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Qin X, Guo M, Qin S, Chen R. [Exploration of cross-cultivar group characteristics of a new cultivar of Prunus mume 'Zhizhang Guhong Chongcui']. Sheng Wu Gong Cheng Xue Bao 2024; 40:239-251. [PMID: 38258644 DOI: 10.13345/j.cjb.230287] [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] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
'Zhizhang Guhong Chongcui' is a new cultivar of Prunus mume with cross-cultivar group characteristics. It has typical characteristics of cinnabar purple cultivar group and green calyx cultivar group. It has green calyx, white flower, and light purple xylem, but the mechanism remains unclear. In order to clarify the causes of its cross-cultivar group traits, the color phenotype, anthocyanin content and the expression levels of genes related to anthocyanin synthesis pathway of 'Zhizhang Guhong Chongcui', 'Yuxi Zhusha' and 'Yuxi Bian Lü'e' were determined. It was found that the red degree of petals, sepals and fresh xylem in branches was positively correlated with the total anthocyanin content. MYBɑ1, MYB1, and bHLH3 were the key transcription factor genes that affected the redness of the three cultivars of flowers and xylem. The transcription factors further promoted the high expression of structural genes F3'H, DFR, ANS and UFGT, thereby promoting the production of red traits. Combined with phenotype, anthocyanin content and qRT-PCR results, it was speculated that the white color of petals of 'Zhizhang Guhong Chongcui' were derived from the high expression of FLS, F3'5'H, LAR and ANR genes in other branches of cyanidin synthesis pathway, and the low expression of GST gene. The green color of sepals might be originated from the relatively low expression of F3'H, DFR and ANS genes. The red color of xylem might be derived from the high expression of ANS and UFGT genes. This study made a preliminary explanation for the characteristics of the cross-cultivar group of 'Zhizhang Guhong Chongcui', and provided a reference for molecular breeding of flower color and xylem color of Prunus mume.
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Affiliation(s)
- Xiaotian Qin
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, National Engineering Research Center for Floriculture, Engineering Research Center of Landscape Environment of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Yuxi Institute of Mei, Sanmenxia 472200, Henan, China
| | - Mengge Guo
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, National Engineering Research Center for Floriculture, Engineering Research Center of Landscape Environment of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Shaohua Qin
- Yuxi Institute of Mei, Sanmenxia 472200, Henan, China
| | - Ruidan Chen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, National Engineering Research Center for Floriculture, Engineering Research Center of Landscape Environment of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
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Zhang J, He X, Zhou J, Dong Z, Yu H, Tang Q, Yuan L, Peng S, Zhong X, He Y. Selection and Verification of Standardized Reference Genes of Angelica dahurica under Various Abiotic Stresses by Real-Time Quantitative PCR. Genes (Basel) 2024; 15:79. [PMID: 38254968 PMCID: PMC10815136 DOI: 10.3390/genes15010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
In traditional Chinese medicine, Angelica dahurica is a valuable herb with numerous therapeutic applications for a range of ailments. There have not yet been any articles on the methodical assessment and choice of the best reference genes for A. dahurica gene expression studies. Real-time quantitative PCR (RT-qPCR) is widely employed as the predominant method for investigating gene expression. In order to ensure the precise determination of target gene expression outcomes in RT-qPCR analysis, it is imperative to employ stable reference genes. In this study, a total of 11 candidate reference genes including SAND family protein (SAND), polypyrimidine tract-binding protein (PTBP), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), TIP41-like protein (TIP41), cyclophilin 2 (CYP2), elongation factor 1 α (EF1α), ubiquitin-protein ligase 9 (UBC9), tubulin β-6 (TUB6), thioredoxin-like protein YLS8 (YLS8), and tubulin-α (TUBA) were selected from the transcriptome of A. dahurica. Subsequently, three statistical algorithms (geNorm, NormFinder, and BestKeeper) were employed to assess the stability of their expression patterns across seven distinct stimulus treatments. The outcomes obtained from these analyses were subsequently amalgamated into a comprehensive ranking using RefFinder. Additionally, one target gene, phenylalanine ammonia-lyase (PAL), was used to confirm the effectiveness of the selected reference genes. According to the findings of this study, the two most stable reference genes for normalizing the expression of genes in A. dahurica are TIP41 and UBC9. Overall, our research has determined the appropriate reference genes for RT-qPCR in A. dahurica and provides a crucial foundation for gene screening and identifying genes associated with the biosynthesis of active ingredients in A. dahurica.
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Affiliation(s)
- Jing Zhang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Xinyi He
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Jun Zhou
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Zhuang Dong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Han Yu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Qi Tang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Lei Yuan
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Siqing Peng
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Xiaohong Zhong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Yuedong He
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
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Li S, Guo K, Wang X, Lin Y, Wang J, Wang Y, Du C, Hu Z, Wang X. Development and evaluation of a real-time quantitative PCR for the detection of equine infectious anemia virus. Microbiol Spectr 2023; 11:e0259923. [PMID: 37811976 PMCID: PMC10715080 DOI: 10.1128/spectrum.02599-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Equine infectious anemia (EIA) has a worldwide distribution and causes significant losses to the equine industry worldwide. A reliable detection method is necessary to control the transmission of EIA virus (EIAV). Currently, most of the available real-time PCR assays, including the qPCR of recommended by WOAH, are developed according to the sequences of European or American EIAV strains; however, the primers and probe sequences have low homology with Asian EIAV strains. To the best of our knowledge, no qPCR method capable of the well detection of Asian EIAV strains, especially Chinese EIAV strains, has been published to date. The development of a sensitive, specific, and rapid qPCR assay for the detection of the EIAV strains is therefore of great importance.
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Affiliation(s)
- Shuaijie Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, Harbin, China
| | - Kui Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, Harbin, China
| | - Xuefeng Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, Harbin, China
| | - Yuezhi Lin
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, Harbin, China
| | - Jinhui Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, Harbin, China
| | - Yaoxin Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, Harbin, China
| | - Cheng Du
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, Harbin, China
| | - Zhe Hu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, Harbin, China
- WOAH Reference Laboratory for Equine Infectious Anemia, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaojun Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, Harbin, China
- WOAH Reference Laboratory for Equine Infectious Anemia, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
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Hammad MI, Conrads G, Abdelbary MMH. Isolation, identification, and significance of salivary Veillonella spp., Prevotella spp., and Prevotella salivae in patients with inflammatory bowel disease. Front Cell Infect Microbiol 2023; 13:1278582. [PMID: 38053528 PMCID: PMC10694262 DOI: 10.3389/fcimb.2023.1278582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/30/2023] [Indexed: 12/07/2023] Open
Abstract
The global prevalence of inflammatory bowel disease (IBD) is on the rise, prompting significant attention from researchers worldwide. IBD entails chronic inflammatory disorders of the intestinal tract, characterized by alternating flares and remissions. Through high-throughput sequencing, numerous studies have unveiled a potential microbial signature for IBD patients showing intestinal enrichment of oral-associated bacteria. Simultaneously, the oral microbiome can be perturbed by intestinal inflammation. Our prior investigation, based on 16S rRNA amplicon sequencing, underscored elevated abundance of Veillonella spp. and Prevotella spp. in the salivary microbiomes of IBD patients. Noteworthy, Prevotella salivae emerged as a distinct species significantly associated with IBD. P. salivae is an under-recognized pathogen that was found to play a role in both oral and systemic diseases. In this study, we delve deeper into the salivary microbiomes of both IBD patients and healthy controls. Employing diverse cultivation techniques and real-time quantitative polymerase chain reactions (RT-qPCR), we gauged the prevalence and abundance of Veillonella spp., Prevotella spp., and P. salivae. Our isolation efforts yielded 407 and 168 strains of Veillonella spp., as well as 173 and 90 strains of Prevotella spp., from the saliva samples of IBD patients and healthy controls, respectively. Veillonella-vancomycin agar emerged as the discerning choice for optimal Veillonella spp. cultivation, while Schaedler kanamycin-vancomycin agar proved to be the most suitable medium for cultivating Prevotella spp. strains. Comparing our RT-qPCR findings to the previous 16S rRNA amplicon sequencing data, the results corroborated the higher abundance of Veillonella spp., Prevotella spp., and P. salivae in the saliva of IBD patients compared to healthy controls. However, it's worth noting that in contrast to RT-qPCR, the 16S rRNA amplicon sequencing data revealed greater absolute abundance of all three bacterial groups in both IBD patients and controls.
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Affiliation(s)
- Moshira I. Hammad
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule University Hospital, Aachen, Germany
| | - Georg Conrads
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule University Hospital, Aachen, Germany
| | - Mohamed M. H. Abdelbary
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule University Hospital, Aachen, Germany
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
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Zhou B, Yang G, Hu Z, Chen K, Guo W, Wang X, Du C. Development of a Real-Time Quantitative PCR Based on a TaqMan-MGB Probe for the Rapid Detection of Theileria haneyi. Microorganisms 2023; 11:2633. [PMID: 38004645 PMCID: PMC10673206 DOI: 10.3390/microorganisms11112633] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Equine piroplasmosis (EP) is a parasitic disease caused by Theileria equi (T. equi), Babesia caballi (B. caballi) and Theileria haneyi (T. haneyi). This disease is considered to be reportable by the World Organization for Animal Health (WOAH). Real-time quantitative PCR (qPCR) is regarded as a straightforward, rapid and sensitive diagnostic method to detect pathogens. However, qPCR has not been employed in the various epidemiological investigations of T. haneyi. In this study, we developed a new qPCR method to detect T. haneyi based on the chr1sco (chromosome 1 single-copy open reading frame (ORF)) gene, which has no detectable orthologs in T. equi or B. caballi. A TaqMan MGB probe was used in the development of the qPCR assay. A plasmid containing the chr1sco gene was constructed and used to establish the standard curves. The novel qPCR technique demonstrated great specificity for detecting additional frequent equine infectious pathogens and sensitivity for detecting diluted standard plasmids. This qPCR was further validated by comparison with an optimized nested PCR (nPCR) assay in the analysis of 96 clinical samples. The agreement between the nPCR assay and the established qPCR assay was 85.42%. The newly established method could contribute to the accurate diagnosis of T. haneyi infections in horses.
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Affiliation(s)
| | | | | | | | | | - Xiaojun Wang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (B.Z.); (G.Y.); (Z.H.); (K.C.); (W.G.)
| | - Cheng Du
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (B.Z.); (G.Y.); (Z.H.); (K.C.); (W.G.)
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Shen XX, Zhang GQ, Zhao YX, Zhu XX, Yu XF, Yang MF, Zhang F. Selection and validation of optimal reference genes for RT-qPCR analyses in Aphidoletes aphidimyza Rondani (Diptera: Cecidomyiidae). Front Physiol 2023; 14:1277942. [PMID: 37954450 PMCID: PMC10634233 DOI: 10.3389/fphys.2023.1277942] [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: 08/15/2023] [Accepted: 10/06/2023] [Indexed: 11/14/2023] Open
Abstract
Aphidoletes aphidimyza is a predator that is an important biological agent used to control agricultural and forestry aphids. Although many studies have investigated its biological and ecological characteristics, few molecular studies have been reported. The current study was performed to identify suitable reference genes to facilitate future gene expression and function analyses via quantitative reverse transcription PCR. Eight reference genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), RPS13, RPL8, RPS3, α-Tub, β-actin, RPL32, and elongation factor 1 alpha (EF1-α) were selected. Their expression levels were determined under four different experimental conditions (developmental stages, adult tissues, sugar treatment, and starvation treatment) using qRT-PCR technology. The stability was evaluated with five methods (Ct value, geNorm, NormFinder, BestKeeper, and RefFinder). The results showed that GAPDH, RPL32, and EF1-α were ranked as the best reference gene combinations for measuring gene expression levels among different developing stages and in various starvation treatments. RPL8 and RPS3 were recommended to normalize the gene expression levels among different adult tissues. RPL32, β-actin, and EF1-α were recommended sugar-feeding conditions. To validate the utility of the selected reference pair, RPL8, and RPS3, we estimated the tissue-biased expression level of a chemosensory protein gene (AaphCSP1). As expected, AaphCSP1 is highly expressed in the antennae and lowly expressed in the abdomen. These findings will lay the foundation for future research on the molecular physiology and biochemistry of A. aphidimyza.
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Affiliation(s)
- Xiu-Xian Shen
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, College of Agriculture, Guizhou University, Guiyang, China
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guo-Qiang Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yu-Xin Zhao
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Xiao Zhu
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Fei Yu
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Mao-Fa Yang
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, College of Agriculture, Guizhou University, Guiyang, China
| | - Feng Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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Han X, Beck K, Bürgmann H, Frey B, Stierli B, Frossard A. Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes. Front Microbiol 2023; 14:1279041. [PMID: 37942081 PMCID: PMC10627841 DOI: 10.3389/fmicb.2023.1279041] [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: 08/17/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.
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Affiliation(s)
- Xingguo Han
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Karin Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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Chen M, Wang Z, Hao Z, Li H, Feng Q, Yang X, Han X, Zhao X. Screening and Validation of Appropriate Reference Genes for Real-Time Quantitative PCR under PEG, NaCl and ZnSO 4 Treatments in Broussonetia papyrifera. Int J Mol Sci 2023; 24:15087. [PMID: 37894768 PMCID: PMC10606616 DOI: 10.3390/ijms242015087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Real-time quantitative PCR (RT-qPCR) has a high sensitivity and strong specificity, and is widely used in the analysis of gene expression. Selecting appropriate internal reference genes is the key to accurately analyzing the expression changes of target genes by RT-qPCR. To find out the most suitable internal reference genes for studying the gene expression in Broussonetia papyrifera under abiotic stresses (including drought, salt, and ZnSO4 treatments), seven different tissues of B. papyrifera, as well as the roots, stems, and leaves of B. papyrifera under the abiotic stresses were used as test materials, and 15 candidate internal reference genes were screened based on the transcriptome data via RT-qPCR. Then, the expression stability of the candidate genes was comprehensively evaluated through the software geNorm (v3.5), NormFinder (v0.953), BestKeeper (v1.0), and RefFinder. The best internal reference genes and their combinations were screened out according to the analysis results. rRNA and Actin were the best reference genes under drought stress. Under salt stress, DOUB, HSP, NADH, and rRNA were the most stable reference genes. Under heavy metal stress, HSP and NADH were the most suitable reference genes. EIF3 and Actin were the most suitable internal reference genes in the different tissues of B. papyrifera. In addition, HSP, rRNA, NADH, and UBC were the most suitable internal reference genes for the abiotic stresses and the different tissues of B. papyrifera. The expression patterns of DREB and POD were analyzed by using the selected stable and unstable reference genes. This further verified the reliability of the screened internal reference genes. This study lays the foundation for the functional analysis and regulatory mechanism research of genes in B. papyrifera.
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Affiliation(s)
- Mengdi Chen
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
| | - Zhengbo Wang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
| | - Ziyuan Hao
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
| | - Hongying Li
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
| | - Qi Feng
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
| | - Xue Yang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
| | - Xiaojiao Han
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xiping Zhao
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China; (M.C.)
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Wen J, Yin X, Zhang X, Lan D, Liu J, Song X, Sun Y, Cao J. Development of a Real-Time qPCR Method for the Clinical Sample Detection of Capripox Virus. Microorganisms 2023; 11:2476. [PMID: 37894134 PMCID: PMC10608805 DOI: 10.3390/microorganisms11102476] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Capripox viruses (CaPVs), including sheep pox virus (SPV), goat pox virus (GPV), and lumpy skin disease virus (LSDV), are the cause of sheep pox (SPP), goat pox (GTP), and lumpy skin disease (LSD) in cattle. These diseases are of great economic significance to farmers, as they are endemic on farms and are a major constraint to international trade in livestock and their products. Capripoxvirus (CaPV) infections produce similar symptoms in sheep and goats, and the three viruses cannot be distinguished serologically. In this study, we developed a real-time quantitative polymerase chain reaction (qPCR) method for identifying CaPV in goats, sheep, and cattle. Clinical samples were tested and verified. The developed assay was highly specific for target viruses, including GPVSPV and LSDV, which had no cross-reaction with other viruses causing similar clinical symptoms. An artificially synthesized positive control plasmid using the CaPV 32 gene inserted into the vector pMD19-T was used as a template, and the correlation coefficient of the linear regression curve (R2) was 0.9916, the estimated amplification efficiency (E) was 96.06%, and the sensitivity (limit of detection, LOD) was 3.80 copies per reaction. Using the clinical samples as a template, the limit of detection (LOD) was 4.91 × 10-5 ng per reaction (1.60 × 10-5-2.13 × 10-3 ng, 95% confidence interval (CI)), which means that this method was one of the most sensitive detection assays for CaPVs. A total of 85 clinical samples from CaPV-infected animals (goats, sheep, and cattle) and 50 clinical samples from healthy animals were used to test and compare the diagnostic results using the Synergy Brands (SYBR) Green-based PCR method recommended by the World Organization of Animal Health (WOAH). Both diagnostic sensitivity (DSe) (95.8-100%, 95% CI) and diagnostic specificity (DSp) (92.9-100%, 95% CI) results of the real-time quantitative PCR (qPCR) and SYBR Green PCR were 100%, and the kappa value (κ) was 1.0 (1-1, 95% CI). In summary, the assay established based on TaqMan probes was advantageous in high specificity, sensitivity, and general applicability and could be a competitive candidate tool for the diagnosis of CaPV in clinically suspected animals.
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Affiliation(s)
- Jiaxin Wen
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China; (J.W.); (X.Y.); (X.Z.)
| | - Xinying Yin
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China; (J.W.); (X.Y.); (X.Z.)
| | - Xiaobo Zhang
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China; (J.W.); (X.Y.); (X.Z.)
| | - Desong Lan
- Liaoning Center for Animal Disease Control and Prevention, Shenyang 110164, China;
| | - Junshan Liu
- School of Mechanical Engineering, Faculty of Mechanical Engineering, Materials and Energy, Dalian University of Technology, Dalian 116024, China;
| | - Xiaohui Song
- China Animal Disease Prevention Control Center, Beijing 100125, China;
| | - Yu Sun
- China Animal Disease Prevention Control Center, Beijing 100125, China;
| | - Jijuan Cao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian 116600, China; (J.W.); (X.Y.); (X.Z.)
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10
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Kumar K, Hallikeri K, Oli A, Goni M, Jain A, Poyya J, Shilpasree AS, Javaregowda PK. Quantitative analysis of lncRNA in formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma. Biotechniques 2023; 75:133-142. [PMID: 37589188 DOI: 10.2144/btn-2023-0033] [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] [Indexed: 08/18/2023] Open
Abstract
The study evaluated expression profiles of few regulatory lncRNAs in oral squamous cell carcinoma and normal mucosa adjacent to oral cancer using paired fresh frozen and formalin-fixed paraffin-embedded (FFPE) tissues stored at a different duration of time (1-5 years) using real-time quantitative PCR. The quantity and quality of total RNA isolated from FFPE tissues was less compared with that of fresh frozen tissues, which resulted in a noncorrelation of quantification cycle values. Following normalization, the expression of lncRNAs in the paired tissues did not differ significantly. The differential expression of the lncRNAs in the study was consistent with The Cancer Genome Atlas head and neck squamous cell carcinoma database. The study findings demonstrate the possibility of performing accurate quantitative analysis of lncRNAs using short amplicons and standardized real-time quantitative PCR assays in oral squamous cell carcinoma FFPE samples.
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Affiliation(s)
- Kiran Kumar
- Department of Oral and Maxillofacial Pathology and Oral Microbiology, SDM College of Dental Sciences and Hospital (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Kaveri Hallikeri
- Department of Oral and Maxillofacial Pathology and Oral Microbiology, SDM College of Dental Sciences and Hospital (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Ajaykumar Oli
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Mallikarjun Goni
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Apoorva Jain
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Jagadeesha Poyya
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Alagilavada S Shilpasree
- Department of Biochemistry, SDM College of Medical Sciences and Hospital (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
| | - Palaksha Kanive Javaregowda
- Department of Biomedical Science, SDM Research Institute for Biomedical Sciences (a constituent unit of Shri Dharmasthala Manjunatheshwara University), Dharwad, Karnataka State, 580009, India
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11
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Jia X, Xiong Y, Xiong Y, Li D, Yu Q, Lei X, You M, Bai S, Zhang J, Ma X. Identification and Validation of Reference Genes for RT-qPCR Analysis in Reed Canary Grass during Abiotic Stress. Genes (Basel) 2023; 14:1790. [PMID: 37761930 PMCID: PMC10530813 DOI: 10.3390/genes14091790] [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: 08/24/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Reed canary grass (Phalaris arundinacea L.) is known for its tolerance to drought, heavy metals, and waterlogging, making it a popular choice for forage production and wetland restoration in the Qinghai-Tibet Plateau (QTP). To accurately assess gene expression in reed canary grass under different abiotic stresses, suitable reference genes need to be identified and validated. Thirteen candidate reference gene sequences were selected and screened using RT-qPCR to detect their expression levels in reed canary grass leaves under drought, salt, cadmium, and waterlogging stresses. Four algorithms were used to assess the stability of the expression levels of the candidate reference genes. The most stably expressed genes were UBC and H3 under drought Cd, ETF and CYT under salt stress, and ETF and TUB under waterlogging stress. GAPDH was found to be less stable under abiotic stresses. PIP-1, PAL, NAC 90, and WRKY 72A were selected as response genes for quantitative expression assessment under drought, salt, Cd, and waterlogging stresses to confirm the accuracy of the selected stable reference genes. These results provide a theoretical reference for assessing gene expression in reed canary grass under abiotic stresses.
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Affiliation(s)
- Xuejie Jia
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
| | - Daxu Li
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Qinqin Yu
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Minghong You
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Shiqie Bai
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621002, China
| | - Jianbo Zhang
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
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12
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Chen J, Li D, Xu Y, Li Z, Ma S, Liu X, Yuan Y, Zhang C, Fu Q, Shi H. Establishment and application of multiplex droplet digital polymerase chain reaction assay for bovine enterovirus, bovine coronavirus, and bovine rotavirus. Front Vet Sci 2023; 10:1157900. [PMID: 37771940 PMCID: PMC10523346 DOI: 10.3389/fvets.2023.1157900] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 08/30/2023] [Indexed: 09/30/2023] Open
Abstract
Bovine enterovirus (BEV), bovine coronavirus (BCoV), and bovine rotavirus (BRV) are still the major worldwide concerns in the health care of cattle, causing serious economic losses in the livestock industry. It is urgent to establish specific and sensitive methods to detect viruses for the early control of diseases. Droplet digital PCR (ddPCR) has been proposed to effectively detect viral particles, and it does not involve Ct values or standard curves. In this study, we designed specific primers and probes, based on conserved regions of viral genomes, to optimize protocols for a dual ddPCR assay for detecting BCoV and BRV and a multiplex ddPCR assay for BEV, BCoV, and BRV. Sensitivity assays revealed that the lower limit of detection for qPCR was 1,000 copies/μL and for ddPCR for BEV, BCoV, and BRV, 2.7 copies/μL, 1 copy/μL and 2.4 copies/μL, respectively. Studying 82 samples collected from diarrheal calves on a farm, our dual ddPCR method detected BCoV, BRV, and co-infection at rates of 18.29%, 14.63%, and 6.1%, respectively. In contrast, conventional qPCR methods detected BCoV, BRV, and co-infection at rates of 10.98%, 12.2%, and 3.66%, respectively. On the other hand, studying 68 samples from another farm, qPCR detected BCoV, BRV, BEV, and co-infection of BCoV and BEV at rates of 14.49%, 1.45%, 5.80%, and 1.45%, respectively. Our multiplex ddPCR method detected BCoV, BRV, BEV, co-infection of BCoV and BEV, and co-infection of BRV and BEV. at rates of 14.49%, 2.9%, 8.7%, 2.9%, and 1.45%, respectively. Studying 93 samples from another farm, qPCR detected BCoV, BRV, BEV, and co-infection of BCoV and BEV was detected at rates of 5.38%, 1.08%, 18.28%, and 1.08%, respectively. Co-infection of BCoV, BRV, BEV, BCoV, and BEV, and co-infection of BRV and BEV, were detected by multiplex ddPCR methods at rates of 5.38%, 2.15%, 20.45%, 1.08%, and 1.08%, respectively. These results indicated that our optimized dual and multiplex ddPCR methods were more effective than conventional qPCR assays to detect these viral infections.
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Affiliation(s)
- Junzhen Chen
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Dan Li
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
- Tecon Biology Co., Ltd., Ürümqi, China
| | - Yafang Xu
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Zeyu Li
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Siqi Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Xinyi Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Yuanyuan Yuan
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Chengyuan Zhang
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Qiang Fu
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Huijun Shi
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
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13
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Hu G, Huang K, Zhou W, Wang R, Zhao W, Zou H, Li W, Wu S, Li M, Wang G. Comparison of droplet digital PCR and real-time quantitative PCR for quantitative detection of the parasitic ciliate Ichthyophthirius multifiliis in the water environment. J Fish Dis 2023; 46:357-367. [PMID: 36606558 DOI: 10.1111/jfd.13749] [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] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Ichthyophthiriasis, caused by the parasitic ciliate Ichthyophthirius multifiliis (Ich), is considered one of the most harmful diseases affecting freshwater fish globally. It can cause mass mortalities of fish in intensive farming systems. In such systems, it is thus necessary to detect and quantify the number of Ich in the water so that control measures can be implemented before Ichthyophthiriasis breaks out. In recent years, molecular diagnostic methods have become increasingly important in aquaculture. Real-time quantitative polymerase chain reaction (qPCR) and droplet digital polymerase chain reaction (ddPCR) have become robust assays for detecting pathogens. In this study, a set of specific primers and a TaqMan-minor groove binder probe targeting the small-subunit rDNA (SSU rDNA) of Ich were developed. They were used in qPCR and ddPCR assays to compare the performance of these two different methods in quantitatively detecting Ich. After optimizing the reaction conditions, both qPCR and ddPCR assays were found to have high linearity and quantitative correlations for standard plasmid DNA. When used for the detection of Ich eDNA in water samples, the qPCR assay had a wider detection range, making it a suitable method to screen for the prevalence of Ichthyophthiriasis. However, the ddPCR approach had higher sensitivity, which would help provide advance notice of the disease in complex water environmental samples.
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Affiliation(s)
- Guangran Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weitian Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Runqiu Wang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Weishan Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hong Zou
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wenxiang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shangong Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guitang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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14
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Yu J, Zhang J, Hong H. Characterization and Expression Analysis of Four Cadmium-Tolerance-Associated Genes of Avicennia marina (Forsk.). Biology (Basel) 2023; 12:biology12020216. [PMID: 36829494 PMCID: PMC9952839 DOI: 10.3390/biology12020216] [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] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/31/2022] [Accepted: 01/09/2023] [Indexed: 01/31/2023]
Abstract
Mangroves colonize the intertidal area of estuaries (e.g., Pichavaram, Payardia, and Mai Po) with remarkable cadmium (Cd) pollution. A study on the mechanism of mangrove plant response to Cd pollution can help to understand the adaptive characteristics of plants under Cd stress. This study explored the roles of peroxidase (PRX), pectate lyase (PL), and phytosulfokine (PSK) genes in cadmium tolerance of mangrove Avicennia marina. Full-length sequences of four genes (i.e., AmPRX1, AmPRX2, AmPL, and AmPSK) associated with metal tolerance were identified with suppression subtractive hybridization and rapid amplification of cDNA ends. These genes showed the characteristic features of the respective protein family, indicating functions similar to other plant proteins. Real-time quantitative PCR analysis demonstrated that cadmium exposure resulted in differences in expression patterns among the tissues. Our findings emphasize the complex regulatory mechanism of these four genes in response to trace metal pollution and reveal their functions in metabolic signaling during the stress response.
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Affiliation(s)
- Jinfeng Yu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
- Xiamen Innovax Biotech, Xiamen 361022, China
| | - Jicheng Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
- Frasergen, Wuhan 430075, China
| | - Hualong Hong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
- Correspondence:
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15
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Li Z, Huang N, Zhang W, Li L. Biological function of C-X-C Motif Chemokine Ligand 1 gene (CXCL1) in ovarian malignant tumors. Hum Exp Toxicol 2023; 42:9603271231203392. [PMID: 37787042 DOI: 10.1177/09603271231203392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
OBJECTIVE To determine the function of the chemokine (C-X-C motif) ligand 1 (CXCL1) gene in ovarian cancer cells and to investigate the relationship between CXCL1 gene mRNA expression and ovarian tumor clinical pathology. METHODS Using bioinformatics methods to identify common differentially expressed genes associated with ovarian cancer in the GEO database. Growth curves of A2780 cells with or without CXCL1 expression were plotted by MTT assay. Cell cycles were measured by flow cytometry. Cell colony formation was enumerated in Transwell chambers. Migration and invasion in vitro were investigated using Cell Counting Kit-8 (CCK8), wound healing and Transwell, respectively. The relationship between CXCL1 gene mRNA expression and ovarian tumor clinical pathology was analyzed. RESULTS CXCL1 was found to be one of the co-upregulated differentially expressed genes in the GEO database. The migration of A2780 cells expressing CXCL1 was significantly higher than that of A2780 cells without CXCL1 expression. CXCL1 mRNA expression in ovarian malignancy was significantly higher than those in benign lesions and the normal control (p < .01). In advanced ovarian cancer (Stages III-IV), CXCL1 mRNA expression was also significantly higher than that in patients with early-stage ovarian cancer (Stages I-II) (p = .005). Kaplan-Meier survival curve showed no correlation between CXCL1 mRNA expression and ovarian cancer prognosis. A Cox proportional hazard model also showed that CXCL1 expression was not an independent prognostic factor for ovarian cancer patients. CONCLUSIONS CXCL1 gene could promotes ovarian cancer A2780 cell proliferation and invasion in vitro, and contributed theoretical knowledge for the target selection in molecular targeted therapy. CXCL1 mRNA over-expression may be correlated with the occurrence and development of ovarian malignancy. Level of plasma CXCL1 might serve as a biomarker for prognosis in ovarian carcinoma patients.
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Affiliation(s)
- Zhuang Li
- Department of Gynecological Oncology, Guangxi Medical University Cancer Hospital, Nanning, P.R. China
| | - Ning Huang
- Department of Gynecological Oncology, Guangxi Medical University Cancer Hospital, Nanning, P.R. China
| | - Wei Zhang
- Department of Gynecological Oncology, Guangxi Medical University Cancer Hospital, Nanning, P.R. China
| | - Li Li
- Department of Gynecological Oncology, Guangxi Medical University Cancer Hospital, Nanning, P.R. China
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16
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Liu Y, Han X, Zhang X, Liu J, Yao L. Development of a droplet digital PCR assay for detection of group A porcine rotavirus. Front Vet Sci 2023; 10:1113537. [PMID: 36950538 PMCID: PMC10025470 DOI: 10.3389/fvets.2023.1113537] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Group A porcine rotavirus (PoRVA) is an important pathogen of acute enteritis in piglets, which has caused severe economic losses in the pig industry worldwide. A convenient, sensitive and specific diagnosis method is an urgent requirement for the surveillance of the PoRVA circulating in clinical samples. In this study, a novel and convenient droplet digital PCR (ddPCR) for the detection of PoRVA was developed using the conserved region of the VP6 gene. The detection limit of ddPCR was 1.81 ± 0.14 copies/rection, ~10 times greater sensitivity than TaqMan real-time quantitative PCR (qPCR). Both ddPCR and qPCR assays exhibited good linearity and repeatability, and the established ddPCR method was highly specific for PoRVA. The results of clinical sample testing showed that the positivity rate of ddPCR (5.6%) was higher than that of qPCR (4.4%). Therefore, the newly developed ddPCR assay could be widely used in clinical diagnosis of PoRVA infections.
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Affiliation(s)
- Yangkun Liu
- Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Xueying Han
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinru Zhang
- Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Jiaxing Liu
- Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Lunguang Yao
- Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- *Correspondence: Lunguang Yao
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17
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Noureen A, Zuhaib Khan M, Amin I, Zainab T, Ahmad N, Haider S, Mansoor S. Broad-spectrum resistance against multiple PVY-strains by CRSIPR/Cas13 system in Solanum tuberosum crop. GM Crops Food 2022; 13:97-111. [PMID: 35652435 PMCID: PMC9176253 DOI: 10.1080/21645698.2022.2080481] [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] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Potato virus Y (PVY) is a deadly environmental constraint that damages productivity of potato (Solanum tuberosum) around the globe. One of the major challenges is to develop resistance against PVY. Emerging clustered regularly short palindromic repeat (CRISPR)/Cas systems have the potential to develop resistance against PVY. In the current research, CRISPR-Cas13 has been exploited to target multiple strains of PVYN, PVYO, and PVYNTN. Multiple genes PI, HC-Pro, P3, Cl1, Cl2, and VPg genes of PVY were targeted by CRISPR/Cas13a. Multiplex gRNA cassettes were developed on the conserved regions of the PVY-genes. Three independent CRISPR/Cas13 transgenic potato lines were developed by applying an optimized concentration of trans-ribo zeatin and indole acetic acid at callus development, rooting, and shooting growth stages. The level of resistance in transgenic plants was confirmed through double-antibody sandwich enzyme-linked immunosorbent assay and real-time quantitative PCR. Our results have shown that efficiency of PVY inhibition was positively correlated with the Cas13a/sgRNA expression. Finding provides the specific functionality of Cas13 with specific gRNA cassette and engineering the potential resistance in potato crop against multiple strains of PVY.
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Affiliation(s)
- Azka Noureen
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), A Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan.,University Institute of Biochemistry and Biotechnology (UIBB), Pir Mehr Ali Shah- Arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Zuhaib Khan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), A Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), A Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Tayyaba Zainab
- University Institute of Biochemistry and Biotechnology (UIBB), Pir Mehr Ali Shah- Arid Agriculture University, Rawalpindi, Pakistan.,National Centre for Industrial Biotechnology (NCIB), Pir Mehr Ali Shah- Arid Agriculture University, Rawalpindi, Pakistan
| | - Nasim Ahmad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), A Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Sibtain Haider
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), A Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), A Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
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Tian Y, Chu Z, Wang L, Wang H, Yuan X, Wu S, Yang Y. Evaluation and validation of reference genes in Cymbidium faberi for real-time quantitative PCR. Biotechniques 2022. [PMID: 36178123 DOI: 10.2144/btn-2022-0025] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
For all organs at all Cymbidium faberi stages, ACT, UBQ3 and GAPDH can be selected as reference genes. For organs of the vegetative stage, UBQ2 and UBQ3 can be chosen for analysis of normalized gene expression. For the bud stage, ACT and UBQ3 can be used for analysis of gene expression. For the full blossom stage, ACT, UBQ3 and UBQ2 can be introduced into relative gene expression analysis. For vegetative organs, UBQ2 and ACT can be used as reference genes. For reproductive organs, ACT, UBQ3 and UBQ2 can be used as a reference for data processing. CfAG1 gene expression is more consistent when UBQ3, GAPDH and ACT are used as reference genes.
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19
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Zhao J, Yang J, Wang X, Xiong Y, Xiong Y, Dong Z, Lei X, Yan L, Ma X. Selection and Validation of Reference Genes for qRT-PCR Gene Expression Analysis in Kengyilia melanthera. Genes (Basel) 2022; 13:genes13081445. [PMID: 36011356 PMCID: PMC9408421 DOI: 10.3390/genes13081445] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
Kengyilia is a newly established genus. Most species in this genus survive in hash environment, which might be an indicator of an acquirement of stress resistance genes and the potential for molecular breeding in Triticeae species. Quantitative real-time PCR (qRT-PCR) is a widely used technique with varied sensitivity heavily dependent on the optimal level of the reference genes. K. melanthera is a typical psammophyte species which has high drought resistance. The reference genes of K. melanthera are not yet reported. This study aims to evaluate the expression stability of 14 candidate reference genes (EF1A, GAPDH, ACT1, UBI, TUBB3, TIPRL, CACS, PPP2R1B, TUBA1A, EIF4A1, CYPA3, TCTP, ABCG11L, and FBXO6L) under five treatments (drought, heat, cold, salt, and ABA) and find the most stable and suitable one even upon stressed conditions. The software NormFinder, GeNorm, BestKeeper, and RefFinder were used for data analysis. In general, the genes CACS and PPP2R1B are concluded to have the best overall performance under the various treatments. With the ABA treatment, TCTP and TIPRL show the best stability. CACS and TCTP, as well as TIPRL and CYPA3, were most stable under the treatments of cold and salt, respectively. CACS and FBXO6L were ranked the highest with the heat treatment and drought treatment, respectively. Finally, the Catalase-1 (CAT1) gene was used to verify the reliability of the above reference genes. Accordingly, CAT1’s expression pattern remained unchanged after normalization with stable reference genes. This study provides beneficial information about the stability and reliability of potential reference genes for qRT-PCR in K. melanthera.
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Affiliation(s)
- Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jian Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoyun Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhixiao Dong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu 611731, China
| | - Lijun Yan
- Sichuan Academy of Grassland Science, Chengdu 611731, China
- Correspondence: (L.Y.); (X.M.)
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (L.Y.); (X.M.)
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Han Y, Liu Q. [Rapid identification of SARS-CoV-2 main variants using real-time quantitative PCR assay]. Sheng Wu Gong Cheng Xue Bao 2022; 38:2224-2235. [PMID: 35786474 DOI: 10.13345/j.cjb.220028] [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] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A TaqMan probe real-time quantitative PCR (RT-qPCR) approach was developed for rapid identification of SARS-CoV-2 main variants. Specific primers and probes were designed based on the sequence of the SARS-CoV-2 wild and main variants alpha (N501Y, HV69-70del), beta (E484K, K417N), gamma (K417T, V1176F), delta (L452R, T478K) and omicron (H655Y, N679K, P681H) genes. The specificity, sensitivity and performance of the RT-qPCR assay were tested. The assay can identify SARS-CoV-2 wild type and main variants efficiently, and has no crossover with a panel of respiratory pathogens (n=21), showing high specificity toward SARS-CoV-2 RNA. The assay's sensitivity was determined to be 2×102 copies/mL. In summary, we developed a simple, rapid and cost-effective RT-qPCR assay that enables identification of SARS-CoV-2 main variants. It can be used to monitor the variation of SARS-CoV-2 strain for accurate identification, prevention and control of outbreaks.
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Affiliation(s)
- Yongjun Han
- Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
- Institute of Radiation Medicine, Academy of Military Medical Sciences, Beijing 100850, China
| | - Qiqi Liu
- Institute of Radiation Medicine, Academy of Military Medical Sciences, Beijing 100850, China
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Cheng MC, Chien WH, Huang YS, Fang TH, Chen CH. Translational Study of Copy Number Variations in Schizophrenia. Int J Mol Sci 2021; 23:ijms23010457. [PMID: 35008879 PMCID: PMC8745588 DOI: 10.3390/ijms23010457] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/11/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Rare copy number variations (CNVs) are part of the genetics of schizophrenia; they are highly heterogeneous and personalized. The CNV Analysis Group of the Psychiatric Genomic Consortium (PGC) conducted a large-scale analysis and discovered that recurrent CNVs at eight genetic loci were pathogenic to schizophrenia, including 1q21.1, 2p16.3 (NRXN1), 3q29, 7q11.23, 15q13.3, distal 16p11.2, proximal 16p11.2, and 22q11.2. We adopted a two-stage strategy to translate this knowledge into clinical psychiatric practice. As a screening test, we first developed a real-time quantitative PCR (RT-qPCR) panel that simultaneously detected these pathogenic CNVs. Then, we tested the utility of this screening panel by investigating a sample of 557 patients with schizophrenia. Chromosomal microarray analysis (CMA) was used to confirm positive cases from the screening test. We detected and confirmed thirteen patients who carried CNVs at these hot loci, including two patients at 1q21.1, one patient at 7q11.2, three patients at 15q13.3, two patients at 16p11.2, and five patients at 22q11.2. The detection rate in this sample was 2.3%, and the concordance rate between the RT-qPCR test panel and CMA was 100%. Our results suggest that a two-stage approach is cost-effective and reliable in achieving etiological diagnosis for some patients with schizophrenia and improving the understanding of schizophrenia genetics.
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Affiliation(s)
- Min-Chih Cheng
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien 981, Taiwan;
| | - Wei-Hsien Chien
- Department of Occupational Therapy, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan;
| | - Yu-Shu Huang
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan;
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Ting-Hsuan Fang
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan;
- Department and Institute of Biomedical Sciences, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence:
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22
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De Falco F, Cutarelli A, D'Alessio N, Cerino P, Catoi C, Roperto S. Molecular Epidemiology of Ovine Papillomavirus Infections Among Sheep in Southern Italy. Front Vet Sci 2021; 8:790392. [PMID: 34881323 PMCID: PMC8645557 DOI: 10.3389/fvets.2021.790392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 10/07/2021] [Accepted: 10/25/2021] [Indexed: 11/21/2022] Open
Abstract
Ovine papillomaviruses (OaPVs) were detected and quantified, for the first time, using droplet digital polymerase chain reaction (ddPCR) and real-time quantitative PCR (qPCR) via blood samples of 165 clinically healthy sheep. OaPV DNA was detected in 126 blood samples (~76.4%). DdPCR detected OaPV DNA in 124 samples; in only two additional samples positive for real-time qPCR, ddPCR failed to detect the presence of any OaPVs. In 70 of the positive samples (~55.6%), a single OaPV infection was observed, 12 of which were caused by OaPV1 (~17.1%) and 14 by OaPV2 (20%). OaPV3 was responsible for 19 single infections (~27.1%), and OaPV4 for 25 single infections (~35.7%). Multiple OaPV coinfections were observed in 56 (~44.4%) positive samples. OaPV coinfections caused by two genotypes were observed in 31 positive samples (~55.4%), with dual OaPV3/OaPV4 infection being the most prevalent as seen in 11 blood samples. In addition, five OaPV1/OaPV4, four OaPV1/OaPV2, four OaPV2/OaPV3, four OaPV1/OaPV3, and three OaPV2/OaPV4 dual coinfections were also detected. OaPV coinfections by triple and quadruple genotypes were detected in 24 (~42.8%) and only one (~1.8%) of coinfected blood samples, respectively. Multiple infections caused by OaPV1/OaPV3/OaPV4 genotypes were the most prevalent, as observed in 12 (50%) blood samples harboring triple OaPV infections. This study showed that ddPCR is the most sensitive and accurate assay for OaPV detection and quantification thus outperforming real-time qPCR in terms of sensitivity and specificity. Therefore, ddPCR may represent the molecular diagnostic tool of choice, ultimately providing useful insights into OaPV molecular epidemiology and field surveillance.
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Affiliation(s)
- Francesca De Falco
- Dipartimento di Medicina Veterinaria e Produzioni Animali, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Anna Cutarelli
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Nicola D'Alessio
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Pellegrino Cerino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Cornel Catoi
- Department of Pathology, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Sante Roperto
- Dipartimento di Medicina Veterinaria e Produzioni Animali, Università degli Studi di Napoli Federico II, Naples, Italy
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Shi Y, Zhao JY, Zhou JR, Ntambo MS, Xu PY, Rott PC, Gao SJ. Molecular Detection and Quantification of Xanthomonas albilineans in Juice from Symptomless Sugarcane Stalks Using a Real-Time Quantitative PCR Assay. Plant Dis 2021; 105:3451-3458. [PMID: 34142842 DOI: 10.1094/pdis-03-21-0468-re] [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] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Leaf scald, a bacterial disease caused by Xanthomonas albilineans (Ashby) Dowson, is a major limiting factor for sugarcane production worldwide. Accurate identification and quantification of X. albilineans is a prerequisite for successful management of this disease. A sensitive and robust quantitative PCR (qPCR) assay was developed in this study for detection and quantification of X. albilineans using TaqMan probe and primers targeting a putative adenosine triphosphate-binding cassette (ABC) transporter gene (abc). The novel qPCR assay was highly specific to the 43 tested X. albilineans strains belonging to different pulsed-field gel electrophoresis groups. The detection thresholds were 100 copies/µl of plasmid DNA, 100 fg/µl of bacterial genomic DNA, and 100 CFU/ml of bacterial suspension prepared from pure culture. This qPCR assay was 100 times more sensitive than a conventional PCR assay. The pathogen was detected by qPCR in 75.1% (410/546) of symptomless stalk samples, whereas only 28.4% (155/546) of samples tested positive by conventional PCR. Based on qPCR data, population densities of X. albilineans in symptomless stalks of the same varieties differed between two sugarcane production areas in China, Beihai (Guangxi Province) and Zhanjiang (Guangdong Province), and no significant correlation between these populations was identified. Furthermore, no relationship was found between these populations of the pathogen in asymptomatic stalks and the resistance level of the sugarcane varieties to leaf scald. The newly developed qPCR assay proved to be highly sensitive and reliable for the detection and quantification of X. albilineans in sugarcane stalks.
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Affiliation(s)
- Yang Shi
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jian-Ying Zhao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing-Ru Zhou
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mbuya Sylvain Ntambo
- Unité de Protection des Plantes, Département de Phytotechnie, Faculté des Sciences Agronomiques, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Peng-Yuan Xu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Philippe C Rott
- CIRAD, UMR PHIM, F-34398 Montpellier, France
- PHIM, Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34398 Montpellier, France
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Sun YL, Dong JF, Song YQ, Wang SL. GOBP1 from the Variegated Cutworm Peridroma saucia (Hübner) (Lepidoptera: Noctuidae) Displays High Binding Affinities to the Behavioral Attractant ( Z)-3-Hexenyl acetate. Insects 2021; 12:939. [PMID: 34680708 DOI: 10.3390/insects12100939] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022]
Abstract
The variegated cutworm Peridroma saucia (Hübner) is a worldwide pest that causes serious damage to many crops. To recognize sex pheromones and host plant volatiles, insects depend on olfactory chemoreception involving general odorant-binding proteins (GOBPs). In this study, PsauGOBP1 was cloned from the adult antennae of P. saucia. RT-qPCR and Western-blot analysis showed that PsauGOBP1 was specifically and equally expressed in the adult antennae of both females and males. Fluorescence competitive-binding assays with sex pheromones and host plant volatiles demonstrated that PsauGOBP1 bound to six host plant volatiles: (Z)-3-hexenyl acetate (KD = 4.0 ± 0.1 μM), citral (KD = 5.6 ± 0.4 μM), farnesol (KD = 6.4 ± 0.6 μM), nonanal (KD = 6.8 ± 0.3 μM), (Z)-3-hexen-1-ol (KD = 8.5 ± 0.6 μM), and benzaldehyde (KD = 9.4 ± 0.5 μM). Electroantennogram recordings with the six host plant volatiles indicated that (Z)-3-hexenyl acetate elicited the strongest responses from both male and female antennae. Further bioassays using Y-tube olfactometers showed that (Z)-3-hexenyl acetate was attractive to adult P. saucia of both sexes. These results suggest that PsauGOBP1 might be involved in detecting host plant volatiles and that (Z)-3-hexenyl acetate might serve as a potential attractant for the biological control of P. saucia.
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25
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Bermond C, Cherrad S, Trainoy A, Ngari C, Poulet V. Real-time qPCR to evaluate bacterial contamination of cosmetic cream and the efficiency of protective ingredients. J Appl Microbiol 2021; 132:2106-2120. [PMID: 34586708 DOI: 10.1111/jam.15310] [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: 05/26/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 02/04/2023]
Abstract
AIMS The absence of objectionable micro-organisms in cosmetics and the efficiency of preservatives are still mainly assessed by time-consuming cultivation-based methods. We explored the applicability of real-time quantitative polymerase chain reaction (qPCR) and reported on the behaviour of different bacteria in artificially contaminated creams. METHODS AND RESULTS Real-time qPCR on DNA from Burkholderia cepacia, Pluribacter gergoviae, Pseudomonas aeruginosa and Sphingomonas paucimobilis identified specific primer pairs that amplify accurately and efficiently two strains/isolates of each species. Using DNeasy mericon Food Kit, we detected bacterial growth in an inoculated cosmetic cream and persistency of DNA from heat-inactivated bacteria. We were also able to monitor the growth inhibitory effect of caprylyl glycol and EDTA, also showing how different bacterial species interact depending on the presence/absence of these ingredients. Finally, creams supplemented with the protective cosmetic ingredients revealed the various behaviour of five strains/isolates from P. aeruginosa. CONCLUSIONS Successfully extracting bacterial DNA from artificially contaminated cosmetic creams, we could perform real-time qPCR to identify and follow the growth of various strains of 4 bacteria species under different conditions. SIGNIFICANCE AND IMPACT OF THE STUDY Real-time qPCR appears as a promising method to detect bacterial contamination in cosmetic creams and/or to monitor growth inhibition by ingredients.
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Hernández-Ochoa B, Fernández-Rosario F, Castillo-Rodríguez RA, Marhx-Bracho A, Cárdenas-Rodríguez N, Martínez-Rosas V, Morales-Luna L, González-Valdez A, Calderón-Jaimes E, Pérez de la Cruz V, Rivera-Gutiérrez S, Meza-Toledo S, Wong-Baeza C, Baeza-Ramírez I, Gómez-Manzo S. Validation and Selection of New Reference Genes for RT-qPCR Analysis in Pediatric Glioma of Different Grades. Genes (Basel) 2021; 12:genes12091335. [PMID: 34573317 PMCID: PMC8468898 DOI: 10.3390/genes12091335] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
Gliomas are heterogeneous, solid, and intracranial tumors that originate from glial cells. Malignant cells from the tumor undergo metabolic alterations to obtain the energy required for proliferation and the invasion of the cerebral parenchyma. The alterations in the expression of the genes related to the metabolic pathways can be detected in biopsies of gliomas of different CNS WHO grades. In this study, we evaluated the expression of 16 candidate reference genes in the HMC3 microglia cell line. Then, statistical algorithms such as BestKeeper, the comparative ΔCT method, geNorm, NormFinder, and RefFinder were applied to obtain the genes most suitable to be considered as references for measuring the levels of expression in glioma samples. The results show that PKM and TPI1 are two novel genes suitable for genic expression studies on gliomas. Finally, we analyzed the expression of genes involved in metabolic pathways in clinical samples of brain gliomas of different CNS WHO grades. RT-qPCR analysis showed that in CNS WHO grade 3 and 4 gliomas, the expression levels of HK1, PFKM, GAPDH, G6PD, PGD1, IDH1, FASN, ACACA, and ELOVL2 were higher than those of CNS WHO grade 1 and 2 glioma biopsies. Hence, our results suggest that reference genes from metabolic pathways have different expression profiles depending on the stratification of gliomas and constitute a potential model for studying the development of this type of tumor and the search for molecular targets to treat gliomas.
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Affiliation(s)
- Beatriz Hernández-Ochoa
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (B.H.-O.); (V.M.-R.)
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Ciudad de México 06720, Mexico;
| | - Fabiola Fernández-Rosario
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (F.F.-R.); (L.M.-L.)
| | - Rosa Angelica Castillo-Rodríguez
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico;
| | - Alfonso Marhx-Bracho
- Departamento de Neurocirugía, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico;
| | - Noemí Cárdenas-Rodríguez
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico;
| | - Víctor Martínez-Rosas
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (B.H.-O.); (V.M.-R.)
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (F.F.-R.); (L.M.-L.)
| | - Laura Morales-Luna
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (F.F.-R.); (L.M.-L.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
| | - Ernesto Calderón-Jaimes
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Ciudad de México 06720, Mexico;
| | - Verónica Pérez de la Cruz
- Neurochemistry and Behavior Laboratory, National Institute of Neurology and Neurosurgery “Manuel Velasco Suárez”, México City 14269, Mexico;
| | - Sandra Rivera-Gutiérrez
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Prolongacion Carpio y Plan de Ayala s/n, Ciudad de México 11340, Mexico;
| | - Sergio Meza-Toledo
- Laboratorio de Quimioterapia Experimental, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico;
| | - Carlos Wong-Baeza
- Laboratorio de Biomembranas, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (C.W.-B.); (I.B.-R.)
| | - Isabel Baeza-Ramírez
- Laboratorio de Biomembranas, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (C.W.-B.); (I.B.-R.)
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (F.F.-R.); (L.M.-L.)
- Correspondence: ; Tel.: +52-55-1084-0900 (ext. 1442)
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Jeyaprakash K, Shanthini T, Kim U, Muthukkaruppan V, Vanniarajan A. Human papillomavirus in retinoblastoma: A tertiary eye care center study from South India. Indian J Ophthalmol 2021; 69:2111-2115. [PMID: 34304188 PMCID: PMC8482879 DOI: 10.4103/ijo.ijo_106_21] [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] [Indexed: 11/14/2022] Open
Abstract
Purpose: This study is aimed to investigate the presence of Human papillomavirus (HPV) DNA in tumors obtained from sporadic retinoblastoma patients. Methods: One hundred six tumor tissues obtained from sporadic RB patients were analyzed for HPV infection by use of both seminested PCR and real-time quantitative PCR. Results: Of 106 RB patients, 55 were male and 51 were female. The mean age at diagnosis was 26.77 ± 15.36 (mean ± Std. dev) months. Almost all patients presented with leukocoria. Molecular investigation by different methods revealed no HPV positivity in any tumor genome. Conclusion: Our study demonstrates no association between HPV and RB, postulating HPV may not be a major risk factor in the etiology of RB.
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Affiliation(s)
- Kumar Jeyaprakash
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai; Department of Molecular Biology, Aravind Medical Research Foundation, Affiliated to Alagappa University, Karaikudi, India
| | - Thennarasu Shanthini
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India
| | - Usha Kim
- Department of Orbit, Oculoplasty and Oncology, Aravind Eye Hospital, Madurai, India
| | - Veerappan Muthukkaruppan
- Department of Stem Cell Biology and Immunology, Aravind Medical Research Foundation, Madurai, India
| | - Ayyasamy Vanniarajan
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai; Department of Molecular Biology, Aravind Medical Research Foundation, Affiliated to Alagappa University, Karaikudi, India
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Luo X, Kong Q, Wang Y, Duan X, Wang P, Li C, Huan Y. Colonization of Clostridium butyricum in Rats and Its Effect on Intestinal Microbial Composition. Microorganisms 2021; 9:1573. [PMID: 34442652 PMCID: PMC8401576 DOI: 10.3390/microorganisms9081573] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 12/31/2022] Open
Abstract
Gut microorganisms participate in many physiological processes. In particular, Clostridium butyricum can modulate gut microorganisms and treat diseases. The colonization and persistence of strains in the gut contribute to beneficial effects, and the colonization by C. butyricum in the gut is currently unknown. We investigated the total intestinal contents of C. butyricum at 12 h, 24 h, 48 h, and four and six days using real-time reverse transcription-PCR, after oral administration of C. butyricum to rats for seven consecutive days. We assessed the bacterial community structure using Illumina MiSeq sequencing. The results showed that C. butyricum was mainly colonized in the colon. The total content of C. butyricum in the gut increased significantly at 12 h after administration. Exogenous C. butyricum could still be detected in the gut six days after administration. Administration of C. butyricum significantly enhanced gut microbial diversity. The relative abundance of short-chain fatty acid-producing bacterial genera was shown to be higher than that of the control group, and treatment with C. butyricum elevated Firmicutes and diminished Bacteroidetes phyla compared with to the control group. These findings laid the foundation for the study of probiotic colonization capacity and the improvement of microflora for the prevention of gut diseases.
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Affiliation(s)
| | - Qing Kong
- School of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; (X.L.); (Y.W.); (X.D.); (P.W.); (C.L.); (Y.H.)
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Kotrova M, Darzentas N, Pott C, Baldus CD, Brüggemann M. Immune Gene Rearrangements: Unique Signatures for Tracing Physiological Lymphocytes and Leukemic Cells. Genes (Basel) 2021; 12:979. [PMID: 34198966 DOI: 10.3390/genes12070979] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/25/2021] [Indexed: 02/07/2023] Open
Abstract
The tremendous diversity of the human immune repertoire, fundamental for the defense against highly heterogeneous pathogens, is based on the ingenious mechanism of immune gene rearrangements. Rearranged immune genes encoding the immunoglobulins and T-cell receptors and thus determining each lymphocyte's antigen specificity are very valuable molecular markers for tracing malignant or physiological lymphocytes. One of their most significant applications is tracking residual leukemic cells in patients with lymphoid malignancies. This so called 'minimal residual disease' (MRD) has been shown to be the most important prognostic factor across various leukemia subtypes and has therefore been given enormous attention. Despite the current rapid development of the molecular methods, the classical real-time PCR based approach is still being regarded as the standard method for molecular MRD detection due to the cumbersome standardization of the novel approaches currently in progress within the EuroMRD and EuroClonality NGS Consortia. Each of the molecular methods, however, poses certain benefits and it is therefore expectable that none of the methods for MRD detection will clearly prevail over the others in the near future.
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30
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Liang H, Yu Z, Wang B, Ndayisenga F, Liu R, Zhang H, Wu G. Synergistic Application of Molecular Markers and Community-Based Microbial Source Tracking Methods for Identification of Fecal Pollution in River Water During Dry and Wet Seasons. Front Microbiol 2021; 12:660368. [PMID: 34194406 PMCID: PMC8236858 DOI: 10.3389/fmicb.2021.660368] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022] Open
Abstract
It is important to track fecal sources from humans and animals that negatively influence the water quality of rural rivers and human health. In this study, microbial source tracking (MST) methods using molecular markers and the community-based FEAST (fast expectation–maximization microbial source tracking) program were synergistically applied to distinguish the fecal contributions of multiple sources in a rural river located in Beijing, China. The performance of eight markers were evaluated using 133 fecal samples based on real-time quantitative (qPCR) technique. Among them, six markers, including universal (BacUni), human-associated (HF183-1 and BacH), swine-associated (Pig-2-Bac), ruminant-associated (Rum-2-Bac), and avian-associated (AV4143) markers, performed well in the study. A total of 96 water samples from the river and outfalls showed a coordinated composition of fecal pollution, which revealed that outfall water might be a potential input of the Fsq River. In the FEAST program, bacterial 16S rRNA genes of 58 fecal and 12 water samples were sequenced to build the “source” library and “sink,” respectively. The relative contribution (<4.01% of sequence reads) of each source (i.e., human, swine, bovine, or sheep) was calculated based on simultaneous screening of the operational taxonomic units (OTUs) of sources and sinks, which indicated that community-based MST methods could be promising tools for identifying fecal sources from a more comprehensive perspective. Results of the qPCR assays indicated that fecal contamination from human was dominant during dry weather and that fecal sources from swine and ruminant were more prevalent in samples during the wet season than in those during the dry season, which were consistent with the findings predicted by the FEAST program using a very small sample size. Information from the study could be valuable for the development of improved regulation policies to reduce the levels of fecal contamination in rural rivers.
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Affiliation(s)
- Hongxia Liang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China
| | - Bobo Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Fabrice Ndayisenga
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Hongxun Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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31
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Yang Z, Zhang R, Zhou Z. Identification and Validation of Reference Genes for Gene Expression Analysis in Schima superba. Genes (Basel) 2021; 12:732. [PMID: 34068362 DOI: 10.3390/genes12050732] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 04/11/2021] [Revised: 05/08/2021] [Accepted: 05/12/2021] [Indexed: 11/29/2022] Open
Abstract
Real-time quantitative PCR (RT-qPCR) is a reliable and high-throughput technique for gene expression studies, but its accuracy depends on the expression stability of reference genes. Schima superba is a fast-growing timber species with strong resistance. However, thus far, reliable reference gene identifications have not been reported in S. superba. In this study, 19 candidate reference genes were selected and evaluated for their expression stability in different tissues of S. superba. Three software programs (geNorm, NormFinder, and BestKeeper) were used to evaluate the reference gene transcript stabilities, and comprehensive stability ranking was generated by the geometric mean method. Our results show that SsuACT was the most stable reference gene and that SsuACT + SsuRIB was the best reference gene combination for different tissues. Finally, the stable and less stable reference genes were verified using SsuSND1 expression in different tissues. To our knowledge, this is the first report to verify appropriate reference genes for normalizing gene expression in S. superba for different tissues, which will facilitate the future elucidation of gene regulations in this species and useful references for relative species.
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32
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Guix S, Fuentes C, Pintó RM, Blanco A, Sabrià A, Anfruns-Estrada E, Garrido VR, Alonso M, Bartolomé R, Cornejo T, Pumarola T, Bosch A. Infectivity of Norovirus GI and GII from Bottled Mineral Water during a Waterborne Outbreak, Spain. Emerg Infect Dis 2021; 26:134-137. [PMID: 31855546 PMCID: PMC6924916 DOI: 10.3201/eid2601.190778] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
During a waterborne outbreak of norovirus in Spain, we estimated 50% illness doses for a group of exposed (secretor) persons to be 556 (95% CI 319–957) genome copies/day for norovirus GI and 2,934 (95% CI 1,683–5,044) genome copies/day for norovirus GII. Use of a propidium monoazide viability assay reduced these values.
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33
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Niu L, Guo W, Song X, Song X, Xie L. Tumor-educated leukocytes mRNA as a diagnostic biomarker for non-small cell lung cancer. Thorac Cancer 2021; 12:737-745. [PMID: 33474835 PMCID: PMC7952788 DOI: 10.1111/1759-7714.13833] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/24/2020] [Accepted: 12/24/2020] [Indexed: 12/24/2022] Open
Abstract
Background This study aimed to investigate the diagnostic and prognostic role of tumor‐educated leukocytes (TELs) mRNA in Chinese patients with non‐small cell lung cancer (NSCLC). Methods The TELs collected underwent total RNA isolation. RNA‐sequencing (RNA‐seq) technology was used to analyze the transcriptome of the TELs. The mRNA expression levels of differential genes were analyzed by RT‐qPCR. Statistical analyses were performed using Prism and SPSS by Mann–Whitney nonparametric test, Kruskal‐Wallis test and one‐way ANOVA. Results We used RNA‐seq technology to screen 95 differential genes (DEGs) from seven NSCLC and four controls, wherein 15 genes were upregulated, and 80 were downregulated. Of these, four genes were selected for further analysis, wherein one was upregulated (GPX1) and three were downregulated (BCL9L, MAP3K7CL, PCSK7). RT‐qPCR was performed in 431 samples (237 NSCLC, 194 healthy donors). The four‐gene panel showed significant differences (p < 0.001) in the expression levels between NSCLC and healthy samples. ROC curves of the panel revealed an AUC of 0.803, with a sensitivity of 73.8% and specificity of 75.3%. GPX1, BCL9L and PCSK7 genes distinguished early‐stage NSCLC patients from healthy group (p < 0.05). When the three genes were combined to diagnose early‐stage NSCLC, the diagnostic efficacy was 0.772, sensitivity was 73.7%, and specificity was 72.2%. In addition, the downregulated gene BCL9L was associated with chemotherapeutic effect. Conclusions The present study provided a systematic description of gene expression profiling in the TELs. It is worth noting that these four genes may be potential candidate genes for NSCLC diagnostic biomarkers and provide a basis for further biological and functional studies.
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Affiliation(s)
- Limin Niu
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Wei Guo
- Ultrasound Diagnosis Department, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xingguo Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.,Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xianrang Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.,Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Li Xie
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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Hou S, Zhao T, Yang D, Li Q, Liang L, Wang G, Ma Q. Selection and Validation of Reference Genes for Quantitative RT-PCR Analysis in Corylus heterophylla Fisch. × Corylus avellana L. Plants (Basel) 2021; 10:plants10010159. [PMID: 33467497 PMCID: PMC7830083 DOI: 10.3390/plants10010159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 11/16/2022]
Abstract
(1) Background: the species of Corylus have sporophytic type of self-incompatibility. Several genes related to recognition reaction between pollen and stigma have been identified in hazelnuts. To better understand the self-incompatibility (SI) response, we screened the suitable reference genes by using quantitative real-time reverse transcription PCR (qRT-PCR) analysis in hazelnut for the first time. (2) Methods: the major cultivar "Dawei" was used as material. A total of 12 candidate genes were identified and their expression profiles were compared among different tissues and in response to various treatments (different times after self- and cross-pollination) by RT-qPCR. The expression stability of these 12 candidate reference genes was evaluated using geNorm, NormFinder, BestKeeper, Delta Ct, and RefFinder programs. (3) Results: the comprehensive ranking of RefFinder indicated that ChaActin, VvActin,
ChaUBQ14, and ChaEF1-α were the most suitable reference genes. According to the stability analysis of 12 candidate reference genes for each sample group based on four software packages, ChaActin and ChaEF1-α were most stable in different times after self-pollination and 4 h after self- and cross-pollination, respectively. To further validate the suitability of the reference genes identified in this study, CavPrx, which the expression profiles in Corylus have been reported, was quantified by using ChaActin and ChaEF1-α as reference genes. (4) Conclusions: our study of reference genes selection in hazelnut shows that the two reference genes, ChaActin and ChaEF1-α, are suitable for the evaluation of gene expression, and can be used for the analysis of pollen-pistil interaction in Corylus. The results supply a reliable foundation for accurate gene quantifications in Corylus species, which will facilitate the studies related to the reproductive biology in Corylus.
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Affiliation(s)
- Sihao Hou
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Tiantian Zhao
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Dan Yang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Qing Li
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Lisong Liang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Guixi Wang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Qinghua Ma
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
- Correspondence: ; Tel.: +86-1381-139-0689
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Ding J, Shi M, Wang L, Qi D, Tao Z, Hayat MA, Liu T, Zhang JT, Wang H. Gene Expression of Metalloproteinases and Endogenous Inhibitors in the Lamellae of Dairy Heifers With Oligofructose-Induced Laminitis. Front Vet Sci 2020; 7:597827. [PMID: 33426020 PMCID: PMC7786368 DOI: 10.3389/fvets.2020.597827] [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: 08/22/2020] [Accepted: 12/02/2020] [Indexed: 12/03/2022] Open
Abstract
Bovine laminitis leads to huge economic losses and animal welfare problems in the dairy industry worldwide. Numerous studies suggested that several metalloproteinases (MPs) may play vital roles in the failure of epidermal attachment. To the best of our knowledge, the present study is the first to investigate and characterize the gene-level changes in distinct MPs and endogenous inhibitors using oligofructose (OF)-induced bovine laminitis model. The objective of this study was to determine aberrant MPs and related inhibitors of bovine laminitis in gene level, and to provide reasonable directions for the further protein-level research. Twelve normal Chinese Holstein dairy heifers were randomly divided into treatment group (n = 6) and control group (n = 6). The heifers in the treatment group were administered with OF solutions at a dose of 17 g/kg of body weight via a stomach tube. The heifers were then humanely euthanized when they met the criteria of bovine laminitis. The heifers in the control group were administered with deionized water at a dose of 2 L/100 kg of body weight. They humanely euthanized at 72 h. The gene expressions of MPs and endogenous inhibitors, namely, matrix metalloproteinases (MMPs), A disintegrin and metalloproteinases (ADAMs), and A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTs), and tissue inhibitors of metalloproteinases (TIMPs) in the lamellae from two groups were determined via real-time quantitative PCR. The gene expressions of MMP-2, MMP-9, ADAMTS-4, and ADAMTS-5 significantly increased (P < 0.05), whereas that of TIMP-2 significantly decreased (P < 0.05) in the treatment group relative to the control group. No significant difference was found in the gene expressions of ADAM-10, ADAM-17, TIMP-1, and TIMP-3. These results indicated that the gene-level imbalanced condition of MPs and their TIMPs may be the basic cause for the failure of epidermal attachment. At the same time, more detailed protein-level studies would be needed to further clarify the roles of MPs and TIMPs in the pathogenesis of bovine laminitis, especially to MMP-2, MMP-9, ADAMTS-4, ADAMTS-5, TIMP-2 as well as related substrates (e.g., aggrecan and versican).
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Affiliation(s)
- Jiafeng Ding
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Mingxian Shi
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Long Wang
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Dongdong Qi
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Ze Tao
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Muhammad A Hayat
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Tao Liu
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Jian-Tao Zhang
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Hongbin Wang
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
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Chen CY, Chen SY, Liu CW, Wu DH, Kuo CC, Lin CC, Chou HP, Wang YY, Tsai YC, Lai MH, Chung CL. Invasion and Colonization Pattern of Fusarium fujikuroi in Rice. Phytopathology 2020; 110:1934-1945. [PMID: 32689901 DOI: 10.1094/phyto-03-20-0068-r] [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: 06/11/2023]
Abstract
Bakanae disease in rice can cause abnormal elongation of the stem and leaves, development of adventitious roots, a larger leaf angle, and even death. Little is known about the infection, colonization, and distribution of Fusarium fujikuroi in rice plants across different growth stages. In this study, microscopic observation and quantitative real-time PCR were combined to investigate the pathogenesis of bakanae, using artificially inoculated seedlings of a susceptible rice cultivar, Zerawchanica karatals (ZK), a resistant cultivar, Tainung 67 (TNG67), naturally infected adult field plants (cultivars Kaohsiung 139, Taikeng 2, and Tainan 11), and an F. fujikuroi isolate expressing green fluorescent protein. In rice seedlings, F. fujikuroi hyphae were found to directly penetrate the epidermis of basal stems and roots, then extend inter- and intracellularly to invade the vascular bundles. Occlusion of vascular bundles and radial hyphal expansion from vascular bundles to surrounding parenchyma were observed in adult plants. Analysis of consecutive 3-cm segments of the whole plant revealed that F. fujikuroi was largely confined to the embryo, basal stem, and basal roots in seedlings, and distributed unevenly in the lower aerial parts (including nodes and internodes) of adult plants. The elongation and development of adventitious roots did not necessarily correlate with the amount of F. fujikuroi in diseased plants. Treatment of rice seeds with gibberellic acid-3 (GA3) at 0.5 mg/liter resulted in significantly more elongation of ZK than TNG67 seedlings, suggesting that the susceptibility of ZK to bakanae is associated with its higher sensitivity to GA3.
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Affiliation(s)
- Chieh-Yi Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan
| | - Szu-Yu Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan
| | - Chun-Wei Liu
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan
| | - Dong-Hong Wu
- Crop Science Division, Taiwan Agricultural Research Institute, Council of Agriculture, No. 189, Chung-Cheng Road, Wufeng, Taichung City 41203, Taiwan
- Department of Agronomy, National Chung Hsing University, No. 145, Xingda Rd., South District, Taichung City 40227, Taiwan
| | - Chien-Chih Kuo
- Crop Environment Section, Taichung District Agricultural Research and Extension Station, Council of Agriculture, No. 370, Song Hwai Road, Tatsuen Hsiang, Changhua County 51544, Taiwan
| | - Chun-Chi Lin
- Crop Environment Section, Taitung District Agricultural Research and Extension Station, Council of Agriculture, No. 675, Chunghua Rd., Sec. 1, Taitung City 95055, Taiwan
| | - Hau-Ping Chou
- Crop Environment Section, Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, No. 2-6 Dehe Rd., Dehe Village, Changjhih Township, Pingtung County 90846, Taiwan
| | - Yu-Yao Wang
- Crop Environment Section, Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, No. 2-6 Dehe Rd., Dehe Village, Changjhih Township, Pingtung County 90846, Taiwan
| | - Yi-Chen Tsai
- Crop Environment Section, Hualien District Agricultural Research and Extension Station, Council of Agriculture, No. 150, Sec. 2, Ji'an Rd., Ji'an Township, Hualien County 97365, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, Council of Agriculture, No. 189, Chung-Cheng Road, Wufeng, Taichung City 41203, Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan
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Khaled S, Gantois N, Ly AT, Senghor S, Even G, Dautel E, Dejager R, Sawant M, Baydoun M, Benamrouz-Vanneste S, Chabé M, Ndiaye S, Schacht AM, Certad G, Riveau G, Viscogliosi E. Prevalence and Subtype Distribution of Blastocystis sp. in Senegalese School Children. Microorganisms 2020; 8:microorganisms8091408. [PMID: 32932661 PMCID: PMC7564003 DOI: 10.3390/microorganisms8091408] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [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: 07/06/2020] [Revised: 09/07/2020] [Accepted: 09/10/2020] [Indexed: 12/12/2022] Open
Abstract
Blastocystis sp. is an enteric protozoan that frequently colonizes humans and many animals. Despite impacting on human health, data on the prevalence and subtype (ST) distribution of Blastocystis sp. remain sparse in Africa. Accordingly, we performed the first multicenter and largest epidemiological survey ever conducted on Blastocystis sp. for this continent. A total of 731 stool samples collected from healthy school children living in 10 villages of the northwestern region of Senegal were tested for the presence of Blastocystis sp. by real-time polymerase chain reaction followed by subtyping of positive samples. Considerable variation in prevalence between villages (51.7 to 100%) was evident with the overall prevalence being 80.4%. Mixed infections were identified in 23% of positive individuals. Among 453 school children with a single infection, ST2 was predominant, followed by ST1, ST3, ST7, ST10, and ST14; this is the first report of ST10 and ST14 in humans. Genetic polymorphisms were evident at the intra-ST level with the identification of numerous ST1 to ST3 genotypes. ST1 showed the greatest intra-ST diversity followed by ST2 and ST3. The prevalence and distribution of STs and genotypes varied among target villages, pointing to several potential infection sources, including human-to-human, zoonotic, and waterborne transmission.
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Affiliation(s)
- Salma Khaled
- Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (S.K.); (N.G.); (E.D.); (R.D.); (M.S.); (M.B.); (S.B.-V.); (M.C.); (A.-M.S.); (G.C.); (G.R.)
| | - Nausicaa Gantois
- Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (S.K.); (N.G.); (E.D.); (R.D.); (M.S.); (M.B.); (S.B.-V.); (M.C.); (A.-M.S.); (G.C.); (G.R.)
| | - Amadou Tidjani Ly
- Biomedical Research Center Espoir Pour La Santé (BRC-EPLS), BP 226 Saint-Louis, Senegal; (A.T.L.); (S.S.)
| | - Simon Senghor
- Biomedical Research Center Espoir Pour La Santé (BRC-EPLS), BP 226 Saint-Louis, Senegal; (A.T.L.); (S.S.)
| | - Gaël Even
- Gènes Diffusion, F-59501 Douai, France;
- PEGASE-Biosciences (Plateforme d’Expertises Génomiques Appliquées aux Sciences Expérimentales), Institut Pasteur de Lille, F-59000 Lille, France
| | - Ellena Dautel
- Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (S.K.); (N.G.); (E.D.); (R.D.); (M.S.); (M.B.); (S.B.-V.); (M.C.); (A.-M.S.); (G.C.); (G.R.)
| | - Romane Dejager
- Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (S.K.); (N.G.); (E.D.); (R.D.); (M.S.); (M.B.); (S.B.-V.); (M.C.); (A.-M.S.); (G.C.); (G.R.)
| | - Manasi Sawant
- Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (S.K.); (N.G.); (E.D.); (R.D.); (M.S.); (M.B.); (S.B.-V.); (M.C.); (A.-M.S.); (G.C.); (G.R.)
| | - Martha Baydoun
- Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (S.K.); (N.G.); (E.D.); (R.D.); (M.S.); (M.B.); (S.B.-V.); (M.C.); (A.-M.S.); (G.C.); (G.R.)
| | - Sadia Benamrouz-Vanneste
- Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (S.K.); (N.G.); (E.D.); (R.D.); (M.S.); (M.B.); (S.B.-V.); (M.C.); (A.-M.S.); (G.C.); (G.R.)
- Laboratoire Ecologie et Biodiversité, Institut Catholique de Lille, Faculté de Gestion Economie et Sciences, F-59000 Lille, France
| | - Magali Chabé
- Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (S.K.); (N.G.); (E.D.); (R.D.); (M.S.); (M.B.); (S.B.-V.); (M.C.); (A.-M.S.); (G.C.); (G.R.)
| | - Seynabou Ndiaye
- Région Médicale de Saint-Louis, MSAS, BP 226 Saint-Louis, Senegal;
| | - Anne-Marie Schacht
- Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (S.K.); (N.G.); (E.D.); (R.D.); (M.S.); (M.B.); (S.B.-V.); (M.C.); (A.-M.S.); (G.C.); (G.R.)
- Biomedical Research Center Espoir Pour La Santé (BRC-EPLS), BP 226 Saint-Louis, Senegal; (A.T.L.); (S.S.)
| | - Gabriela Certad
- Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (S.K.); (N.G.); (E.D.); (R.D.); (M.S.); (M.B.); (S.B.-V.); (M.C.); (A.-M.S.); (G.C.); (G.R.)
- Délégation à la Recherche Clinique et à l’Innovation, Groupement des Hôpitaux de l’Institut Catholique de Lille, F-59000 Lille, France
| | - Gilles Riveau
- Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (S.K.); (N.G.); (E.D.); (R.D.); (M.S.); (M.B.); (S.B.-V.); (M.C.); (A.-M.S.); (G.C.); (G.R.)
- Biomedical Research Center Espoir Pour La Santé (BRC-EPLS), BP 226 Saint-Louis, Senegal; (A.T.L.); (S.S.)
| | - Eric Viscogliosi
- Institut Pasteur de Lille, U1019–UMR 9017–CIIL–Centre d’Infection et d’Immunité de Lille, University of Lille, CNRS, Inserm, CHU Lille, F-59000 Lille, France; (S.K.); (N.G.); (E.D.); (R.D.); (M.S.); (M.B.); (S.B.-V.); (M.C.); (A.-M.S.); (G.C.); (G.R.)
- Correspondence:
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Chhalliyil P, Ilves H, Kazakov SA, Howard SJ, Johnston BH, Fagan J. A Real-Time Quantitative PCR Method Specific for Detection and Quantification of the First Commercialized Genome-Edited Plant. Foods 2020; 9:foods9091245. [PMID: 32906573 PMCID: PMC7556030 DOI: 10.3390/foods9091245] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 11/30/2022] Open
Abstract
Discussion regarding the regulatory status of genome-edited crops has focused on precision of editing and on doubts regarding the feasibility of analytical monitoring compliant with existing GMO regulations. Effective detection methods are important, both for regulatory enforcement and traceability in case of biosafety, environmental or socio-economic impacts. Here, we approach the analysis question for the first time in the laboratory and report the successful development of a quantitative PCR detection method for the first commercialized genome-edited crop, a canola with a single base pair edit conferring herbicide tolerance. The method is highly sensitive and specific (quantification limit, 0.05%), compatible with the standards of practice, equipment and expertise typical in GMO laboratories, and readily integrable into their analytical workflows, including use of the matrix approach. The method, validated by an independent laboratory, meets all legal requirements for GMO analytical methods in jurisdictions such as the EU, is consistent with ISO17025 accreditation standards and has been placed in the public domain. Having developed a qPCR method for the most challenging class of genome edits, single-nucleotide variants, this research suggests that qPCR-based method development may be applicable to virtually any genome-edited organism. This advance resolves doubts regarding the feasibility of extending the regulatory approach currently employed for recombinant DNA-based GMOs to genome-edited organisms.
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Affiliation(s)
- Pradheep Chhalliyil
- Health Research Institute, 505 Dimick Drive, P.O. Box 370, Fairfield, IA 52556, USA;
| | - Heini Ilves
- Somagenics, Inc., 2161 Delaware Ave, Suite E, Santa Cruz, CA 95060, USA; (H.I.); (S.A.K.); (B.H.J.)
| | - Sergei A. Kazakov
- Somagenics, Inc., 2161 Delaware Ave, Suite E, Santa Cruz, CA 95060, USA; (H.I.); (S.A.K.); (B.H.J.)
| | - Stephanie J. Howard
- The Sustainability Council of New Zealand, P.O. Box 24304, Wellington 6142, New Zealand;
| | - Brian H. Johnston
- Somagenics, Inc., 2161 Delaware Ave, Suite E, Santa Cruz, CA 95060, USA; (H.I.); (S.A.K.); (B.H.J.)
| | - John Fagan
- Health Research Institute, 505 Dimick Drive, P.O. Box 370, Fairfield, IA 52556, USA;
- Correspondence: ; Tel.: +1-641-451-5454
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Cardoso FDO, Zaverucha-do-Valle T, Almeida-Souza F, Abreu-Silva AL, Calabrese KDS. Modulation of Cytokines and Extracellular Matrix Proteins Expression by Leishmania amazonensis in Susceptible and Resistant Mice. Front Microbiol 2020; 11:1986. [PMID: 32983013 PMCID: PMC7487551 DOI: 10.3389/fmicb.2020.01986] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 05/07/2020] [Accepted: 07/27/2020] [Indexed: 12/24/2022] Open
Abstract
Leishmaniases are a complex of diseases with a broad spectrum of clinical forms, which depend on the parasite species, immunological status, and genetic background of the host. In the Leishmania major model, susceptibility is associated with the Th2 pattern of cytokines production, while resistance is associated with Th1 response. However, the same dichotomy does not occur in L. amazonensis-infected mice. Cytokines are key players in these diseases progression, while the extracellular matrix (ECM) components participate in the process of parasite invasion as well as lesion healing. In this article, we analyzed the influence of host genetics on the expression of cytokines, inducible nitric oxide synthase (iNOS), and ECM proteins, as well as the parasite load in mice with different genetic backgrounds infected by L. amazonensis. C57BL/10 and C3H/He mice were subcutaneously infected with 106L. amazonensis promastigotes. Lesion kinetics, parasite load, cytokines, iNOS, and ECM proteins expression were measured by quantitative PCR (qPCR) in the footpad, draining lymph nodes, liver, and spleen at early (24 h and 30 days) and late phase (120 and 180 days) of infection. Analysis of lesion kinetics showed that C57BL/10 mice developed ulcerative lesions at the inoculation site after L. amazonensis infection, while C3H/He showed slight swelling in the footpad 180 days after infection. C57BL/10 showed progressive enhancement of parasite load in all analyzed organs, while C3H/He mice showed extremely low parasite loads. Susceptible C57BL/10 mice showed high levels of TGF-β mRNA in the footpad early in infection and high levels of proinflammatory cytokines mRNA (IL-12, TNF-α, and IFN-γ) and iNOS in the late phase of the infection. There is an association between increased expression of fibronectin, laminin, collagen III and IV, and TGF-β. On the other hand, resistant C3H/He mice presented a lower repertory of cytokines mRNA expression when compared with susceptible C57BL/10 mice, basically producing TNF-α, collagen IV, and laminin early in infection. The findings of our study indicate that L. amazonensis infection induces different cytokine expression in resistant and susceptible mice but not like the L. major model. An organ-compartmentalized cytokine response was observed in our model. Host genetics determine this response, which modulates ECM proteins expression.
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Affiliation(s)
- Flávia de Oliveira Cardoso
- Laboratório de Imunomodulação e Protozoologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Tânia Zaverucha-do-Valle
- Laboratório de Imunomodulação e Protozoologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Fernando Almeida-Souza
- Laboratório de Imunomodulação e Protozoologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratório de Anatomopatologia, Departamento de Patologia, Universidade Estadual do Maranhão, São Luís, Brazil
| | - Ana Lúcia Abreu-Silva
- Laboratório de Anatomopatologia, Departamento de Patologia, Universidade Estadual do Maranhão, São Luís, Brazil
| | - Kátia da Silva Calabrese
- Laboratório de Imunomodulação e Protozoologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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Ding J, Li S, Jiang L, Li Y, Zhang X, Song Q, Hayat MA, Zhang JT, Wang H. Laminar Inflammation Responses in the Oligofructose Overload Induced Model of Bovine Laminitis. Front Vet Sci 2020; 7:351. [PMID: 32766286 PMCID: PMC7381234 DOI: 10.3389/fvets.2020.00351] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/20/2020] [Indexed: 01/02/2023] Open
Abstract
Bovine laminitis causes substantial economic losses and animal welfare problems in dairy farms worldwide. Previously published studies have reported that the inflammatory response plays a central role in the pathogenesis of the disease. To our knowledge, inflammation associated with bovine laminitis induced by high levels of exposure to oligofructose (OF) has not been reported and characterized. In fact, the disease manifestations in this model closely approximate those of clinical laminitis. The objective of this study was to characterize the inflammatory response in OF-induced bovine laminitis. A total of 12 Chinese Holstein dairy heifers were utilized in this study. The heifers were randomly divided into two groups, treatment (n = 6) and control (n = 6). The treatment group heifers were administered OF solutions via a stomach tube (dose: 17 g/kg of body weight). Upon development of a lameness score of 2 with consecutive positive reactions in the same claw, they would be humanely euthanized. Control heifers were administered deionized water (dose: 2 L/100 kg of body weight) and humanely euthanized at 72 h. Real-time quantitative PCR (qPCR) assays were performed to determine the messenger RNA (mRNA) concentrations of inflammatory mediators in the lamellae. Concentrations of interleukin (IL)-1β, IL-6, IL-8, C-X-C motif chemokine ligand-1 (CXCL-1), macrophage cationic peptide-2 (MCP-2), E-selectin, intercellular adhesion molecule-1 (ICAM-1), cyclooxygenase-2 (COX-2), inducible nitric oxide synthase-1 (iNOS-1), and plasminogen activator inhibitor-1 (PAI-1) were significantly increased (P < 0.05) in the treatment group. No significant difference was found for tumor necrosis factor alpha (TNF-α), IL-10, CXCL-6, and MCP-1. These results demonstrated and characterized the laminar inflammatory response leading to the pathogenesis of bovine laminitis at the early stages.
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Affiliation(s)
- Jiafeng Ding
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Shuaichen Li
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Lihong Jiang
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Yuepeng Li
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Xianhao Zhang
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Qiaozhi Song
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Muhammad A Hayat
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Jian-Tao Zhang
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
| | - Hongbin Wang
- Department of Veterinary Surgery, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, China
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Liu J, Liu JP. A method for efficient quantitative analysis of genomic subtelomere Y' element abundance in yeasts. Yeast 2020; 37:373-388. [PMID: 32639041 DOI: 10.1002/yea.3511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 04/01/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 01/09/2023] Open
Abstract
Subtelomere Y' elements get amplified by homologous recombination in sustaining the survival and division of the budding yeast Saccharomyces cerevisiae. However, current method for measurement of the subtelomere structures uses Southern blotting with labelled specific probes, which is laborious and time-consuming. By multiple sequence alignment analysis of all 19 subtelomere Y' elements across the 13 chromosomes of the sequenced S288C strain deposited in the yeast genome SGD database, we identified 12 consensus and relative longer fragments and 14 pairs of unique primers for real-time quantitative PCR analysis. With a PAC2 or ACT1 located near the centromere of chromosome V and VI as internal controls, these primers were applied to real-time quantitative PCR analysis, so the relative Y' element intensity normalised to that of wild type (WT) cells was calculated for subtelomere Y' element copy numbers across all different chromosomes using the formula: 2^[-((CTmutant Y' - CTmutant control ) - (CTWT Y' - CTWT control ))]. This novel quantitative subtelomere amplification assay across chromosomes by real-time PCR proves to be a much simpler and more sensitive way than the traditional Southern blotting method to analyse the Y' element recombination events in survivors derived from telomerase deficiency or recruitment failure.
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Affiliation(s)
- Jun Liu
- Institute of Ageing Research, College of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Jun-Ping Liu
- Institute of Ageing Research, College of Medicine, Hangzhou Normal University, Hangzhou, China
- Department of Immunology, Faculty of Medicine, Monash University, Prahran, Victoria, Australia
- Hudson Institute of Medical Research, Clayton, Victoria, Australia
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Nikitina E, Kuznetsova V, Kroupin P, Karlov GI, Divashuk MG. Development of Specific Thinopyrum Cytogenetic Markers for Wheat-Wheatgrass Hybrids Using Sequencing and qPCR Data. Int J Mol Sci 2020; 21:E4495. [PMID: 32599865 PMCID: PMC7349979 DOI: 10.3390/ijms21124495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/15/2020] [Accepted: 06/21/2020] [Indexed: 01/19/2023] Open
Abstract
The cytogenetic study of wide hybrids of wheat has both practical and fundamental values. Partial wheat-wheatgrass hybrids (WWGHs) are interesting as a breeding bridge to confer valuable genes to wheat genome, as well as a model object that contains related genomes of Triticeae. The development of cytogenetic markers is a process that requires long and laborious fluorescence in situ hybridization (FISH) testing of various probes before a suitable probe is found. In this study, we aimed to find an approach that allows to facilitate this process. Based on the data sequencing of Thinopyrum ponticum, we selected six tandem repeat (TR) clusters using RepeatExplorer2 pipeline and designed primers for each of them. We estimated the found TRs' abundance in the genomes of Triticum aestivum, Thinopyrum ponticum, Thinopyrum intermedium and four different WWGH accessions using real-time qPCR, and localized them on the chromosomes of the studied WWGHs using fluorescence in situ hybridization. As a result, we obtained three tandem repeat cytogenetic markers that specifically labeled wheatgrass chromosomes in the presence of bread wheat chromosomes. Moreover, we designed and tested primers for these repeats, and demonstrated that they can be used as qPCR markers for quick and cheap monitoring of the presence of certain chromosomes of wheatgrass in breeding programs.
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Affiliation(s)
- Ekaterina Nikitina
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
| | - Victoria Kuznetsova
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
| | - Pavel Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
| | - Gennady I. Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
| | - Mikhail G. Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia; (E.N.); (V.K.); (P.K.); (G.I.K.)
- Kurchatov Genomics Center—ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia
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Zhu L, Zeng C, Yang S, Hou Z, Wang Y, Hu X, Senoo K, Wei W. Diversity and specificity of the bacterial community in Chinese horse milk cheese. Microbiologyopen 2020; 9:e1066. [PMID: 32741094 PMCID: PMC7424250 DOI: 10.1002/mbo3.1066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 03/23/2020] [Revised: 04/24/2020] [Accepted: 05/12/2020] [Indexed: 11/15/2022] Open
Abstract
The nutrition and flavor of cheese are generated by the microbial community. Thus, horse milk cheese with unique nutrition and flavor, an increasingly popular local cheese of the Xinjiang Uygur Autonomous Region of China, is considered to have diverse and specific bacterial community. To verify this hypothesis, horse, cow, and goat milk cheese samples produced under the same environmental conditions and manufacturing process were collected, and the 16S rRNA gene was targeted to determine the bacterial population size and community composition by real‐time quantitative PCR and high‐throughput sequencing. The bacterial community of horse milk cheese had a significantly larger bacterial population size, greater species richness, and a more diverse composition than those of cow and goat milk cheeses. Unlike the absolute dominance of Lactococcus and Streptococcus in cow and goat milk cheeses, Lactobacillus and Streptococcus dominated the bacterial community as the starter lactic acid bacteria in horse milk cheese. Additionally, horse milk cheese also contains a higher abundance of unclassified secondary bacteria and specific secondary bacteria (e.g., Psychrobacter, Sulfurisoma, Halomonas, and Brevibacterium) than cow and goat milk cheeses. These abundant, diverse, and specific starter lactic acid bacteria and secondary bacteria may generate unique nutrition and flavor of horse milk cheese.
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Affiliation(s)
- Lin Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Chunlin Zeng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Sai Yang
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
| | - Zhaozhi Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yuan Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Xinyu Hu
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Wei Wei
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
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González-Domínguez E, Berlanas C, Gramaje D, Armengol J, Rossi V, Berbegal M. Temporal Dispersal Patterns of Phaeomoniella chlamydospora, Causal Agent of Petri Disease and Esca, in Vineyards. Phytopathology 2020; 110:1216-1225. [PMID: 32129711 DOI: 10.1094/phyto-10-19-0400-r] [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] [Indexed: 06/10/2023]
Abstract
Although the fungus Phaeomoniella chlamydospora is the most commonly detected causal agent of Petri disease and esca, two important fungal grapevine trunk diseases, little is known about the dispersal patterns of P. chlamydospora inoculum. In this work, we studied the dispersal of P. chlamydospora airborne inoculum from 2016 to 2018 in two viticultural areas of eastern (Ontinyent) and northern (Logroño) Spain. The vineyards were monitored weekly from November to April using microscope slide traps, and P. chlamydospora was detected and quantified by a specific real-time quantitative (qPCR) method set up in this work. The method was found to be sensitive, and a good correlation was observed between numbers of P. chlamydospora conidia (counted by microscope) and DNA copy numbers (quantified by qPCR). We consistently detected DNA of P. chlamydospora at both locations and in all seasons but in different quantities. In most cases, DNA was first detected in the last half of November, and most of the DNA was detected from December to early April. When rain was used as a predictor of P. chlamydospora DNA detection in traps, false-negative detections were observed, but these involved only 4% of the total. The dispersal pattern of P. chlamydospora DNA over time was best described (R2 = 0.765 and concordance correlation coefficient = 0.870) by a Gompertz equation, with time expressed as hydrothermal time (a physiological time accounting for the effects of temperature and rain). This equation could be used to predict periods with a high risk of dispersal of P. chlamydospora.
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Affiliation(s)
| | - Carmen Berlanas
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas-Universidad de la Rioja-Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain
| | - David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas-Universidad de la Rioja-Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain
| | - Josep Armengol
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Vittorio Rossi
- Department of Sustainable Crop Production (DIPROVES), Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
| | - Mónica Berbegal
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
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Pan J, Feng R, Hu Q, Chen H, Zhang S, Sun J, Ji S. TaqMan real-time quantitative PCR for identification of antlers in tradition Chinese medicine. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:173-177. [PMID: 32378441 DOI: 10.1080/24701394.2020.1741560] [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] [Indexed: 10/24/2022]
Abstract
In this study, a method was established for discriminating the true Cervus antlers from its counterfeits using TaqMan real-time quantitative PCR. The method combines the use of true Cervus antlers-specific primers, that amplify a 226 bp fragment from true Cervus antlers DNA, and mammalian-specific primers amplifying a 146 bp fragment from mammalian species DNA, which are used as endogenous control. A TaqMan probe that hybridizes in the 'Cervus antler' and also in the 'mammalian' DNA fragments is used to monitor the amplification of the target gene. The Cervus antler mitochondrial DNA was used as target gene to design the primers and TaqMan probes. The data revealed that the TaqMan real-time PCR-based assay can be used for identification of the true Cervus antlers from counterfeits in a single step. The limit of detection (LOD) was lower than 1 pg of DNA per reaction.
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Affiliation(s)
- Jie Pan
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Shanghai Insititute for Food and Drug Control, Shanghai, NMPA Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai, China
| | - Rui Feng
- Shanghai Insititute for Food and Drug Control, Shanghai, NMPA Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai, China
| | - Qing Hu
- Shanghai Insititute for Food and Drug Control, Shanghai, NMPA Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai, China
| | - Hong Chen
- Shanghai Insititute for Food and Drug Control, Shanghai, NMPA Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai, China
| | - Su Zhang
- Shanghai Insititute for Food and Drug Control, Shanghai, NMPA Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai, China
| | - Jian Sun
- Shanghai Insititute for Food and Drug Control, Shanghai, NMPA Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai, China
| | - Shen Ji
- Shanghai Insititute for Food and Drug Control, Shanghai, NMPA Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai, China
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46
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Zhao J, Zhou M, Meng Y. Identification and Validation of Reference Genes for RT-qPCR Analysis in Switchgrass under Heavy Metal Stresses. Genes (Basel) 2020; 11:E502. [PMID: 32375288 PMCID: PMC7291066 DOI: 10.3390/genes11050502] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 11/22/2022] Open
Abstract
Switchgrass (Panicum Virgatum L.) has been recognized as the new energy plant, which makes it ideal for the development of phytoremediation on heavy metal contamination in soils with great potential. This study aimed to screen the best internal reference genes for the real-time quantitative PCR (RT-qPCR) in leaves and roots of switchgrass for investigating its response to various heavy metals, such as cadmium (Cd), lead (Pb), mercury (Hg), chromium (Cr), and arsenic (As). The stability of fourteen candidate reference genes was evaluated by BestKeeper, GeNorm, NormFinder, and RefFinder software. Our results identified U2AF as the best reference gene in Cd, Hg, Cr, and As treated leaves as well as in Hg, Pb, As, and Cr stressed root tissues. In Pb treated leaf tissues, 18S rRNA was demonstrated to be the best reference gene. CYP5 was determined to be the optimal reference gene in Cd treated root tissues. The least stable reference gene was identified to be CYP2 in all tested samples except for root tissues stressed by Pb. To further validate the initial screening results, we used the different sets of combinatory internal reference genes to analyze the expression of two metal transport associated genes (PvZIP4 and PvPDB8) in young leaves and roots of switchgrass. Our results demonstrated that the relative expression of the target genes consistently changed during the treatment when CYP5/UBQ1, U2AF/ACT12, eEF1a/U2AF, or 18S rRNA/ACT12 were combined as the internal reference genes. However, the time-dependent change pattern of the target genes was significantly altered when CYP2 was used as the internal reference gene. Therefore, the selection of the internal reference genes appropriate for specific experimental conditions is critical to ensure the accuracy and reliability of RT-qPCR. Our findings established a solid foundation to further study the gene regulatory network of switchgrass in response to heavy metal stress.
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Affiliation(s)
- Junming Zhao
- Department of Grassland Science, Sichuan Agricultural University, Chengdu 611130, China;
| | - Man Zhou
- Zonation Fringe Technology Co., Metro Vancouver, BC V5C 2A0, Canada;
| | - Yu Meng
- College of Science and Technology, Wenzhou-Kean University, Wenzhou 325060, China
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Viudez‐Martínez A, García‐Gutiérrez MS, Manzanares J. Gender differences in the effects of cannabidiol on ethanol binge drinking in mice. Addict Biol 2020; 25:e12765. [PMID: 31074060 DOI: 10.1111/adb.12765] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 05/28/2018] [Revised: 02/27/2019] [Accepted: 03/27/2019] [Indexed: 12/13/2022]
Abstract
The purpose of this study was to explore the effects of cannabidiol (CBD) on binge drinking and evaluate potential gender-related differences. To this aim, male and female C57BL/6J mice (n = 60 per sex) were exposed to the drinking in the dark (DID) model for 4 weeks (DID-1 to DID-4). Dose-response effects of CBD on the ethanol intake were tested by acute (day-4 of DID-3) or repeated administration (day-1 to 4 of DID-4) (experiment 1: CBD 15, 30, and 60 mg/kg, i.p.; experiment 2: CBD 90 mg/kg, i.p.). Finally, we analyzed the relative gene expression of tyrosine hydroxylase (TH) and μ-opioid receptor (OPRM1) and cannabinoid CB1 receptor (CB1 r) in the ventral tegmental area (VTA) and in the nucleus accumbens (NAc), respectively, by real-time quantitative PCR. Females exhibited higher ethanol intake during each DID session. Interestingly, females also showed higher expression of TH and OPRM1, without any difference in CB1 r. Only the acute administration of CBD at the highest dose (90 mg/kg) reduced significantly ethanol consumption in both sexes. Chronic CBD administration (30, 60 and 90 mg/kg) reduced ethanol intake in males, whereas in females a significant reduction was only achieved with the highest dose (90 mg/kg). Repeated administration with CBD (60 mg/kg) significantly reduced TH and OPRM1 in males. In addition, CBD (30 and 60 mg/kg) significantly reduced CB1 r in males. No effect was observed in females. Taken together, these findings suggest that CBD may be of interest for treating binge-drinking patterns and that gender-related difference may affect the treatment outcome.
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Affiliation(s)
| | - María S. García‐Gutiérrez
- Instituto de Neurociencias, Universidad Miguel Hernández‐CSIC Spain
- Red Temática de Investigación Cooperativa en Salud (RETICS), Red de Trastornos AdictivosInstituto de Salud Carlos III, MICINN and FEDER Spain
| | - Jorge Manzanares
- Instituto de Neurociencias, Universidad Miguel Hernández‐CSIC Spain
- Red Temática de Investigación Cooperativa en Salud (RETICS), Red de Trastornos AdictivosInstituto de Salud Carlos III, MICINN and FEDER Spain
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Ma X, Zhang L, Zhang L, Wang C, Guo X, Yang Y, Wang L, Li X, Ma N. Validation and identification of reference genes in Chinese hamster ovary cells for Fc-fusion protein production. Exp Biol Med (Maywood) 2020; 245:690-702. [PMID: 32216463 DOI: 10.1177/1535370220914058] [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] [Indexed: 11/15/2022] Open
Abstract
IMPACT STATEMENT In order to reveal potential genotype-phenotype relationship, RT-qPCR reactions are frequently applied which require validated and reliable reference genes. With the investigation on long-term passage and fed-batch cultivation of CHO cells producing an Fc-fusion protein, four new reference genes-Akr1a1, Gpx1, Aprt, and Rps16, were identified from 20 candidates with the aid of geNorm, NormFinder, BestKeeper, and ΔCt programs and methods. This article provided more verified options in reference gene selection in related research on CHO cells.
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Affiliation(s)
- Xiaonan Ma
- Wuya college of Innovation; College of life science and biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Ling Zhang
- Wuya college of Innovation; College of life science and biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Luming Zhang
- Wuya college of Innovation; College of life science and biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Chenglong Wang
- Wuya college of Innovation; College of life science and biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiaorui Guo
- Wuya college of Innovation; College of life science and biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yu Yang
- Wuya college of Innovation; College of life science and biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lin Wang
- Wuya college of Innovation; College of life science and biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiangru Li
- Wuya college of Innovation; College of life science and biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Ningning Ma
- Wuya college of Innovation; College of life science and biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, China
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Morinha F, Magalhães P, Blanco G. Standard guidelines for the publication of telomere qPCR results in evolutionary ecology. Mol Ecol Resour 2020; 20. [PMID: 32133733 DOI: 10.1111/1755-0998.13152] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 12/14/2022]
Abstract
Telomere length has been used as a proxy of fitness, aging and lifespan in vertebrates. In the last decade, dozens of articles reporting on telomere dynamics in the fields of ecology and evolution have been published for a wide range of taxa. With this growing interest, it is necessary to ensure the accuracy and reproducibility of telomere length measurement techniques. Real-time quantitative PCR (qPCR) is routinely applied to measure relative telomere length. However, this technique is highly sensitive to several methodological variables and the optimization of qPCR telomere assays remains highly variable between studies. Therefore, standardized guidelines are required to enable the optimization of robust protocols, and to help in judging the validity of the presented results. This review provides an overview of preanalytical and analytical factors that can lead to qPCR inconsistencies and biases, including: (a) sample type, collection and storage; (b) DNA extraction, storage and quality; (c) qPCR primers, laboratory reagents, and assay conditions; and (d) data analysis. We propose a minimum level of information for publication of qPCR telomere assays in evolutionary ecology considering the methodological pitfalls and sources of error. This review highlights the complexity of the optimization and validation of qPCR for telomere measurement per se, demonstrating the importance of transparency and clarity of reporting methodological details required for reliable, reproducible and comparable qPCR telomere assays. We encourage efforts to implement standardized protocols that ensure the rigour and quality of telomere dynamics studies.
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Affiliation(s)
- Francisco Morinha
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
| | - Paula Magalhães
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Guillermo Blanco
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid, Spain
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Gantois N, Lamot A, Seesao Y, Creusy C, Li LL, Monchy S, Benamrouz-Vanneste S, Karpouzopoulos J, Bourgain JL, Rault C, Demaret F, Baydoun M, Chabé M, Fréalle E, Aliouat-Denis CM, Gay M, Certad G, Viscogliosi E. First Report on the Prevalence and Subtype Distribution of Blastocystis sp. in Edible Marine Fish and Marine Mammals: A Large Scale-Study Conducted in Atlantic Northeast and on the Coasts of Northern France. Microorganisms 2020; 8:microorganisms8030460. [PMID: 32213897 PMCID: PMC7144014 DOI: 10.3390/microorganisms8030460] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 02/11/2020] [Revised: 03/03/2020] [Accepted: 03/22/2020] [Indexed: 12/18/2022] Open
Abstract
Blastocystis is frequently identified in humans and animal hosts and exhibits a large genetic diversity with the identification of 17 subtypes (STs). Despite its zoonotic potential, its prevalence and ST distribution in edible marine fish and marine mammals remain unknown. A large-scale survey was thus conducted by screening 345 fish caught in Atlantic Northeast and 29 marine mammals stranded on the coasts of northern France for the presence of the parasite using real-time Polymerase Chain Reaction PCR. The prevalence of the parasite was about 3.5% in marine fish. These animals were mostly colonized by poikilotherm-derived isolates not identified in humans and corresponding to potential new STs, indicating that fish are natural hosts of Blastocystis. Marine fishes are also carriers of human STs and represent a likely limited source of zoonotic transmission. 13.8% of the marine mammals tested were colonized and 6 different STs were identified including 3 potential new STs. The risk of zoonotic transmission through marine mammals is insignificant due to the lack of repeated contact with humans. The present survey represents the first data regarding the prevalence and ST distribution of Blastocystis in marine fish and marine mammals and provides new insights into its genetic diversity, host range and transmission.
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Affiliation(s)
- Nausicaa Gantois
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 – CIIL – Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France; (N.G.); (A.L.); (S.B.-V.); (M.B.); (M.C.); (E.F.); (C.-M.A.-D.); (G.C.)
| | - Angélique Lamot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 – CIIL – Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France; (N.G.); (A.L.); (S.B.-V.); (M.B.); (M.C.); (E.F.); (C.-M.A.-D.); (G.C.)
| | - Yuwalee Seesao
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety, F-62200 Boulogne-sur-mer, France; (Y.S.); (L.-L.L.); (M.G.)
| | - Colette Creusy
- Service d’Anatomie et de Cytologie Pathologiques, Groupement des Hôpitaux de l’Institut Catholique de Lille (GHICL), F-59000 Lille, France;
| | - Luen-Luen Li
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety, F-62200 Boulogne-sur-mer, France; (Y.S.); (L.-L.L.); (M.G.)
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d’Océanologie et de Géosciences, F-62930 Wimereux, France;
| | - Sébastien Monchy
- Univ. Littoral Côte d’Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d’Océanologie et de Géosciences, F-62930 Wimereux, France;
| | - Sadia Benamrouz-Vanneste
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 – CIIL – Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France; (N.G.); (A.L.); (S.B.-V.); (M.B.); (M.C.); (E.F.); (C.-M.A.-D.); (G.C.)
- Laboratoire Ecologie et Biodiversité, Faculté de Gestion Economie et Sciences, Institut Catholique de Lille, F-59000 Lille, France
| | - Jacky Karpouzopoulos
- Coordination Mammalogique du Nord de la France, Groupe Mammifères Marins, F-62850 Alembon, France; (J.K.); (J.-L.B.); (C.R.)
| | - Jean-Luc Bourgain
- Coordination Mammalogique du Nord de la France, Groupe Mammifères Marins, F-62850 Alembon, France; (J.K.); (J.-L.B.); (C.R.)
| | - Célia Rault
- Coordination Mammalogique du Nord de la France, Groupe Mammifères Marins, F-62850 Alembon, France; (J.K.); (J.-L.B.); (C.R.)
| | - Fabien Demaret
- Observatoire PELAGIS - UMS 3462, La Rochelle Université/CNRS, F-17000 La Rochelle, France;
| | - Martha Baydoun
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 – CIIL – Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France; (N.G.); (A.L.); (S.B.-V.); (M.B.); (M.C.); (E.F.); (C.-M.A.-D.); (G.C.)
| | - Magali Chabé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 – CIIL – Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France; (N.G.); (A.L.); (S.B.-V.); (M.B.); (M.C.); (E.F.); (C.-M.A.-D.); (G.C.)
| | - Emilie Fréalle
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 – CIIL – Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France; (N.G.); (A.L.); (S.B.-V.); (M.B.); (M.C.); (E.F.); (C.-M.A.-D.); (G.C.)
| | - Cécile-Marie Aliouat-Denis
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 – CIIL – Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France; (N.G.); (A.L.); (S.B.-V.); (M.B.); (M.C.); (E.F.); (C.-M.A.-D.); (G.C.)
| | - Mélanie Gay
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), Laboratory for Food Safety, F-62200 Boulogne-sur-mer, France; (Y.S.); (L.-L.L.); (M.G.)
| | - Gabriela Certad
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 – CIIL – Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France; (N.G.); (A.L.); (S.B.-V.); (M.B.); (M.C.); (E.F.); (C.-M.A.-D.); (G.C.)
- Délégation à la Recherche Clinique et à l’Innovation, Groupement des Hôpitaux de l’Institut Catholique de Lille, F-59000 Lille, France
| | - Eric Viscogliosi
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 9017 – CIIL – Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France; (N.G.); (A.L.); (S.B.-V.); (M.B.); (M.C.); (E.F.); (C.-M.A.-D.); (G.C.)
- Correspondence:
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