of CmBGALs expressed in tissues with vigorous cell wall remodeling/disassembly. In addition, cis-acting regulatory elements analysis in promoters inferred that CmBGALs might participate in diverse responsiveness to phytohormone, biotic and abiotic signaling. CONCLUSIONS A novel clade of CmBGAL members (Clade F) related to melon fruit softening was discovered, since their expression showed a specific surge in the mature fruit of 'HPM' with mealy texture (softening sharply), but not in 'HDB' with crisp texture (softening bluntly). The homologous CmBGAL7-11 in Clade F exhibited identical spatiotemporal expression patterns may multiple genes leading to melon fruit softening.
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Affiliation(s)
- Haobin Pan
- grid.412557.00000 0000 9886 8131College of Horticulture, Shenyang Agricultural University, No.120 Dongling Road, Shenhe District, Shenyang, Liaoning 110866 People’s Republic of China ,Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang, Liaoning 110866 People’s Republic of China ,Northern National & Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology (Liaoning), Shenyang, Liaoning 110866 People’s Republic of China
| | - Yinhan Sun
- grid.412557.00000 0000 9886 8131College of Horticulture, Shenyang Agricultural University, No.120 Dongling Road, Shenhe District, Shenyang, Liaoning 110866 People’s Republic of China ,Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang, Liaoning 110866 People’s Republic of China ,Northern National & Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology (Liaoning), Shenyang, Liaoning 110866 People’s Republic of China
| | - Miaomiao Qiao
- grid.412557.00000 0000 9886 8131College of Horticulture, Shenyang Agricultural University, No.120 Dongling Road, Shenhe District, Shenyang, Liaoning 110866 People’s Republic of China ,Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang, Liaoning 110866 People’s Republic of China ,Northern National & Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology (Liaoning), Shenyang, Liaoning 110866 People’s Republic of China
| | - Hongyan Qi
- grid.412557.00000 0000 9886 8131College of Horticulture, Shenyang Agricultural University, No.120 Dongling Road, Shenhe District, Shenyang, Liaoning 110866 People’s Republic of China ,Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang, Liaoning 110866 People’s Republic of China ,Northern National & Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology (Liaoning), Shenyang, Liaoning 110866 People’s Republic of China
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Liu H, Xu X, Bai X, Li Y, Wang J, Lv A, Luo Z. Development of a TaqMan real-time quantitative PCR assay to detect Metschnikowia bicuspidata in Chinese mitten crab Eriocheir sinensis. Dis Aquat Organ 2022; 152:17-25. [PMID: 36394137 DOI: 10.3354/dao03704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Milky disease of Chinese mitten crab Eriocheir sinensis caused by Metschnikowia bicuspidata is a novel disease with high mortality. No effective treatment is currently available, but a rapid, accurate detection method is required for the prevention and control of the disease. In this study, the genome-sequencing results of M. bicuspidata and similar species were used for comparative genomic analysis for genes specific to M. bicuspidata. A quantitative PCR (qPCR) detection method for M. bicuspidata was then established using the specific primers and probes designed according to the sequence of a hypothetical protein gene specific to M. bicuspidata. The assay was found to have a high degree of repeatability and reproducibility, with a linear dynamic range (R2 = 0.998) extending over 9 log10 dilutions and a high efficiency (100.7%). Furthermore, the method showed high sensitivity, being able to detect at least 11.3 copies μl-1 of recombinant plasmid, and strong specificity, without any cross-reaction with any of the 9 species of yeast that are closely related to M. bicuspidata or any of 16 species of pathogenic bacteria commonly observed in aquatic animals. The established method was used to examine 138 apparently healthy crabs collected from 22 farms, with 21 samples (15.2%) found to be M. bicuspidata-positive. Thus, the developed qPCR assay is a specific, sensitive, stable, and rapid diagnostic method for the detection and quantification of M. bicuspidata DNA from E. sinensis tissues.
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Affiliation(s)
- Houfu Liu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, PR China
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23
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Bakker R, Ekelmans A, Xie L, Vooijs R, Roelofs D, Ellers J, Hoedjes KM, van Gestel CAM. Biomarker development for neonicotinoid exposure in soil under interaction with the synergist piperonyl butoxide in Folsomia candida. Environ Sci Pollut Res Int 2022; 29:80897-80909. [PMID: 35729387 PMCID: PMC9596504 DOI: 10.1007/s11356-022-21362-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
Pesticide toxicity is typically assessed by exposing model organisms to individual compounds and measuring effects on survival and reproduction. These tests are time-consuming, labor-intensive, and do not accurately capture the effect of pesticide mixtures. Moreover, it is unfeasible to screen the nearly infinite combinations of mixtures for synergistic effects on model organisms. Therefore, reliable molecular indicators of pesticide exposure have to be identified, i.e., biomarkers. These biomarkers can form the basis of rapid and economical screening procedures to assess the toxicity of pesticides even under synergistic interaction with other pollutants. In this study, we screened the expression patterns of eight genes for suitability as a biomarker for neonicotinoid exposure in the soil ecotoxicological model Folsomia candida (springtails). Springtails were exposed to the neonicotinoids imidacloprid and thiacloprid either alone or with various levels of piperonyl butoxide (PBO), which inhibits cytochrome P450 enzymes (CYPs): a common point of synergistic interaction between neonicotinoid and other pesticides. First, we confirmed PBO as a potency enhancer for neonicotinoid toxicity to springtail fecundity, and then used it as a tool to confirm biomarker robustness. We identified two genes that are reliably indicative for neonicotinoid exposure even under metabolic inhibition of CYPs by PBO, nicotinic acetylcholine receptor-subunit alpha 1 (nAchR) and sodium-coupled monocarboxylate transporter (SMCT). These results can form the basis for developing high-throughput screening procedures for neonicotinoid exposure in varying mixture compositions.
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Affiliation(s)
- Ruben Bakker
- Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands.
| | - Astrid Ekelmans
- Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Liyan Xie
- Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Riet Vooijs
- Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Dick Roelofs
- Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
- Keygene N.V., Agro Business Park 90, Wageningen, 6708, PW, The Netherlands
| | - Jacintha Ellers
- Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Katja M Hoedjes
- Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Cornelis A M van Gestel
- Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
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Sezgin E, Terlemez G, Bozkurt B, Bengi G, Akpinar H, Büyüktorun İ. Quantitative real-time PCR analysis of bacterial biomarkers enable fast and accurate monitoring in inflammatory bowel disease. PeerJ 2022; 10:e14217. [PMID: 36275453 PMCID: PMC9586115 DOI: 10.7717/peerj.14217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/20/2022] [Indexed: 01/24/2023] Open
Abstract
Inflammatory bowel diseases (IBD) affect millions of people worldwide with increasing incidence. Ulcerative colitis (UC) and Crohn's disease (CD) are the two most common IBDs. There is no definite cure for IBD, and response to treatment greatly vary among patients. Therefore, there is urgent need for biomarkers to monitor therapy efficacy, and disease prognosis. We aimed to test whether qPCR analysis of common candidate bacteria identified from a patient's individual fecal microbiome can be used as a fast and reliable personalized microbial biomarker for efficient monitoring of disease course in IBD. Next generation sequencing (NGS) of 16S rRNA gene region identified species level microbiota profiles for a subset of UC, CD, and control samples. Common high abundance bacterial species observed in all three groups, and reported to be associated with IBD are chosen as candidate marker species. These species, and total bacteria amount are quantified in all samples with qPCR. Relative abundance of anti-inflammatory, beneficial Faecalibacterium prausnitzii, Akkermansia muciniphila, and Streptococcus thermophilus was significantly lower in IBD compared to control samples. Moreover, the relative abundance of the examined common species was correlated with the severity of IBD disease. The variance in qPCR data was much lower compared to NGS data, and showed much higher statistical power for clinical utility. The qPCR analysis of target common bacterial species can be a powerful, cost and time efficient approach for monitoring disease status and identify better personalized treatment options for IBD patients.
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Affiliation(s)
- Efe Sezgin
- Izmir Institute of Technology, Izmir, Turkey
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Chengula AA, Mugimba KK, Tal S, Levi RT, Dubey S, Mutoloki S, Dishon A, David L, Evensen Ø, Munang'andu HM. Efficiency, sensitivity and specificity of a quantitative real-time PCR assay for Tilapia Lake virus (TiLV). J Virol Methods 2022; 307:114567. [PMID: 35709972 DOI: 10.1016/j.jviromet.2022.114567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022]
Abstract
Tilapia lake virus (TiLV) is an emerging viral pathogen of tilapiines worldwide in wild and farmed tilapia. TiLV is an orthomyxo-like, negative sense segmented RNA virus, belonging to genus Tilapinevirus, family Amnoonviridae. Here we developed a quantitative real-time PCR (qRT-PCR) assay testing primer sets targeting the 10 segments of TiLV. Sensitivity, specificity, efficiency and reproducibility of these assays were examined. Detection sensitivity was equivalent to 2 TCID50/ml when tested on supernatants from cell culture-grown TiLV. Specificity tests showed that all primer sets amplified their respective TiLV segments, and standard curves showed linear correlation of R2 > 0.998 and amplification efficiencies between 93 % and 98 %. Intra- and inter-assay coefficients of variation (CV %) were in the range of 0.0 %- 2.6 % and 0.0 %- 5.9 %, respectively. Sensitivity tests showed that primer sets targeting segments 1, 2, 3 and 4 had the highest detection sensitivities (100.301 TCID50/ml). The qRT-PCR used for detection of viral genome in TiLV infected organs gave virus titers equivalent to 3.80 log10, 3.94 log10 and 3.52 log10 TCID50/ml for brain, kidney and liver tissues, respectively as calculated on the basis of Ct values. These findings suggest that primer optimization for qPCR should not only focus on attaining high amplification efficiency but also sensitivity comparison of primer sets targeting different viral segments in order to develop a method with the highest sensitivity.
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Affiliation(s)
- Augustino Alfred Chengula
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, PO Box 5003, N-1432 Ås, Norway; Sokoine University of Agriculture, College of Veterinary Medicine and Biomedical Sciences, Department of Microbiology, Parasitology and Biotechnology, P.O. Box 3019, Morogoro, Tanzania
| | - Kizito Kahoza Mugimba
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, PO Box 5003, N-1432 Ås, Norway; Makerere University, College of Veterinary Medicine Animal Resources and Biosecurity, Department of Biotechnical and Diagnostic Sciences, Kampala, Uganda
| | - Shlomit Tal
- Phibro Animal Health Corporation, R&D Vaccines, Ha'melacha St. 3, POB 489, West Industrial Zone, Beit-Shemesh 99100, Israel
| | - Roni Tadmor Levi
- Department of Animal Sciences, R.H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
| | - Saurabh Dubey
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, PO Box 5003, N-1432 Ås, Norway
| | - Stephen Mutoloki
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, PO Box 5003, N-1432 Ås, Norway
| | - Arnon Dishon
- Phibro Animal Health Corporation, R&D Vaccines, Ha'melacha St. 3, POB 489, West Industrial Zone, Beit-Shemesh 99100, Israel
| | - Lior David
- Department of Animal Sciences, R.H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
| | - Øystein Evensen
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, PO Box 5003, N-1432 Ås, Norway
| | - Hetron Mweemba Munang'andu
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, PO Box 5003, N-1432 Ås, Norway; Department of Biosciences and Aquaculture, Nord University, PB 1490, 8049 Bodø, Norway.
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Ahmad SM, Ahmed BS, Khidhir KG, Rahman HS. Prospective quantitative gene expression analysis of kallikrein-related peptidase KLK10 as a diagnostic biomarker for childhood acute lymphoblastic leukemia. PeerJ 2022; 10:e13489. [PMID: 35669967 PMCID: PMC9165590 DOI: 10.7717/peerj.13489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/03/2022] [Indexed: 01/17/2023] Open
Abstract
Background The most common malignancy in children is acute lymphoblastic leukemia (ALL). This study aimed to explore KLK10 mRNA expression as a potential diagnostic biomarker for ALL in children and to examine the effect of chemotherapy on KLK10 mRNA expression following the induction and after three months of receiving chemotherapy. Methods In this prospective study, total RNA was extracted from blood samples of 23 pediatric ALL patients on diagnosis, after one month and three months of receiving chemotherapy. Healthy pediatric volunteers (n = 12) were selected as control individuals. After cDNA synthesis, KLK10 mRNA gene expression levels were quantified using quantitative real-time PCR (qRT-PCR). Results KLK10 mRNA expression levels were significantly decreased in leukemic cells compared to their levels in cells of normal blood samples (p = 0.0001). KLK10 expression levels in ALL patients after one month and three months of receiving chemotherapy decreased compared to normal blood samples (p < 0.0001 and p = 0.0175 respectively). The expression level of KLK10 mRNA in ALL patients after one month of chemotherapy was decreased compared to their level on diagnosis (p = 0.4413). KLK10 mRNA expression levels in ALL patients after three months of chemotherapy were increased compared to their level on diagnosis (p = 0.0602). The ROC curve illustrated that KLK10 mRNA expression could very efficiently discriminate ALL patients from normal counterparts (AUC=0.886, 95% CI [0.7720-1.000], SE = 0.0582, p = 0.0004). Conclusion KLK10 mRNA expression could serve as a potential diagnostic molecular biomarker for ALL in children.
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Affiliation(s)
- Shwan Majid Ahmad
- Department of Biochemistry, College of Medicine, University of Sulaimani, Sulaimaniyah, Iraq
| | - Basima Sadq Ahmed
- Department of Biochemistry & Clinical Chemistry, College of Pharmacy, University of Sulaimani, Sulaimaniyah, Iraq
| | - Karzan Ghafur Khidhir
- Department of Biology, College of Science, University of Sulaimani, Sulaimaniyah, Iraq
| | - Heshu Sulaiman Rahman
- Department of Physiology, College of Medicine, University of Sulaimani, Sulaimaniyah, Iraq
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Franconi I, Leonildi A, Erra G, Fais R, Falcone M, Ghelardi E, Lupetti A. Comparison of different microbiological procedures for the diagnosis of Pneumocystis jirovecii pneumonia on bronchoalveolar-lavage fluid. BMC Microbiol 2022; 22:143. [PMID: 35597925 PMCID: PMC9123786 DOI: 10.1186/s12866-022-02559-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The current diagnostic gold standard for Pneumocystis jirovecii is represented by microscopic visualization of the fungus from clinical respiratory samples, as bronchoalveolar-lavage fluid, defining "proven" P. jirovecii pneumonia, whereas qPCR allows defining "probable" diagnosis, as it is unable to discriminate infection from colonization. However, molecular methods, such as end-point PCR and qPCR, are faster, easier to perform and interpret, thus allowing the laboratory to give back the clinician useful microbiological data in a shorter time. The present study aims at comparing microscopy with molecular assays and beta-D-glucan diagnostic performance on bronchoalveolar-lavage fluids from patients with suspected Pneumocystis jirovecii pneumonia. Bronchoalveolar-lavage fluid from eighteen high-risk and four negative control subjects underwent Grocott-Gomori's methenamine silver-staining, end-point PCR, RT-PCR, and beta-D-glucan assay. RESULTS All the microscopically positive bronchoalveolar-lavage samples (50%) also resulted positive by end-point and real time PCR and all, but two, resulted positive also by beta-D-glucan quantification. End-point PCR and RT-PCR detected 10 (55%) and 11 (61%) out of the 18 samples, respectively, thus showing an enhanced sensitivity in comparison to microscopy. All RT-PCR with a Ct < 27 were confirmed microscopically, whereas samples with a Ct ≥ 27 were not. CONCLUSIONS Our work highlights the need of reshaping and redefining the role of molecular diagnostics in a peculiar clinical setting, like P. jirovecii infection, which is a rare but also severe and rapidly progressive clinical condition affecting immunocompromised hosts that would largely benefit from a faster diagnosis. Strictly selected patients, according to the inclusion criteria, resulting negative by molecular methods could be ruled out for P. jirovecii pneumonia.
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Affiliation(s)
- Iacopo Franconi
- Department of Traslational Research and of New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
| | - Alessandro Leonildi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Gianluca Erra
- Department of Traslational Research and of New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
| | - Roberta Fais
- Department of Traslational Research and of New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
| | - Marco Falcone
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Emilia Ghelardi
- Department of Traslational Research and of New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
| | - Antonella Lupetti
- Department of Traslational Research and of New Technologies in Medicine and Surgery, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy.
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Xu CQ, Chen XL, Zhang DS, Wang JW, Yuan H, Chen WF, Xia H, Zhang ZY, Peng FH. Diagnosis of cytomegalovirus encephalitis using metagenomic next-generation sequencing of blood and cerebrospinal fluid: A case report. World J Clin Cases 2022; 10:4601-4607. [PMID: 35663067 PMCID: PMC9125273 DOI: 10.12998/wjcc.v10.i14.4601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/23/2021] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cytomegalovirus (CMV) infections in the population are mostly subclinical, inapparent, or latent. However, it is rare in brain tissue. Most reported CMV encephalitis cases were patients with immunodeficiency. The diagnosis and detection rate of CMV encephalitis in patients with normal immune function needs to be further improved. CASE SUMMARY An 86-year-old male was admitted due to a sudden onset of unconsciousness for 3 h. The patient developed status epilepticus and was relieved after antiepileptic treatment. Encephalitis was considered due to the high signals of diffusion-weighted imaging sequences in the right central region by magnetic resonance imaging. Metagenomic next-generation sequencing (mNGS) of blood and cerebrospinal fluid revealed CMV, with unique reads number being 614 and 1, respectively. Simultaneous quantitative PCR results showed CMV positive in blood samples and negative in cerebrospinal fluid samples. The patient was finally diagnosed as CMV encephalitis with status epilepticus. After the antiviral, hormonal, and γ-globulin pulse therapy, the patient's condition improved, and he was finally discharged. CONCLUSION mNGS could be a reliable approach for the diagnosis of CMV encephalitis, with high efficiency, sensitivity, and specificity.
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Affiliation(s)
- Chang-Qing Xu
- Department of Neurology, Dongguan Kanghua Hospital, Dongguan 523080, Guangdong Province, China
| | - Xia-Ling Chen
- Department of Neurology, Dongguan Kanghua Hospital, Dongguan 523080, Guangdong Province, China
| | - Dong-Sheng Zhang
- Department of Neurology, Dongguan Kanghua Hospital, Dongguan 523080, Guangdong Province, China
| | - Jia-Wei Wang
- Department of Neurology, Dongguan Kanghua Hospital, Dongguan 523080, Guangdong Province, China
| | - Hong Yuan
- Department of Neurology, Dongguan Kanghua Hospital, Dongguan 523080, Guangdong Province, China
| | - Wei-Fan Chen
- Department of Neurology, Dongguan Kanghua Hospital, Dongguan 523080, Guangdong Province, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing 100176, China
| | - Zhong-Yin Zhang
- Department of Neurology, Dongguan Kanghua Hospital, Dongguan 523080, Guangdong Province, China
| | - Fu-Hua Peng
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, Guangdong Province, China
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Shirakawa D, Shirasaki N, Matsushita T, Matsui Y, Yamashita R, Matsumura T, Koriki S. Evaluation of reduction efficiencies of pepper mild mottle virus and human enteric viruses in full-scale drinking water treatment plants employing coagulation-sedimentation-rapid sand filtration or coagulation-microfiltration. Water Res 2022; 213:118160. [PMID: 35151086 DOI: 10.1016/j.watres.2022.118160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Here, we evaluated the reduction efficiencies of indigenous pepper mild mottle virus (PMMoV, a potential surrogate for human enteric viruses to assess virus removal by coagulation-sedimentation-rapid sand filtration [CS-RSF] and coagulation-microfiltration [C-MF]) and representative human enteric viruses in four full-scale drinking water treatment plants that use CS-RSF (Plants A and B) or C-MF (Plants C and D). First, we developed a virus concentration method by using an electropositive filter and a tangential-flow ultrafiltration membrane to effectively concentrate and recover PMMoV from large volumes of water: the recovery rates of PMMoV were 100% when 100-L samples of PMMoV-spiked dechlorinated tap water were concentrated to 20 mL; even when spiked water volume was 2000 L, recovery rates of >30% were maintained. The concentrations of indigenous PMMoV in raw and treated water samples determined by using this method were always above the quantification limit of the real-time polymerase chain reaction assay. We therefore were able to determine its reduction ratios: 0.9-2.7-log10 in full-scale CS-RSF and 0.7-2.9-log10 in full-scale C-MF. The PMMoV reduction ratios in C-MF at Plant C (1.0 ± 0.3-log10) were lower than those in CS-RSF at Plants A (1.7 ± 0.5-log10) and B (1.4 ± 0.7-log10), despite the higher ability of MF for particle separation in comparison with RSF owing to the small pore size in MF. Lab-scale virus-spiking C-MF experiments that mimicked full-scale C-MF revealed that a low dosage of coagulant (polyaluminum chloride [PACl]) applied in C-MF, which is determined mainly from the viewpoint of preventing membrane fouling, probably led to the low reduction ratios of PMMoV in C-MF. This implies that high virus reduction ratios (>4-log10) achieved in previous lab-scale virus-spiking C-MF studies are not necessarily achieved in full-scale C-MF. The PMMoV reduction ratios in C-MF at Plant D (2.2 ± 0.6-log10) were higher than those at Plant C, despite similar coagulant dosages. In lab-scale C-MF, the PMMoV reduction ratios increased from 1-log10 (with PACl [basicity 1.5], as at Plant C) to 2-4-log10 (with high-basicity PACl [basicity 2.1], as at Plant D), suggesting that the use of high-basicity PACl probably resulted in higher reduction ratios of PMMoV at Plant D than at Plant C. Finally, we compared the reduction ratios of indigenous PMMoV and representative human enteric viruses in full-scale CS-RSF and C-MF. At Plant D, the concentrations of human norovirus genogroup II (HuNoV GII) in raw water were sometimes above the quantification limit; however, whether its reduction ratios in C-MF were higher than those of PMMoV could not be judged since reduction ratios were >1.4-log10 for HuNoV GII and 2.3-2.9-log10 for PMMoV. At Plant B, the concentrations of enteroviruses (EVs) and HuNoV GII in raw water were above the quantification limit on one occasion, and the reduction ratios of EVs (>1.2-log10) and HuNoV GII (>1.5-log10) in CS-RSF were higher than that of PMMoV (0.9-log10). This finding supports the usefulness of PMMoV as a potential surrogate for human enteric viruses to assess virus removal by CS-RSF.
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Affiliation(s)
- D Shirakawa
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - N Shirasaki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan.
| | - T Matsushita
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Y Matsui
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - R Yamashita
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - T Matsumura
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - S Koriki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
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Mattox AK, D'Souza G, Khan Z, Allen H, Henson S, Seiwert TY, Koch W, Pardoll DM, Fakhry C. Comparison of next generation sequencing, droplet digital PCR, and quantitative real-time PCR for the earlier detection and quantification of HPV in HPV-positive oropharyngeal cancer. Oral Oncol 2022; 128:105805. [PMID: 35334415 PMCID: PMC9058207 DOI: 10.1016/j.oraloncology.2022.105805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 02/02/2022] [Accepted: 03/01/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Human papillomavirus (HPV) causes nearly 80% of oropharynx cancers diagnosed in the United States, with incidence increasing each year. Analysis of cfDNA in plasma and oral rinse has the potential to detect these cases earlier than their typical presentation, but their utility and the best method to detect HPV in plasma and oral rinse samples is unknown. MATERIALS AND METHODS We directly compared next generation sequencing (NGS), droplet digital PCR (ddPCR), and quantitative real-time PCR (qPCR) for their ability to detect HPV16 DNA in plasma and oral rinse from 66 patients diagnosed with HPV16-positive oropharyngeal cancer (HPV16-OPC). RESULTS HPV DNA detection by NGS and ddPCR in plasma samples both had good sensitivity (70%) for HPV16-OPC compared to 20.6% sensitivity by qPCR (p < 0.001). In oral rinse, NGS demonstrated a superior sensitivity of 75.0% as compared to both ddPCR (8.3%, p < 0.001) and qPCR (2.1%, p < 0.001). In a limited cohort of follow up patients, HPV levels detected in plasma by NGS but not ddPCR or qPCR reflected disease remission or progression. CONCLUSIONS These results suggest that NGS has the best sensitivity for detecting HPV in both plasma and oral rinse and may play a role in monitoring patients for disease recurrence. Additional studies are needed to define the specificity of NGS for similar patient cohorts.
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Affiliation(s)
- Austin K Mattox
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gypsyamber D'Souza
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Zubair Khan
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hailey Allen
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephanie Henson
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tanguy Y Seiwert
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wayne Koch
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Drew M Pardoll
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carole Fakhry
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Bachmann A, Lavstsen T. Analysis of var Gene Transcript Patterns by Quantitative Real-Time PCR. Methods Mol Biol 2022; 2470:149-171. [PMID: 35881345 DOI: 10.1007/978-1-0716-2189-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Quantitative real-time PCR (qPCR) is a simple and sensitive method for determining the amount of a specific target DNA sequence present in a sample. Compared to RNA-seq, reverse transcription qPCR (RT-qPCR) is fast, requires only low input material and is easy to analyze. Therefore, qPCR is widely used to analyze gene expression in P. falciparum, including analyses of the multicopy gene families encoding variant surface antigens (VSAs), whose expression is clonally variant and prone to changes over time. In the recent years, several P. falciparum genomes of culture-adapted strains have been sequenced, providing the knowledge to design variable gene family-specific qPCR primers for each P. falciparum genetic background. Here, we describe the required materials, methods and key factors to perform RT-qPCR experiments to determine VSA transcript abundances in the P. falciparum clones 3D7/NF54, IT4, HB3, and 7G8.
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Affiliation(s)
- Anna Bachmann
- Molecular Biology and Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
- Centre for Structural Systems Biology, Hamburg, Germany.
- Biology Department, University of Hamburg, Hamburg, Germany.
- German Center for Infection Research (DZIF), Partner Site Hamburg-Borstel-Lübeck-Riems, Hamburg, Germany.
| | - Thomas Lavstsen
- Centre for Medical Parasitology at Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
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Mohsin M, Li Y, Zhang X, Wang Y, Huang Z, Yin G, Zhang Z. Development of CRISPR-CAS9 based RNA drugs against Eimeria tenella infection. Genomics 2021; 113:4126-4135. [PMID: 34740777 DOI: 10.1016/j.ygeno.2021.10.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/16/2021] [Accepted: 10/31/2021] [Indexed: 11/29/2022]
Abstract
Parasitic diseases are major trouble in many parts of the world. We consider that if a chemical can break a DNA barcode sequence, it might be used to develop a species-specific anti-parasitic agent. To examine this hypothesis, we constructed sgRNAs that target both the control (5.8S rDNA) and a DNA barcode (ITS) sequence in Eimeria tenella. In vitro experiment showed that Cas9 mRNA combined with sgRNAs could reduce the sporulation percentage of oocysts and the survival rate of sporulated oocysts and sporozoites. Quantitative real-time PCR showed that the DNAs of parasites exposed to Cas9 mRNA and sgRNAs were significantly affected, regardless of whether they were exposed to a combination of two sgRNAs or just a single sgRNA. The DNA sequencing also indicated that the experimental group exposed to two sgRNAs mixed with Cas9-induced deletion of large parts and a single sgRNA mixed with Cas9-induced mutation at sgRNA targeted fragments. In vivo trial, the effect of sgRNA and Cas9 RNA on the pathogenicity of E. tenella in chicken showed less lesion score and oocysts score (P < 0.05) in experimental groups than control groups. The results and concepts presented in this research can lead to discovering novel nucleic acid therapeutic drugs for Eimeriasis and other parasitic infections, which provide insights into the development of species-specific anti-parasitic agents.
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Affiliation(s)
- Muhammad Mohsin
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; Department of Parasitology, University of Agriculture, Faisalabad, Pakistan
| | - Yige Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yilei Wang
- College of Fisheries, Jimei University, Xiamen, Fujian, China
| | - Zhijian Huang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Guangwen Yin
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
| | - Ziping Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China.
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Eshghifar N, Rouhollah F, Barikrow N, Pouresmaeili F, Taheri M. The role of long noncoding RNAs in patients with Luminal A invasive breast ductal carcinoma. Pathol Res Pract 2021; 227:153645. [PMID: 34678601 DOI: 10.1016/j.prp.2021.153645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 12/25/2022]
Abstract
Breast cancer is the most common form of cancer in women around the world. The molecular mechanisms of this heterogeneous disease have been extensively investigated; but yet; It requires a lot of sensitive and specific markers for prognosis and early detection approaches. Non-protein coding RNAs known as lncRNAs have been reported in tumorigenic involvement so they can be used for therapeutic purposes. In the present study, the expression levels of CCAT1, PDCD4, PDCD4-AS1, and MEG3 LncRNA in adjacent tumor and breast tissue in 88 Iranian patients were evaluated by quantitative real-time PCR. CCAT1 was significantly expressed and PDCD4-AS1 decreased in tumor samples, PDCD4 and PDCD4-AS1 showed a positive correlation with each other, higher levels of PDCD4-AS1 were associated with better survival, tumor samples showed lower levels of PDCD4 in Showed comparisons with normal tissue. Our findings suggest that lncRNAs play an important role in controlling gene expression after transcription of major tumor suppressors or carcinogenic genes, leading to the development of triple-negative breast cancer (TNBC). In conclusion, this study investigated the prognostic role of lncRNA in breast cancer patients.
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Affiliation(s)
- Nahal Eshghifar
- Department of Cellular and Molecular Sciences, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Fatemeh Rouhollah
- Department of Cellular and Molecular Sciences, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Nooshin Barikrow
- Department of Cellular and Molecular Sciences, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Farkhondeh Pouresmaeili
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Merker Breyer G, Malvessi Cattani A, Silveira Schrank I, Maboni Siqueira F. The influence of regulatory elements on Mycoplasma hyopneumoniae 7448 transcriptional response during oxidative stress and heat shock. Mol Biol Rep 2021; 49:139-147. [PMID: 34676505 DOI: 10.1007/s11033-021-06851-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/15/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND The comprehension of genome organization and gene modulation is essential for understanding pathogens' infection mechanisms. Mycoplasma hyopneumoniae 7448 genome is organized in transcriptional units (TUs), which are flanked by regulatory elements such as putative promoters, terminators and repetitive sequences. Yet the relationship between the presence of these elements and bacterial responses during stress conditions remains unclear. Thus, in this study, in silico and RT-qPCR analyses were associated to determine the effect of regulatory elements in gene expression regulation upon heat shock and oxidative stress conditions. METHODS AND RESULTS Thirteen TU's organizational profiles were found based on promoters and terminators distribution. Differential expression in genes sharing the same TUs was observed, suggesting the activity of internal regulatory elements. Moreover, 88.8% of tested genes were differentially expressed under oxidative stress in comparison to the control condition, being 81.3% of them surrounded by their own regulatory elements. Similarly, under heat shock, 44.4% of the genes showed regulation when compared to control condition, being 75.0% of them surrounded by their own regulatory elements. CONCLUSIONS Altogether, this data suggests the activity of internal regulatory elements in gene modulation of M. hyopneumoniae 7448 transcription.
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Affiliation(s)
- Gabriela Merker Breyer
- Laboratory of Veterinary Bacteriology, Veterinary Pathology Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Amanda Malvessi Cattani
- Graduate Program in Cell and Molecular Biology, Biotechnology Center, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Irene Silveira Schrank
- Graduate Program in Cell and Molecular Biology, Biotechnology Center, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Franciele Maboni Siqueira
- Laboratory of Veterinary Bacteriology, Veterinary Pathology Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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Ma Y, Zhao H, Shan Q, Xu Y, Yu M, Cui J, Liu T, Qiao L, He X. K-strategy species plays a pivotal role in the natural attenuation of petroleum hydrocarbon pollution in aquifers. J Hazard Mater 2021; 420:126559. [PMID: 34252660 DOI: 10.1016/j.jhazmat.2021.126559] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
The natural attenuation of petroleum hydrocarbons is inseparable from the action of microorganisms, while the degradation methods and ecological strategies of microorganisms in petroleum-contaminated aquifers are still under debate. In the present study, 16 S rRNA sequencing and quantitative real-time polymerase chain reaction were used to assess the potential microbial degradation of petroleum hydrocarbons, and the ecological strategy of microorganisms under petroleum stress was analyzed through a co-occurrence network. The results showed that the microbial community in sediments exhibit higher efficiency and stability and stronger ecological function than that in groundwater. Keystone species coordinated with the community to execute ecosystem processes and tended to choose a K-strategy to survive, with the aquifer sediment being the main site of petroleum hydrocarbon degradation. Under natural conditions, the presence of petroleum hydrocarbons at concentrations higher than 126 μg kg-1 and 5557 μg kg-1 was not conducive to the microbial degradation of polycyclic aromatic hydrocarbons and alkanes, respectively. These results can be used as a reference for an enhanced bioremediation of contaminated groundwater. Overall, these findings provide support to managers for developing environmental management strategies.
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Affiliation(s)
- Yan Ma
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Hangzheng Zhao
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Qianjuan Shan
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanqiu Xu
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Minda Yu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jun Cui
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Tong Liu
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Longkai Qiao
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Xiaosong He
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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Kong W, Zhao G, Chen H, Wang W, Shang X, Sun Q, Guo F, Ma X. Analysis of therapeutic targets and prognostic biomarkers of CXC chemokines in cervical cancer microenvironment. Cancer Cell Int 2021; 21:399. [PMID: 34321012 PMCID: PMC8317415 DOI: 10.1186/s12935-021-02101-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/17/2021] [Indexed: 12/30/2022] Open
Abstract
Background The tumor microenvironment (TME) has received an increasing amount of attention. CXC chemokines can regulate immune cell transport and tumor cell activity to exert anti-tumor immunity. However, studies on the expression and prognosis of CXC chemokines in cervical cancer (CC) are more limited. Methods The study investigated the role of CXC chemokines in TME of CC by using public databases. Moreover, quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC) of CXC chemokines were performed to further verify. Results The transcriptional levels of CXCL1/3/5/6/8/9/10/11/13/16/17 in CC tissues were significantly elevated while the transcriptional levels of CXCL12/14 were significantly reduced. We reached a consistent conclusion that the expression of CXCL9/10/11/13 was verified by quantitative real-time PCR and immunohistochemistry. Moreover, CC patients with low transcriptional levels of CXCL1/2/3/4/5/8 were significantly associated with longer overall survival (OS). The CCL family was related to CXC chemokines neighboring alteration. RELA, NFKB1, LCK and PAK2 were the key transcription factors and kinase targets of CXC chemokines, respectively. We also found there were significant correlations between the expression of CXCL9/10/11 and the infiltration of immune cells (CD8+ T cell, CD4+ T cell, neutrophils and dendritic cells). Conclusions In brief, we conducted a comprehensive analysis of CXC chemokines via clinical data and some online public databases. Our results may provide a new idea for the selection of immunotherapeutic targets and prognostic biomarkers for cervical cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02101-9.
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Affiliation(s)
- Weina Kong
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, No 789 Suzhou Road, Ürümqi, China
| | - Gang Zhao
- Department of Blood Transfusion, Affiliated Traditional Chinese Medicine Hospital of Xinjiang Medical University, Ürümqi, China
| | - Haixia Chen
- Department of Pathology, Tumor Hospital Affiliated to Xinjiang Medical University, Ürümqi, China
| | - Weina Wang
- Department of Pathology, Tumor Hospital Affiliated to Xinjiang Medical University, Ürümqi, China
| | - Xiaoqian Shang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, No 789 Suzhou Road, Ürümqi, China
| | - Qiannan Sun
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, No 789 Suzhou Road, Ürümqi, China
| | - Fan Guo
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, No 789 Suzhou Road, Ürümqi, China.
| | - Xiumin Ma
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, No 789 Suzhou Road, Ürümqi, China.
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Srivastava R, Sirohi P, Chauhan H, Kumar R. The enhanced phosphorus use efficiency in phosphate-deficient and mycorrhiza-inoculated barley seedlings involves activation of different sets of PHT1 transporters in roots. Planta 2021; 254:38. [PMID: 34312721 DOI: 10.1007/s00425-021-03687-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Transcriptional activation of subfamily II PHT1 members in roots is associated with the enhanced phosphorus use efficiency and growth promotion of barley seedlings inoculated with Glomus species. The arbuscular mycorrhizal (AM) fungi symbiotic associations in cereal crops are known to regulate growth in cultivar-specific manner and induce phosphate (Pi) transporters (PHT1) in roots. In the present study, we observed that both AM colonization of roots by Glomus species and phosphate starvation enhanced phosphorus use efficiency (PUE) in barley seedlings. Our search for the full complement of PHT1 members in the recently sequenced barley genome identified six additional genes, totaling their number to 17. Both AM colonization and Pi starvation triggered activation of common as well as different PHT1s. Pi starvation led to the robust upregulation of HvPHT1;6.2/6.3 at 7d and weak activation of HvPHT1;1 in shoots at 3d time-point. In roots, only HvPHT1;1, HvPHT1;6.2/6.3, HvPHT1;7, HvPHT1;8, HvPHT1;11.2 and HvPHT12 were induced at least one of the time-points. AM colonization specifically upregulated HvPHT1;11, HvPHT1;11.2, HvPHT1;12 and HvPHT1;13.1/13.2, members belonging to subfamily II, in roots. Sucrose availability seems to be obligatory for the robust activation of HvPHT1;1 as unavailability of this metabolite generally weakened its upregulation under Pi starvation. Intriguingly, lack of sucrose supply also led to induction of HvPHT1;5, HvPHT1;8, and HvPHT1;11.2 in either roots or shoot or both. The mRNA levels of HvPHT1;5 and HvPHT1;11.2 were not severely affected under combined deficiency of Pi and sucrose. Taken together, this study not only identify additional PHT1 members in barley, but also ascertain their AM, Pi and sucrose-specific transcript accumulation. The beneficial role of AM fungi in the promotion of PUE and barley seedlings' growth is also demonstrated.
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Affiliation(s)
- Rajat Srivastava
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, 500046, India
| | - Parul Sirohi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247 667, India
| | - Harsh Chauhan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247 667, India.
| | - Rahul Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, 500046, India.
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Lu X, Liu Y, Zhang D, Liu K, Wang Q, Wang H. Determination of the panel of reference genes for quantitative real-time PCR in fetal and adult rat intestines. Reprod Toxicol 2021; 104:68-75. [PMID: 34242779 DOI: 10.1016/j.reprotox.2021.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/17/2021] [Revised: 06/30/2021] [Accepted: 07/04/2021] [Indexed: 02/07/2023]
Abstract
In quantitative real-time PCR (qRT-PCR) detection, the stability of reference genes varies with different organs, tissue locations, sex and developmental stages. This study aimed to screen out and determine the optimal panel of reference genes of the intestine in pre- and post-natal rats of different sex. We used qRT-PCR to detect the mRNA expression of six commonly used reference genes (ACTB, GAPDH, HPRT1, B2M, RPLPO and SDHA) in rat intestines at gestational day 21 (GD21) and postnatal week 12 (PW12). Using GeNorm, BestKeeper and NormFinder software comprehensively analyzed the stability of candidate reference genes and screened out stable reference genes. Further, we used the pathological model of prenatal dexamethasone exposure (PDE) to verify the stability of the selected panel of reference genes. Based on the results of the software analysis, the optimal panel of reference genes in the fetal rat intestine was SDHA + ACTB, and the adult rat small intestine and colon were ACTB + HPRT1 and RPLP0 + GAPDH, respectively. There was no significant sex difference in the above results. Besides, in the PDE model, the results were consistent with those under physiological conditions. Therefore, the stability of intestinal reference genes in fetal rats and adult rats was different, and the intestinal reference genes of adult rats were intestinal segments-specific. The selected panel of reference genes was still stable under pathological conditions. This study determined the optimal panel of reference genes of pre- and post-natal rat intestines and provided reliable reference genes for the qRT-PCR analysis of rat intestines.
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Affiliation(s)
- Xiaoqian Lu
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, 430071, China
| | - Yi Liu
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, 430071, China
| | - Dingmei Zhang
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, 430071, China
| | - Kexin Liu
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, 430071, China
| | - Qian Wang
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, 430071, China
| | - Hui Wang
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, 430071, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China.
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Shi J, Chi H, Cao A, Song Y, Zhu M, Zhang L, Xu F, Huang J. Development of IMBs-qPCR detection method for Yersinia enterocolitica based on the foxA gene. Arch Microbiol 2021; 203:4653-4662. [PMID: 34173855 DOI: 10.1007/s00203-021-02459-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 11/29/2022]
Abstract
Yersinia enterocolitica is an important zoonotic pathogen, which seriously endangers food-safety risk. In this study, the recombinant outer membrane protein OmpF and its antibody were prepared and coupled with immunomagnetic beads (IMBs) to capture Y. enterocolitica in food samples, combining the quantitative PCR detection with primers of virulence factor gene foxA for Yersinia enterocolitica contamination. The results showed that the capture efficiency of approximately 80% using anti-OmpF antibody-immunomagnetic beads and linearly dependent capture under 101-105 CFU/mL Y. enterocolitica compared with less than 10% capture of other bacteria. The detection limit of 64 CFU/mL was obtained based on foxA gene PCR detection combined with capture of the anti-OmpF antibody-immunomagnetic beads to detect Yersinia enterocolitica in artificially contaminated milk and pork samples. Compared to the culture method, the developed IMBs-qPCR method has higher consistency, was less time consuming, which taken together provides an effective alternative method for rapid detection of Y. enterocolitica in food.
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Affiliation(s)
- Jingxuan Shi
- School of Life Sciences, Tianjin University, China. No. 92, Weijin road, Nankai District, Tianjin, 300072, China
| | - Heng Chi
- School of Life Sciences, Tianjin University, China. No. 92, Weijin road, Nankai District, Tianjin, 300072, China
| | - Aiping Cao
- School of Life Sciences, Tianjin University, China. No. 92, Weijin road, Nankai District, Tianjin, 300072, China
| | - Yinna Song
- School of Life Sciences, Tianjin University, China. No. 92, Weijin road, Nankai District, Tianjin, 300072, China
| | - Min Zhu
- School of Life Sciences, Tianjin University, China. No. 92, Weijin road, Nankai District, Tianjin, 300072, China
| | - Lilin Zhang
- School of Life Sciences, Tianjin University, China. No. 92, Weijin road, Nankai District, Tianjin, 300072, China
| | - Fuzhou Xu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, 100097, Beijing, People's Republic of China.
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, China. No. 92, Weijin road, Nankai District, Tianjin, 300072, China.
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Stadnik CMB, Caurio CFB, Rodrigues-Filho EM, Nedel WL, Cantisani GPC, Zanotelli ML, Pasqualotto AC. Impact of cytomegalovirus reactivation just before liver transplantation: A prospective cohort study. World J Gastrointest Pathophysiol 2021; 12:51-58. [PMID: 34084592 PMCID: PMC8160598 DOI: 10.4291/wjgp.v12.i3.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/30/2020] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cytomegalovirus (CMV) is the most common viral pathogen after liver transplantation (LT). Although reactivation of CMV infection is generally described in the context of immunosuppression, it has also been described in critically ill immunocompetent patients including cirrhotic patients.
AIM To determine the incidence of reactivated CMV prior to LT.
METHODS This was a prospective cohort study evaluating adult patients who underwent LT between 2014 and 2016. A plasma sample was obtained from all patients for CMV quantitative real-time PCR testing right before transplantation. Patients were followed for at least 1 year to assess the following outcomes: Incidence of CMV infection, organ rejection and overall mortality.
RESULTS A total of 72 patients were enrolled. Four patients died before transplantation, thus 68 patients were followed up for a median of 44 mo (20-50 mo). In 23/72 patients (31.9%) CMV was reactivated before transplantation. Post-transplantation, 16/68 (23.5%) patients had CMV infection and that was significantly associated with the recipient being CMV negative and a CMV-positive donor. Pre-transplant CMV reactivation was not associated with overall mortality (log rank: 0.9).
CONCLUSION This study shows that CMV infection is common in patients with chronic liver disease just before LT, but the clinical impact of this infection seems to be negligible.
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Affiliation(s)
- Claudio Marcel B Stadnik
- Infection Control Department, Santa Casa de Misericordia de Porto Alegre, Porto Alegre 90075075, RS, Brazil
| | - Cassia Ferreira B Caurio
- Molecular Biology Laboratory, Santa Casa de Misericordia de Porto Alegre, Porto Alegre 90075075, RS, Brazil
| | | | - Wagner L Nedel
- Intensive Care, Santa Casa de Misericordia de Porto Alegre, Porto Alegre 90075075, RS, Brazil
| | - Guido PC Cantisani
- Liver Transplant Unit, Santa Casa de Misericordia de Porto Alegre, Porto Alegre 90075075, RS, Brazil
| | - Maria L Zanotelli
- Liver Transplant Unit, Santa Casa de Misericordia de Porto Alegre, Porto Alegre 90075075, RS, Brazil
| | - Alessandro C Pasqualotto
- Molecular Biology Laboratory, Santa Casa de Misericordia de Porto Alegre, Porto Alegre 90075075, RS, Brazil
- Infectious Diseases Unit, Universidade Federal de Ciencias da Saude de Porto Alegre, Porto Alegre 90035075, RS, Brazil
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Chiodi C, Concheri G, Squartini A, Ravi S, Broccanello C, Moro M, Stevanato P. Quantification of rhizomania virus by automated RNA isolation and PCR based methods in sugar beet. Virusdisease 2021;:1-6. [PMID: 33758773 DOI: 10.1007/s13337-021-00674-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/20/2021] [Indexed: 11/05/2022] Open
Abstract
Rhizomania is a grave disease affecting sugar beet (Beta vulgaris L.). It is caused by the Beet Necrotic Yellow Vein Virus (BNYVV), an RNA virus transmitted by the plasmodiophorid vector Polymyxa betae. Genetic resistance to the virus has been accomplished mostly using phenotype-genotype association studies. As yet, the most convenient method to ascertain plant resistance has been the quantification of viral titer in roots through the ELISA test. This method is particularly time-consuming and clashes with the necessities of modern plant breeding. Here, we propose an alternative and successful phenotyping method based on the automatic extraction of the viral RNA from sugar beet roots and its relative and absolute quantification by quantitative real-time PCR (qRT-PCR) and digital PCR (dPCR), respectively. Such a method enables an improved standardization of the study, as well as an accurate quantification of the virus also in those samples presenting low virus titer, with respect to the ELISA test.
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Abstract
Specific quantification of root-colonizing arbuscular mycorrhizal fungi (AMF) by quantitative real-time PCR is a high-throughput technique, most suitable for determining abundances of AMF species or isolates in previously characterized experimental systems. The principal steps are the choice and validation of an appropriate assay to specifically amplify a gene fragment of the target AMF, preparation of templates from root samples, and quantification of the fungal gene copy numbers in these templates. The use of a suitable assay is crucial for a correct data collection but also highly specific for each experimental system and is therefore covered by general recommendations. Subsequently, specific steps are described for the validation of the assay using a standard dilution series, the determination of appropriate dilutions of DNA extracts from roots, and the quantification of the gene copy numbers in samples including calculations.
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El-Far A, Samir S, El-Gebaly E, Taha NY, Fahmy EM, Diab TM, El-Shenawy A. Assessment of eugenol inhibitory effect on biofilm formation and biofilm gene expression in methicillin resistant Staphylococcus aureus clinical isolates in Egypt. Infect Genet Evol 2021; 89:104722. [PMID: 33444856 DOI: 10.1016/j.meegid.2021.104722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/19/2020] [Accepted: 01/08/2021] [Indexed: 10/22/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) biofilm infection is a major threat in Healthcare facilities. The search for biofilm inhibitors is essential to overcome the antibiotic resistance. Eugenol is a phyto-compound that possesses many biological properties. In this study, the aim was to estimate the effect of eugenol on biofilms of MRSA through quantifying the level of gene expression of three genes (IcaA, IcaD and SarA) involved in biofilm development.. Fifty MRSA biofilm producers collected from the microbiology lab at Theodor Bilharz Research Institute were incubated with different concentrations of eugenol for 24 h. The minimum inhibitory concentration of eugenol (MIC) that eradicates the biofilms growth was detected. mRNA was extracted from all isolates before and after the application of eugenol at 0.5 x MIC, and then subjected to quantitative real-time PCR (qPCR). Results showed that fourteen isolates out of 50 (28%) exhibited intermediate biofilm formation ability, and 36 out of 50 (72%) were strong biofilm producers. The MIC values of eugenol for MRSA ranged from 3.125% to 0.01%. The mean values of MIC in both strong and intermediate biofilm forming MRSA isolates were statistically comparable (p = 0.202). qPCR results revealed that the levels of expression of the studied genes IcaA, IcaD, and SarA were decreased after eugenol treatment when compared with their corresponding values before treatment (p = 0.001). Eugenol inhibited the formation of biofilm of MRSA isolates, indicating it could be used to control infections associated with MRSA biofilms.
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Affiliation(s)
- Amira El-Far
- Microbiology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
| | - Safia Samir
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt.
| | - Eman El-Gebaly
- Microbiology and Immunology Department, Faculty of Pharmacy, Beni-Suif University, Egypt.
| | - Nahed Y Taha
- Microbiology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
| | - Ehab M Fahmy
- Medical Microbiology and Immunology Department, Faculty of Medicine, Aswan University, Egypt
| | - Tarek M Diab
- Parasitology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
| | - Ahmed El-Shenawy
- Microbiology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
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Huang X, Green S, Sook Chung J. The presence of an insulin-like peptide-binding protein (ILPBP) in the ovary and its involvement in the ovarian development of the red deep-sea crab, Chaceon quinquedens. Gen Comp Endocrinol 2021; 301:113653. [PMID: 33122036 DOI: 10.1016/j.ygcen.2020.113653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/06/2020] [Accepted: 10/22/2020] [Indexed: 11/30/2022]
Abstract
Invertebrate insulin-like peptide-binding proteins (ILPBPs) are structurally homologous to vertebrate insulin-like growth factor binding protein 7 (IGFBP7). One of the invertebrate ILPBPs is considered as a potential binding protein of insulin-like androgenic gland factor (IAG) in males of crayfish, Cherax quadricarinatus. However, the ILPBP expression is not limited in the androgenic gland and found in most examined tissues, implicating that ILPBP may have additional functions in crustaceans. Here, the full-length cDNA sequence of ILPBP (termed ChqILPBP) is isolated from the ovary of the red deep-sea crab, Chaceon quinquedens. ChqILPBP transcripts are present in the various tissues, as similar to other crab species. The crustacean ILPBPs have their putative amino acid sequences conserved much less than vertebrate IGFBP7s. To understand if ChqILPBP is involved in ovarian development, examined are levels of ChqILPBP, together with vitellogenin (ChqVTG) in the same ovary and hepatopancreas of adult females at the different ovarian stages: 2, 3, and 5. Chaceon hepatopancreas exhibits as the primary VTG synthesis site, while VTG transcript levels do not differ by the ovarian stages. The ovary contains ChqILPBP transcripts ~10-fold higher than hepatopancreas that changes significantly from stage 2 to 3. Such an expression pattern mirrors that of ovarian ChqVTG. In hepatopancreas, ChqILPBP transcripts are similar at stages 2 and 3 and increase significantly at stage 5. The data indicate that ovarian ILPBP may function differently from that of the hepatopancreas and may play a role in ovarian development. ChqAK transcripts are ~six folds higher in the ovary than the hepatopancreas. While they do not differ by ovarian stages, suggesting that AK may not be involved in vitellogenesis of the cold water crustacean species.
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Affiliation(s)
- X Huang
- Institute of Marine and Environmental TechnologyUniversity of Maryland Center for Environmental Science, 701 E. Pratt Street Columbus Center, Baltimore, MD 21202, USA
| | - S Green
- Institute of Marine and Environmental TechnologyUniversity of Maryland Center for Environmental Science, 701 E. Pratt Street Columbus Center, Baltimore, MD 21202, USA
| | - J Sook Chung
- Institute of Marine and Environmental TechnologyUniversity of Maryland Center for Environmental Science, 701 E. Pratt Street Columbus Center, Baltimore, MD 21202, USA.
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Zhang F, Luo J, Teng M, Xing G, Guo J, Zhang Y. Study on the Dynamic Proliferation of JEV in BHK-21 Cells. Intervirology 2021; 64:1-7. [PMID: 33401269 DOI: 10.1159/000510585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/29/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Epidemic Japanese encephalitis is one of the most important zoonotic diseases that cause central nervous system damage. The vaccination has become the most effective and economical measure for its control. Hence, real-time monitoring of Japanese encephalitis virus (JEV) proliferation is crucial to optimize virus inoculation, culturing conditions, and virus harvest time. METHODS The proliferation dynamics of JEV in BHK-21 cells was studied by combining the established quantitative PCR method with the conventional TCID50 assay in this study. RESULTS The proliferation curve determined by the 2 methods has a definite parallel relationship, but the quantitative real-time PCR method (4 h) is faster and more sensitive than the TCID50 method (3-4 days). The determination results of TCID50 showed that the highest viral titer was 105.44 TCID50/0.1 mL and 104.86 TCID50/0.1 mL in cell suspension and culture supernate, respectively, while the virus RNA copies reached the peak at 1.0 × 107.5 copies/µL and 1.0 × 105.6 copies/µL in cell suspension and culture supernate, respectively. CONCLUSION The comprehensive analysis showed that the best time for JEV proliferation in BHK-21 cell was 60 h post infection.
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Affiliation(s)
- Fuliang Zhang
- College of Veterinary Medicine, Northwest A & F University, Yangling, China
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Jun Luo
- Henan Provincial Key Laboratory of Animal Immunology, Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Academy of Agriculture Sciences, Zhengzhou, China
| | - Man Teng
- Henan Provincial Key Laboratory of Animal Immunology, Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Academy of Agriculture Sciences, Zhengzhou, China
| | - Guangxu Xing
- Henan Provincial Key Laboratory of Animal Immunology, Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Academy of Agriculture Sciences, Zhengzhou, China
| | - Junqing Guo
- Henan Provincial Key Laboratory of Animal Immunology, Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Academy of Agriculture Sciences, Zhengzhou, China
| | - Yihua Zhang
- College of Veterinary Medicine, Northwest A & F University, Yangling, China,
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Kaplan E, Aktaş D, Döğen A, Hilmioğlu-Polat S, Gümral R, Hagen F, Ilkit M, de Hoog GS. Development and Analysis of qPCR for the Identification of Arthroconidial Yeasts of the Genus Magnusiomyces. Mycopathologia 2021; 186:41-51. [PMID: 33392857 DOI: 10.1007/s11046-020-00510-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 11/19/2020] [Indexed: 10/20/2022]
Abstract
The arthroconidial yeasts Magnusiomyces capitatus and M. clavatus are emerging opportunistic pulmonary pathogens. They are closely related and difficult to distinguish based on morphological and physiological traits. We applied an SYBR® green-based quantitative PCR (qPCR) assay to identify the species. We analyzed 30 reference strains originating from clinical and environmental sources by targeting the Rpb2 gene encoding the second largest subunit of RNA polymerase II. The qPCR assays were tested by direct identification of M. capitatus and M. clavatus in spiked sputum and household dishwasher swabs, respectively, as models for clinical and environmental samples. The assays were proved to be reliable for species-level identification of both species, with 100% sensitivity and 100% specificity, lowest inter-assay deviations (RSDr ≤ 1.65%, R2 values >0.99), detection limit of 10 theoretical copy number of target DNA, and detection cell limit of ≥5000 yeast cells from spiked sputum samples. The developed qPCR assay is a practical molecular approach for the detection of M. capitatus and M. clavatus that can be used as a stand-alone assay or in conjunction with culture-dependent approaches.
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Zuo S, Jiang K, Li D, Yan X, Nie H. Transcriptomic analysis of Manila clam Ruditapes philippinarum under lipopolysaccharide challenge provides molecular insights into immune response. Fish Shellfish Immunol 2020; 106:110-119. [PMID: 32755682 DOI: 10.1016/j.fsi.2020.07.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 06/14/2020] [Accepted: 07/11/2020] [Indexed: 06/11/2023]
Abstract
The Manila clam, Ruditapes philippinarum, is an economically important shellfish in marine aquaculture. A better understanding of the immune system in R. philippinarum will provide the basis for the development of strategies to mitigate the impact of infectious diseases affecting this species but can also be of relevance for other bivalves of commercial interest. In this study, the transcriptional response of the Manila clam under lipopolysaccharide (LPS) challenge was characterized using RNA sequencing. The transcriptomes of LPS challenged group of clams (LH1, LH2 and LH3), and the PBS control group (CH1, CH2 and CH3), were sequenced with the Illumina HiSeq platform. Compared with the unigene expression profile of the control group, 223 unigenes were up-regulated and 389 unigenes were down-regulated in the LPS challenged group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that signal transduction, defense response, and immune-related pathways such as Chemokine signaling pathway, Complement and coagulation cascades, NOD-like receptor signaling pathway, and Inflammatory mediator regulation of TRP channels in sensory system were the most highly enriched pathways among the genes that were differentially expressed under LPS challenge. This study present understanding of the molecular basis underpinning response to LPS challenge and provides useful information for future work on the molecular mechanism of pathogen resistance and immunity in Manila clam.
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Affiliation(s)
- Shuqi Zuo
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Kunyin Jiang
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Dongdong Li
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Xiwu Yan
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China.
| | - Hongtao Nie
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China.
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Shirasaki N, Matsushita T, Matsui Y, Koriki S. Suitability of pepper mild mottle virus as a human enteric virus surrogate for assessing the efficacy of thermal or free-chlorine disinfection processes by using infectivity assays and enhanced viability PCR. Water Res 2020; 186:116409. [PMID: 32942179 DOI: 10.1016/j.watres.2020.116409] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/02/2020] [Accepted: 09/06/2020] [Indexed: 05/05/2023]
Abstract
Evaluating the efficacy of disinfection processes to inactivate human enteric viruses is important for the prevention and control of waterborne diseases caused by exposure to those viruses via drinking water. Here, we evaluated the inactivation of two representative human enteric viruses (adenovirus type 40 [AdV] and coxsackievirus B5 [CV]) by thermal or free-chlorine disinfection. In addition, we compared the infectivity reduction ratio of a plant virus (pepper mild mottle virus [PMMoV], a recently proposed novel surrogate for human enteric viruses for the assessment of virus removal by coagulation‒rapid sand filtration and membrane filtration) with that of the two human enteric viruses to assess the suitability of PMMoV as a human enteric virus surrogate for use in thermal and free-chlorine disinfection processes. Finally, we examined whether conventional or enhanced viability polymerase chain reaction (PCR) analysis using propidium monoazide (PMA) or improved PMA (PMAxx) with or without an enhancer could be used as alternatives to infectivity assays (i.e., plaque-forming unit method for AdV and CV; local lesion count assay for PMMoV) for evaluating virus inactivation by disinfection processes. We found that PMMoV was more resistant to heat treatment than AdV and CV, suggesting that PMMoV is a potential surrogate for these two enteric viruses with regard to thermal disinfection processes. However, PMMoV was much more resistant to chlorine treatment compared with AdV and CV (which is chlorine-resistant) (CT value for 4-log10 inactivation: PMMoV, 84.5 mg-Cl2·min/L; CV, 1.15-1.19 mg-Cl2·min/L), suggesting that PMMoV is not useful as a surrogate for these enteric viruses with regard to free-chlorine disinfection processes. For thermal disinfection, the magnitude of the signal reduction observed with PMAxx-Enhancer-PCR was comparable with the magnitude of reduction in infectivity, indicating that PMAxx-Enhancer-PCR is a potential alternative to infectivity assay. However, for free-chlorine disinfection, the magnitude of the signal reduction observed with PMAxx-Enhancer-PCR was smaller than the magnitude of the reduction in infectivity, indicating that PMAxx-Enhancer-PCR underestimated the efficacy of virus inactivation (i.e., overestimated the infectious virus concentration) by chlorine treatment. Nevertheless, among the PCR approaches examined in the present study (PCR alone, PMA-PCR or PMAxx-PCR either with or without enhancer), PMAxx-Enhancer-PCR provided the most accurate assessment of the efficacy of virus inactivation by thermal or free chlorine disinfection processes.
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Affiliation(s)
- N Shirasaki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan.
| | - T Matsushita
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan
| | - Y Matsui
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan
| | - S Koriki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan
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Alfred Compaoré CF, Ilboudo H, Kaboré J, Kaboré JW, Camara O, Bamba M, Sakande H, Koné M, Camara M, Kaba D, Gaston Belem AM, Deborggraeve S, Büscher P, Bucheton B, Lejon V, Jamonneau V. Analytical sensitivity of loopamp and quantitative real-time PCR on dried blood spots and their potential role in monitoring human African trypanosomiasis elimination. Exp Parasitol 2020; 219:108014. [PMID: 33011238 DOI: 10.1016/j.exppara.2020.108014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 05/28/2020] [Revised: 09/19/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022]
Abstract
The objective set by WHO to reach elimination of human African trypanosomiasis (HAT) as a public health problem by 2020 is being achieved. The next target is the interruption of gambiense-HAT transmission in humans by 2030. To monitor progress towards this target, in areas where specialized local HAT control capacities will disappear, is a major challenge. Test specimens should be easily collectable and safely transportable such as dried blood spots (DBS). Monitoring tests performed in regional reference centres should be reliable, cheap and allow analysis of large numbers of specimens in a high-throughput format. The aim of this study was to assess the analytical sensitivity of Loopamp, M18S quantitative real-time PCR (M18S qPCR) and TgsGP qPCR as molecular diagnostic tests for the presence of Trypanosoma brucei gambiense in DBS. The sensitivity of the Loopamp test, with a detection limit of 100 trypanosomes/mL, was in the range of parasitaemias commonly observed in HAT patients, while detection limits for M18S and TgsGP qPCR were respectively 1000 and 10,000 trypanosomes/mL. None of the tests was entirely suitable for high-throughput use and further development and implementation of sensitive high-throughput molecular tools for monitoring HAT elimination are needed.
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Affiliation(s)
- Charlie Franck Alfred Compaoré
- Centre International of Recherche-Développement sur l'Élevage en Zone Subhumide, Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, 01 BP 454, Bobo-Dioulasso 01, Burkina Faso; Université Nazi Boni, Unité de Formation et de Recherche Sciences et Techniques, 01 BP 1091, Bobo-Dioulasso, Burkina Faso
| | - Hamidou Ilboudo
- Institut de Recherche en Sciences de la Santé, Unité de Recherche Clinique de Nanoro, 11 BP 218, Ouagadougou CMS 11, Burkina Faso
| | - Jacques Kaboré
- Centre International of Recherche-Développement sur l'Élevage en Zone Subhumide, Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, 01 BP 454, Bobo-Dioulasso 01, Burkina Faso; Université Nazi Boni, Unité de Formation et de Recherche Sciences et Techniques, 01 BP 1091, Bobo-Dioulasso, Burkina Faso
| | - Justin Windingoudi Kaboré
- Centre International of Recherche-Développement sur l'Élevage en Zone Subhumide, Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, 01 BP 454, Bobo-Dioulasso 01, Burkina Faso; Programme National de Lutte Contre la Trypanosomiase Humaine Africaine, BP 581, Conakry, Guinea
| | - Oumou Camara
- Programme National de Lutte Contre la Trypanosomiase Humaine Africaine, BP 581, Conakry, Guinea
| | - Mohamed Bamba
- Centre International of Recherche-Développement sur l'Élevage en Zone Subhumide, Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, 01 BP 454, Bobo-Dioulasso 01, Burkina Faso
| | - Hassane Sakande
- Centre International of Recherche-Développement sur l'Élevage en Zone Subhumide, Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, 01 BP 454, Bobo-Dioulasso 01, Burkina Faso
| | - Minayégninrin Koné
- Institut Pierre Richet, Unité de Recherche « Trypanosomoses », 01 BP 1500, Bouake, West Africa
| | - Mamadou Camara
- Programme National de Lutte Contre la Trypanosomiase Humaine Africaine, BP 581, Conakry, Guinea
| | - Dramane Kaba
- Institut Pierre Richet, Unité de Recherche « Trypanosomoses », 01 BP 1500, Bouake, West Africa
| | - Adrien Marie Gaston Belem
- Université Nazi Boni, Unité de Formation et de Recherche Sciences et Techniques, 01 BP 1091, Bobo-Dioulasso, Burkina Faso
| | - Stijn Deborggraeve
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Philippe Büscher
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Bruno Bucheton
- Programme National de Lutte Contre la Trypanosomiase Humaine Africaine, BP 581, Conakry, Guinea; Institut de Recherche pour le Développement, UMR INTERTRYP IRD-CIRAD, Université de Montpellier, TA A-17/G, Campus International de Baillarguet, F-34398, Montpellier, France
| | - Veerle Lejon
- Institut de Recherche pour le Développement, UMR INTERTRYP IRD-CIRAD, Université de Montpellier, TA A-17/G, Campus International de Baillarguet, F-34398, Montpellier, France
| | - Vincent Jamonneau
- Institut Pierre Richet, Unité de Recherche « Trypanosomoses », 01 BP 1500, Bouake, West Africa; Institut de Recherche pour le Développement, UMR INTERTRYP IRD-CIRAD, Université de Montpellier, TA A-17/G, Campus International de Baillarguet, F-34398, Montpellier, France.
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He J, Shen C, Liang H, Fang X, Lu J. Antimicrobial properties and immune-related gene expression of a C-type lectin isolated from Pinctada fucata martensii. Fish Shellfish Immunol 2020; 105:330-340. [PMID: 32712228 DOI: 10.1016/j.fsi.2020.07.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
C-type lectins are carbohydrate-binding proteins that play important roles in the innate immune response to pathogen infections. Here, multi-step high performance liquid chromatography (HPLC), combined with mass spectrometry (MS), was used to isolate and identify proteins with antibacterial activity from the serum of Pinctada fucata martensii. Using this method, we obtained a novel isoform of C-type lectin (PmCTL-1). PmCTL-1 strongly inhibited gram-positive bacteria. The complete cDNA sequence of PmCTL-1 was 636 bp in length, and encoded a protein 149 amino acids long, containing a typical carbohydrate recognition domain (CRD). A phylogenetic analysis based on a multiple sequence alignment indicated that PmCTL-1 was highly similar to C-type lectins from other mollusks. Fluorescent quantitative real-time PCR analysis showed that PmCTL-1 mRNA was strongly upregulated in the mantle of healthy P.f. martensii, but was expressed only at low levels in the gill, gonad, hepatopancreas, adductor muscle, and hemocytes. PmCTL-1 expression levels in the mantle and hemocytes increased significantly in response to bacterial stimulation. This study provides a valuable framework for further explorations of innate immunity and the immune response in mollusks.
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Affiliation(s)
- Junjun He
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, PR China; Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, PR China
| | - Chenghao Shen
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, PR China; Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, PR China
| | - Haiying Liang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, Guangdong, PR China; Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, PR China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, Guangdong, PR China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, Guangdong, PR China.
| | - Xiaochen Fang
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, PR China
| | - Jinzhao Lu
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, PR China
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