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Ateutchia-Ngouanet S, Nanfack-Minkeu F, Mavridis K, Wanji S, Demanou M, Vontas J, Djouaka R. Monitoring Aedes populations for arboviruses, Wolbachia, insecticide resistance and its mechanisms in various agroecosystems in Benin. Acta Trop 2024; 253:107178. [PMID: 38461924 DOI: 10.1016/j.actatropica.2024.107178] [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: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
Aedes mosquitoes are the main vectors of arboviruses in Benin. Cases of dengue have been reported in Benin with all four serotypes of the virus actively circulating in this region. Some agricultural settings are known to harbor Aedes vectors responsible for the transmission of arboviruses. The massive use of certain insecticides in agricultural settings has probably contributed to insecticide resistance in these vectors. In Benin, the susceptibility of arbovirus vectors to insecticides is poorly studied. In addition, the distribution of Wolbachia spp., which is used against some arboviruses is unknown. Moreover, there is limited information regarding the vectors responsible for the transmission of arboviruses in Benin. This present study monitored the species composition, arboviruses, and Wolbachia symbiont status, as well as the phenotypic and molecular insecticide resistance profile of Aedes populations from three agroecosystems in Benin. Aedes species identification was performed morphologically and confirmed using qPCR. (RT)-qPCR assay was applied for monitoring the presence of DENV, CHIKV, ZIKV, and WNV pathogens as well as for naturally occurring Wolbachia symbionts. Insecticide resistance was assessed phenotypically, by permethrin (0.75%) exposure of Adults (F0) using World Health Organization (WHO) bioassay protocols, and at the molecular level, using TaqMan (RT)-qPCR assays for assessing knock-down resistance (kdr) mutations (F1534C, V1016G/I, and S989P) and the expression levels of eight detoxification genes (P450s from the CYP9 and CYP6 families, carboxylesterases and glutathione-S-transferases). Aedes aegypti (Ae. aegypti) mosquitoes were the most abundant (93.9%) in the three agroecosystems studied, followed by Aedes albopictus (Ae. albopictus) mosquitoes (6.1%). No arboviruses were detected in the study's mosquito populations. Naturally occurring Wolbachia symbionts were present in 7 pools out of 15 pools tested. This could influence the effectiveness of vector control strategies based on exogenously introduced Wolbachia, all present in the three agroecosystems. Full susceptibility to permethrin was observed in all tested populations of Ae. albopictus. On the contrary, Ae. aegypti were found to be resistant in all three agroecosystem sites except for banana plantation sites, where full susceptibility was observed. Molecular analysis revealed that individual target site resistance kdr mutations F1534C and V1016G/I were detected in most Ae. aegypti populations. Additionally, double mutant (F1534C + V1016G/I) mosquitoes were found in some populations, and in one case, triple mutant (F1534C + V1016G/I + S989P) mosquitoes were detected. Metabolic resistance, as reflected by overexpression of three P450 genes (CYP6BB2, CYP9J26, and CYP9J32), was also detected in Ae. aegypti mosquitoes. Our study provides information that could be used to strategize future vector control strategies and highlights the importance of continuing vector surveillance. Future studies should assess the effect of piperonyl butoxide (PBO) on metabolic resistance and identify the different strains of Wolbachia spp., to choose the best vector control strategies in Benin.
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Affiliation(s)
- S Ateutchia-Ngouanet
- International Institute of Tropical Agriculture (IITA), 08 Tri-Postal, P.O. Box 0932, Cotonou, Benin; Department Microbiology and Parasitology, Faculty of Science, University of Buea, P.O. BOX 63, Buea, Cameroon.
| | - F Nanfack-Minkeu
- International Institute of Tropical Agriculture (IITA), 08 Tri-Postal, P.O. Box 0932, Cotonou, Benin; Department of Biology, The College of Wooster, OH, USA
| | - K Mavridis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | - S Wanji
- Department Microbiology and Parasitology, Faculty of Science, University of Buea, P.O. BOX 63, Buea, Cameroon
| | - M Demanou
- Regional Yellow Fever Laboratory Coordinator World Health Organization, Inter-Country Support Team West Africa, 03 PO BOX 7019 Ouagadougou 03, Burkina Faso
| | - J Vontas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece; Department of Crop Science, Pesticide Science Laboratory, Agricultural University of Athens, Athens 11855, Greece
| | - R Djouaka
- International Institute of Tropical Agriculture (IITA), 08 Tri-Postal, P.O. Box 0932, Cotonou, Benin
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Ibrahim F, Natasha A, Yasmon A, Rizal CT, Fithriyah, Karuniawati A, Saharman YR, Sudarmono P. Evaluation of SARS-CoV-2 quantification from oropharyngeal swabs, nasopharyngeal swabs, and naso-oropharyngeal swabs: A cross-sectional study. Heliyon 2024; 10:e28647. [PMID: 38586376 PMCID: PMC10998208 DOI: 10.1016/j.heliyon.2024.e28647] [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: 04/02/2022] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024] Open
Abstract
The current naso-oropharyngeal swab for SARS-CoV-2 detection faces several problems, such as waste issues and its use for quantitative studies. This study aimed to evaluate the total RNA and viral loads from different upper respiratory tract swabs types and whether SARS-CoV-2 quantification can use the current internal control for normalization. This cross-sectional study collected positive specimens with single oropharyngeal or nasopharyngeal swabs and naso-oropharyngeal swabs. The samples were extracted, tested with qualitative RT‒PCR, and then tested with quantitative RT‒PCR. The RNA eluate was measured for the total RNA concentration. The total RNA concentration, viral load, and RNaseP Ct values were collected and analysed statistically. The positive results came from 41 oropharyngeal swabs, 34 nasopharyngeal swabs, and 36 naso-oropharyngeal swabs. The total RNA increased significantly from oropharyngeal swabs to nasopharyngeal swabs to naso-oropharyngeal swabs. Significant differences in RNaseP Ct values between groups and their correlations with total RNA were found. In addition, the increase in the total RNA and the RNaseP Ct values were unrelated to the viral load. The physical features in the naso-oropharyngeal area and the swabbing procedures could affect the total RNA but not the viral load. However, since the virus particles could present inside and outside human cells, the increase in collected human cells may not always be followed by the viral load increase. Normalization using the RNaseP Ct value became unnecessary due to the factors mentioned above. Therefore, a careful approach is needed in viral load studies of swab specimens.
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Affiliation(s)
- Fera Ibrahim
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Augustine Natasha
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Andi Yasmon
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Chairunnisa Tawadhu Rizal
- Jakarta Health Laboratory Center, Ministry of Health, Percetakan Negara No.23B street, Central Jakarta, Indonesia
| | - Fithriyah
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Anis Karuniawati
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Yulia Rosa Saharman
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Pratiwi Sudarmono
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
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Ren J, Liu K, Hu L, Yang R, Liu Y, Wang S, Chen X, Zhao S, Jing L, Liu T, Hu B, Zhang X, Wang H, Li H. An Efficient Probe-Based Quantitative PCR Assay Targeting Human-Specific DNA in ST6GALNAC3 for the Quantification of Human Cells in Preclinical Animal Models. Mol Biotechnol 2024:10.1007/s12033-024-01115-8. [PMID: 38456963 DOI: 10.1007/s12033-024-01115-8] [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: 03/05/2023] [Accepted: 02/04/2024] [Indexed: 03/09/2024]
Abstract
Precise quantification of human cells in preclinical animal models by a sensitive and specific approach is warranted. The probe-based quantitative PCR (qPCR) assay as a sensitive and swift approach is suitable for the quantification of human cells by targeting human-specific DNA sequences. In this study, we developed an efficient qPCR assay targeting human-specific DNA in ST6GALNAC3 (termed ST6GAL-qPCR) for the quantification of human cells in preclinical animal models. ST6GAL-qPCR probe was synthesized with FAM and non-fluorescent quencher-minor groove binder conjugated to the 5' and 3' end of the probe, respectively. Genomic DNA from human, rhesus monkeys, cynomolgus monkeys, New Zealand White rabbits, SD rats, C57BL/6, and BALB/c mice were utilized for analyzing the specificity and sensitivity of the ST6GAL-qPCR assay. The ST6GAL-qPCR assay targeted human-specific DNA was cloned to pUCM-T vector and released by EcoR I/Hind III digestion for generating a calibration curve. Cell mixing experiment was performed to validate the ST6GAL-qPCR assay by analysis of 0.1%, 0.01%, and 0.001% of human leukocytes mixed with murine thymocytes. The ST6GAL-qPCR assay detected human DNA rather than DNA from the tested animal species. The amplification efficiency of the ST6GAL-qPCR assay was 93% and the linearity of calibration curve was R2 = 0.999. The ST6GAL-qPCR assay detected as low as 5 copies of human-specific DNA and is efficient to specially amplify as low as 30-pg human DNA in the presence of 1 μg of DNA from the tested species, respectively. The ST6GAL-qPCR assay was able to quantify as low as 0.01% of human leukocytes within murine thymocytes. This ST6GAL-qPCR assay can be used as an efficient approach for the quantification of human cells in preclinical animal models.
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Affiliation(s)
- Jinfeng Ren
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Ke Liu
- Department of Gastroenterology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Lang Hu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Ruoning Yang
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Yuting Liu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Siyu Wang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Xinzhu Chen
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Shuli Zhao
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Luyao Jing
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Tiantian Liu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Bin Hu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Xuefeng Zhang
- Jiangsu Tripod Preclinical Research Laboratories Inc, Nanjing, China
| | - Hui Wang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
| | - Hui Li
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Department of Pathogenic Biology and Immunology, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, China.
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Mohamed AA, Fayyad DM, El-Telbany M, Mohamed DAA. Antibacterial biofilm efficacy of calcium hydroxide loaded on Gum Arabic nanocarrier: an in-vitro study. BMC Oral Health 2024; 24:215. [PMID: 38341565 PMCID: PMC10859034 DOI: 10.1186/s12903-024-03941-3] [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: 07/10/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND An innovative intracanal medication formulation was introduced in the current study to improve the calcium hydroxide (Ca(OH)2) therapeutic capability against resistant Enterococcus faecalis (E. faecalis) biofilm. This in-vitro study aimed to prepare, characterize, and evaluate the antibacterial efficiency of Ca(OH)2 loaded on Gum Arabic (GA) nanocarrier (Ca(OH)2-GA NPs) and to compare this efficiency with conventional Ca(OH)2, Ca(OH)2 nanoparticles (NPs), GA, and GA NPs. MATERIALS AND METHODS The prepared nanoparticle formulations for the tested medications were characterized using Transmission Electron Microscope (TEM) and Fourier-Transform Infrared Spectroscopy (FTIR). 141 human mandibular premolars were selected, and their root canals were prepared. Twenty-one roots were then sectioned into 42 tooth slices. All prepared root canals (n = 120) and teeth slices (n = 42) were divided into six groups according to the intracanal medication used. E. faecalis was inoculated in the samples for 21 days to form biofilms, and then the corresponding medications were applied for 7 days. After medication application, the residual E. faecalis bacteria were assessed using CFU, Q-PCR, and SEM. Additionally, the effect of Ca(OH)2-GA NPs on E. faecalis biofilm genes (agg, ace, and efaA) was investigated using RT-PCR. Data were statistically analyzed at a 0.05 level of significance. RESULTS The synthesis of NPs was confirmed using TEM. The results of the FTIR proved that the Ca(OH)2 was successfully encapsulated in the GA NPs. Ca(OH)2-GA NPs caused a significant reduction in the E. faecalis biofilm gene expression when compared to the control (p < 0.001). There were significant differences in the E. faecalis CFU mean count and CT mean values between the tested groups (p < 0.001) except between the Ca(OH)2 and GA CFU mean count. Ca(OH)2-GA NPs showed the least statistical E. faecalis mean count among other groups. SEM observation showed that E. faecalis biofilm was diminished in all treatment groups, especially in the Ca(OH)2-GA NPS group when compared to the control group. CONCLUSIONS Ca(OH)2 and GA nanoparticles demonstrate superior anti-E. faecalis activity when compared to their conventional counterparts. Ca(OH)2-GA NPs showed the best antibacterial efficacy in treating E. faecalis biofilm. The tested NP formulations could be considered as promising intracanal medications.
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Affiliation(s)
- Alshafey Alsayed Mohamed
- Department of Endodontics, Faculty of Dentistry, Suez Canal University, 4.5 Ring Road, Ismailia, 41522, Egypt
| | - Dalia Mukhtar Fayyad
- Department of Endodontics, Faculty of Dentistry, Suez Canal University, 4.5 Ring Road, Ismailia, 41522, Egypt
| | - Mohamed El-Telbany
- Microbiology and Botany Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka, 819-0395, Japan
| | - Dalia Abd-Allah Mohamed
- Department of Endodontics, Faculty of Dentistry, Suez Canal University, 4.5 Ring Road, Ismailia, 41522, Egypt.
- Department of Endodontics, Faculty of Dentistry, Sinai University, Kantara, Ismailia, Egypt.
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Roch B, Pisareva E, Mirandola A, Sanchez C, Pastor B, Tanos R, Frayssinoux F, Diab-Assaf M, Anker P, Al Amir Dache Z, Thierry AR. Impact of platelet activation on the release of cell-free mitochondria and circulating mitochondrial DNA. Clin Chim Acta 2024; 553:117711. [PMID: 38101467 DOI: 10.1016/j.cca.2023.117711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND Research on circulating mitochondrial DNA (cir-mtDNA) based diagnostic is insufficient, as to its function, origin, structural features, and particularly its standardization of isolation. To date, plasma preparation performed in previous studies do not take into consideration the potential bias resulting from the release of mitochondria by activated platelets. METHODS To tackle this, we compared the mtDNA amount determined by a standard plasma preparation method or a method optimally avoiding platelet activation. MtDNA extracted from the plasma of seven healthy individuals was quantified by Q-PCR in the course of the process of both methods submitted to filtration, freezing or differential centrifugation. RESULTS 98.7 to 99.4% of plasma mtDNA corresponded to extracellular mitochondria, either free or into large extracellular vesicles. Without platelet activation, the proportion of both types of entities remained preponderant (76-80%), but the amount of detected mtDNA decreased 67-fold. CONCLUSION We show the high capacity of platelets to release free mitochondria in "in vitro" conditions. This represents a potent confounding factor when extracting mtDNA for cir-mtDNA investigation. Platelet activation during pre-analytical conditions should therefore be avoided when studying cir-mtDNA. Our findings lead to a profound revision of the assumptions previously made by most works in this field. Overall, our data suggest the need to characterize or isolate mtDNA associated various structural forms, as well as to standardize plasma preparation, to better circumscribe cir-mtDNA's diagnostic capacity.
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Affiliation(s)
- Benoit Roch
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France; Thoracic Oncology Unit, Arnaud de Villeneuve Hospital, University Hospital of Montpellier, Montpellier F-34295, France
| | - Ekaterina Pisareva
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Alexia Mirandola
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Cynthia Sanchez
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Brice Pastor
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Rita Tanos
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Florence Frayssinoux
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Mona Diab-Assaf
- Faculty of Sciences II, Lebanese University Fanar, Beirut, Lebanon
| | - Philippe Anker
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Zahra Al Amir Dache
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Alain R Thierry
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France; ICM, Institut Régional du Cancer de Montpellier, Montpellier F-34298, France.
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Antonisamy N, Boddu D, John R, Korrapolu RSA, Balasubramanian P, Arunachalam AK, Joseph LL, Srinivasan HN, Mathew LG, Totadri S. The Outcome of Pediatric Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia: Experience from a Referral Center in South India. Indian J Hematol Blood Transfus 2024; 40:61-67. [PMID: 38312177 PMCID: PMC10830957 DOI: 10.1007/s12288-023-01684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/30/2023] [Indexed: 02/06/2024] Open
Abstract
Although improved survival in children with Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph-ALL) has been demonstrated in trials, the outcome appears to be inferior in low- and middle-income countries (LMIC). Methods A file review of children aged ≤ 15 years diagnosed with Ph-ALL from 2010 to 2019 was performed. Minimal residual disease (MRD) was assessed by flow-cytometry. Real-time polymerase chain reaction (qRT-PCR) was used to quantify the BCR::ABL1 transcripts during treatment. Results The mean age of the 20 patients in the study was 91 months. Of 19 patients in whom the BCR::ABL1 transcript was confirmed, 10(50%) had P210, 7(35%) had P190, and two showed dual expression. The mean dose of imatinib that was administered was 294 ± 41 mg/m2/day. qRT-PCR for BCR::ABL1 was < 0.01% in all patients who were in remission or had a late relapse and was ≥ 0.01% in patients who had an early relapse. Two patients underwent HSCT. The 3-year event-free survival (EFS) was 35.0 ± 10.7%. Patients with a good prednisolone response (GPR) and a negative end-of-induction MRD demonstrated a superior EFS to those who lacked either or both (80.0 ± 17.9% vs. 16.7 ± 15.2%, P = 0.034). Conclusion The 3-year EFS of 20 children with Ph-ALL treated with chemotherapy and TKI was < 50%. An unusually high proportion of patients with p210 transcript expression; sub-optimal TKI dosing and lesser intensity of chemotherapy, due to the concern of high treatment-related mortality in LMIC are possible reasons for the poor outcome. Conventional treatment response parameters such as GPR and MRD predict outcomes in Ph-ALL. qRT-PCR for BCR::ABL1 may have a role in predicting early relapse. Supplementary Information The online version contains supplementary material available at 10.1007/s12288-023-01684-9.
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Affiliation(s)
- Nikita Antonisamy
- Paediatric Haematology-Oncology unit, Department of Paediatrics, Christian Medical College, Vellore, India
| | - Deepthi Boddu
- Paediatric Haematology-Oncology unit, Department of Paediatrics, Christian Medical College, Vellore, India
| | - Rikki John
- Paediatric Haematology-Oncology unit, Department of Paediatrics, Christian Medical College, Vellore, India
| | | | | | | | - Leenu Lizbeth Joseph
- Paediatric Haematology-Oncology unit, Department of Paediatrics, Christian Medical College, Vellore, India
| | - Hema Nalapullu Srinivasan
- Paediatric Haematology-Oncology unit, Department of Paediatrics, Christian Medical College, Vellore, India
| | - Leni Grace Mathew
- Paediatric Haematology-Oncology unit, Department of Paediatrics, Christian Medical College, Vellore, India
| | - Sidharth Totadri
- Paediatric Haematology-Oncology unit, Department of Paediatrics, Christian Medical College, Vellore, India
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Butzler MA, Reed JL, Knapton KM, Afzal T, Agarwal AK, Schaeffer J, Saraiya N, Oti L, White ER, Giacobbe E, Simons LM, Ozer EA, McFall SM. Evaluation of the analytical performance of the 15-minute point-of-care DASH™ SARS-CoV-2 RT-qPCR test. Diagn Microbiol Infect Dis 2024; 108:116120. [PMID: 37898036 PMCID: PMC10842742 DOI: 10.1016/j.diagmicrobio.2023.116120] [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: 08/30/2023] [Revised: 10/10/2023] [Accepted: 10/21/2023] [Indexed: 10/30/2023]
Abstract
Accurate and timely diagnosis for COVID-19 diagnosis allows highly effective antiviral medications to be prescribed. The DASH™ Rapid PCR System is a sample-to-answer point-of-care platform combining state-of-the-art PCR kinetics with sequence specific hybridization. The platform's first assay, the DASH™ SARS-CoV-2/S test for anterior nares direct swab specimens, received FDA Emergency Use Authorization in March 2022 for point-of-care use. Here we report the analytical characteristics of the assay including limit of detection, dynamic range, and robustness of SARS-CoV-2 variant detection. The limit of detection was determined by testing swabs contrived with one hundred copies of wild type or Omicron BA.5 virus and detecting 20/20 and 19/20, respectively. The dynamic range was assessed with contrived swabs containing 102-106 copies; the log-linear relationship between Cq and copy input was plotted, and the qPCR efficiency calculated from the slope of the line was 101.4%. Detection of seven SARS-CoV-2 variants was demonstrated.
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Affiliation(s)
- Matthew A Butzler
- Center for Innovation in Global Health Technologies (CIGHT), Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208 United States
| | - Jennifer L Reed
- Center for Innovation in Global Health Technologies (CIGHT), Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208 United States
| | - Kirsten M Knapton
- Center for Innovation in Global Health Technologies (CIGHT), Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208 United States
| | - Tania Afzal
- Center for Innovation in Global Health Technologies (CIGHT), Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208 United States
| | - Abhishek K Agarwal
- Center for Innovation in Global Health Technologies (CIGHT), Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208 United States
| | - Jakob Schaeffer
- Center for Innovation in Global Health Technologies (CIGHT), Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208 United States
| | - Neeraj Saraiya
- Center for Innovation in Global Health Technologies (CIGHT), Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208 United States
| | - Lisa Oti
- Center for Innovation in Global Health Technologies (CIGHT), Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208 United States
| | - Ezekiel R White
- Center for Innovation in Global Health Technologies (CIGHT), Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208 United States
| | - Emilie Giacobbe
- Center for Innovation in Global Health Technologies (CIGHT), Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208 United States
| | - Lacy M Simons
- Center for Pathogen Genomics and Microbial Evolution (CPGME), Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States; Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States
| | - Egon A Ozer
- Center for Pathogen Genomics and Microbial Evolution (CPGME), Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States; Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States
| | - Sally M McFall
- Center for Innovation in Global Health Technologies (CIGHT), Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 United States; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208 United States.
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Abagero BR, Rama R, Obeid A, Tolossa T, Legese F, Lo E, Yewhalaw D. Detection of Duffy Blood Group Genotypes and Submicroscopic Plasmodium Infections Using Molecular Diagnostic Assays in Febrile Malaria Patients. Res Sq 2023:rs.3.rs-3706814. [PMID: 38105972 PMCID: PMC10723540 DOI: 10.21203/rs.3.rs-3706814/v1] [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] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Background Malaria remains a severe parasitic disease, posing a significant threat to public health and hindering economic development in sub-Saharan Africa. Ethiopia, a malaria endemic country, is facing a resurgence of the disease with a steadily rising incidence. Conventional diagnostic methods, such asmicroscopy, have become less effective due to low parasite density, particularly among Duffy-negative human populations in Africa. To develop comprehensive control strategies, it is crucial to generate data on the distribution and clinical occurrence of Plasmodium vivax and P. falciparum infections in regions where the disease is prevalent. This study assessed Plasmodium infections and Duffy antigen genotypes in febrile patients in Ethiopia. Methods Three hundred febrile patients visiting four health facilities in Jimma town of southwestern Ethiopia were randomly selected during the malaria transmission season (Apr-Oct). Sociodemographic information was collected, and microscopic examination was performed for all study participants. Plasmodiumspecies and parasitemia as well as the Duffy genotype were assessed by quantitative polymerase chain reaction (qPCR) for all samples. Data were analyzed using Fisher's exact test and kappa statistics. Results The Plasmodium infection rate by qPCR was 16% (48/300) among febrile patients, of which 19 (39.6%) were P. vivax, 25 (52.1%) were P. falciparum, and 4 (8.3%) were mixed (P. vivax and P. falciparum) infections. Among the 48 qPCR-positive samples, 39 (13%) were negative by microscopy. The results of bivariate logistic regression analysis showed that agriculture-related occupation, relapse and recurrence were significantly associated withPlasmodium infection (P<0.001). Of the 300 febrile patients, 85 (28.3%) were Duffy negative, of whom two had P. vivax, six had P. falciparum, and one had mixed infections.Except for one patient with P. falciparum infection, Plasmodium infections in Duffy-negative individuals were all submicroscopic with low parasitemia. Conclusions The present study revealed a high prevalence of submicroscopic malaria infections. Plasmodium vivax infections in Duffy-negative individuals were not detected due to low parasitemia. Here, we recommend an improved molecular diagnostic tool to detect and characterize plasmodium infections, with the goal of quantifyingP. vivax infection in Duffy-negative individuals.
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Affiliation(s)
- Beka Raya Abagero
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA
| | - Rei Rama
- University of North Carolina at Charlotte
| | | | | | | | - Eugenia Lo
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA
| | - Delenasaw Yewhalaw
- Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
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9
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Teixeira AM, Vaz-Moreira I, Calderón-Franco D, Weissbrodt D, Purkrtova S, Gajdos S, Dottorini G, Nielsen PH, Khalifa L, Cytryn E, Bartacek J, Manaia CM. Candidate biomarkers of antibiotic resistance for the monitoring of wastewater and the downstream environment. Water Res 2023; 247:120761. [PMID: 37918195 DOI: 10.1016/j.watres.2023.120761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
Urban wastewater treatment plants (UWTPs) are essential for reducing the pollutants load and protecting water bodies. However, wastewater catchment areas and UWTPs emit continuously antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), with recognized impacts on the downstream environments. Recently, the European Commission recommended to monitor antibiotic resistance in UWTPs serving more than 100 000 population equivalents. Antibiotic resistance monitoring in environmental samples can be challenging. The expected complexity of these systems can jeopardize the interpretation capacity regarding, for instance, wastewater treatment efficiency, impacts of environmental contamination, or risks due to human exposure. Simplified monitoring frameworks will be essential for the successful implementation of analytical procedures, data analysis, and data sharing. This study aimed to test a set of biomarkers representative of ARG contamination, selected based on their frequent human association and, simultaneously, rare presence in pristine environments. In addition to the 16S rRNA gene, ten potential biomarkers (intI1, sul1, ermB, ermF, aph(3'')-Ib, qacEΔ1, uidA, mefC, tetX, and crAssphage) were monitored in DNA extracts (n = 116) from raw wastewater, activated sludge, treated wastewater, and surface water (upstream and downstream of UWTPs) samples collected in the Czech Republic, Denmark, Israel, the Netherlands, and Portugal. Each biomarker was sensitive enough to measure decreases (on average by up to 2.5 log-units gene copy/mL) from raw wastewater to surface water, with variations in the same order of magnitude as for the 16S rRNA gene. The use of the 10 biomarkers allowed the typing of water samples whose origin or quality could be predicted in a blind test. The results show that, based on appropriate biomarkers, qPCR can be used for a cost-effective and technically accessible approach to monitoring wastewater and the downstream environment.
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Affiliation(s)
- A Margarida Teixeira
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, Porto 4169-005, Portugal
| | - Ivone Vaz-Moreira
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, Porto 4169-005, Portugal
| | - David Calderón-Franco
- Department of Biotechnology, Environmental Biotechnology Section, Delft University of Technology, van der Maasweg 9, Delft, HZ 2629, the Netherlands
| | - David Weissbrodt
- Department of Biotechnology, Environmental Biotechnology Section, Delft University of Technology, van der Maasweg 9, Delft, HZ 2629, the Netherlands; Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim 7034, Norway
| | - Sabina Purkrtova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, 5 Technická, Prague 166 28, Czech Republic
| | - Stanislav Gajdos
- Department of Water Technology and Environmental Engineering, Faculty of Environmental Technology, University of Chemistry and Technology Prague, 5 Technická, Prague 166 28, Czech Republic
| | - Giulia Dottorini
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg 9220, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg 9220, Denmark
| | - Leron Khalifa
- Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agricultural Research Organization, P.O Box 15159, Rishon Lezion 7528809, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agricultural Research Organization, P.O Box 15159, Rishon Lezion 7528809, Israel
| | - Jan Bartacek
- Department of Water Technology and Environmental Engineering, Faculty of Environmental Technology, University of Chemistry and Technology Prague, 5 Technická, Prague 166 28, Czech Republic
| | - Célia M Manaia
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, Porto 4169-005, Portugal.
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10
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Liu K, Hu L, Wang S, Chen X, Liu Y, Zhao S, Wang H, Li L, Li H. An efficient qPCR assay for the quantification of human cells in preclinical animal models by targeting human specific DNA in the intron of BRCA1. Mol Biol Rep 2023; 50:9229-9237. [PMID: 37805662 DOI: 10.1007/s11033-023-08853-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/26/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND Precise quantification of grafted human cells in preclinical animal models such as non-human primates, rodents and rabbits is needed for the evaluations of the safety and efficacy of cell therapy. Quantitative PCR (qPCR) as a swift, sensitive and powerful assay is suitable for human cell quantification. However, it is a formidable challenge due to that the genome of non-human primates share more than 95% of similarity as human. METHODS In the present study, we developed a probe-based quantitative PCR (qPCR) assay for the quantification of human cells in preclinical animal models via targeting human specific DNA in the intron of BRCA1 (termed BRCA1-qPCR). The 5' and 3' end of BRCA1-qPCR probe was conjugated with FAM and non-fluorescent quencher-minor groove binder (NFQ-MGB), respectively. 1 µg of genomic DNA from human and preclinical animal models including rhesus monkeys, cynomolgus monkeys, New Zealand white rabbits, SD rats, C57BL/6 and BALB/c mice were used for determining the specificity and sensitivity of the BRCA1-qPCR assay. A calibration curve was generated by BRCA1-qPCR analysis of linearized plasmid containing targeted human specific DNA in BRCA1. The BRCA1-qPCR assay was validated by analysis of 0.003%, 0.03% and 0.3% of human leukocytes mixed within murine leukocytes. RESULTS The BRCA1-qPCR assay detected human DNA rather than DNA from tested species. The amplification efficiency of the BRCA1-qPCR assay was 95.4% and the linearity of the calibration curve was R2 = 0.9997. The BRCA1-qPCR assay detected as low as 5 copies of human specific DNA and is efficient to specially amplify 30 pg human DNA in the presence of 1 µg of genomic DNA from tested species, respectively. The BRCA1-qPCR assay was able to quantify as low as 0.003% of human cells within murine leukocytes. CONCLUSION The BRCA1-qPCR assay is efficient for the quantification of human cells in preclinical animal models.
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Affiliation(s)
- Ke Liu
- Department of Gastroenterology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Lang Hu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Siyu Wang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Xinzhu Chen
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Yuting Liu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Shuli Zhao
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hui Wang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Li Li
- Department of Gastroenterology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China.
| | - Hui Li
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
- National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Department of Biotechnology, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
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11
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Hong X, Wang K, Ji L, Liu X, Yu L, Wei J, Wang Y, Wei C, Li W, Zhu X. Exploring the relationship between environmental DNA concentration and biomass in Asian giant softshell turtle ( Pelochelys cantorii). PeerJ 2023; 11:e16218. [PMID: 37810767 PMCID: PMC10559886 DOI: 10.7717/peerj.16218] [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: 11/14/2022] [Accepted: 09/11/2023] [Indexed: 10/10/2023] Open
Abstract
In recent years, environmental DNA (eDNA) technology has become an accepted approach for investigating rare and endangered species because of its economic efficiency, high sensitivity, and non-invasiveness. The Asian giant softshell turtle (Pelochelys cantorii) is a first-class protected aquatic animal in China, and traditional resource survey methods have not identified its natural populations for many years. In this study, primers and a TaqMan probe targeting ND5 were designed, reaction conditions were optimized, a standard curve was constructed using synthetic DNA, and an eDNA quantitative PCR (qPCR) detection method was established. The eDNA detection technology for P. cantorii revealed that the number of species in the experimental pools showed a significant linear relationship with the eDNA concentration (p < 0.05). The eDNA concentration was negatively correlated with the length of time after the removal of P. cantorii and retention in the water body for 9 days. The qPCR detection method for P. cantorii eDNA established in this study can be applied to the qualitative detection of P. cantorii in water bodies, as well as to preliminary evaluation of its relative biomass. This can serve as a baseline for the investigation of natural P. cantorii population and the evaluation of its wild release effects.
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Affiliation(s)
- Xiaoyou Hong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Kaikuo Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Liqin Ji
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Xiaoli Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Lingyun Yu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jie Wei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Yakun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chengqing Wei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Wei Li
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Xinping Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
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12
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Ochiai I, Harada T, Jomori S, Kouzuma A, Watanabe K. Bioaugmentation of microbial electrolysis cells with Geobacter sulfurreducens YM18 for enhanced hydrogen production from starch. Bioresour Technol 2023; 386:129508. [PMID: 37468016 DOI: 10.1016/j.biortech.2023.129508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Double-chamber microbial electrolysis cells (MECs) were operated using starch-based medium as the anolyte and rice paddy-field soil as the anode inoculum, and hydrogen production from the cathode chamber was examined. In order to enhance current generation and hydrogen production, the anode chamber was bioaugmented with Geobacter sulfurreducens strain YM18, and its effects were evaluated based on the performances of non-bioaugmented controls. Results show that the bioaugmented MEC generated threefold greater current during one-month operation and produced sixfold greater amounts of hydrogen than those of the non-bioaugmented control. Quantitative PCR and metabarcoding analyses confirmed successful colonization of anode surfaces with YM18, suggesting the utility of bioaugmentation with YM18 for enhancing the performance of bioelectrochemical systems, including MECs treating biomass wastes.
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Affiliation(s)
- Itta Ochiai
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Tomoka Harada
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Shinji Jomori
- Advanced Material Engineering Division, Toyota Motor Corporation, Susono, Shizuoka 410-1193, Japan
| | - Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.
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13
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Zhu X, Gopurenko D, Galea F, Marsh IB, McDougall S, Thotagamuwa A. High-quality DNA isolation protocol for detection of Khapra beetle (Dermestidae: Trogoderma granarium Everts, 1898) in standard wheat germ trap. Mol Biol Rep 2023; 50:8757-8762. [PMID: 37541998 PMCID: PMC10520210 DOI: 10.1007/s11033-023-08673-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/07/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND Khapra beetle (Dermestidae: Trogoderma granarium Everts, 1898) is an internationally significant pest of grain crops and stored grain products. Wheat germ traps, routinely used in surveillance sampling of Khapra beetle provide feed-substrates used by the pest throughout its life cycle. However, Khapra beetle larvae, eggs and other traces of the pest, such as larval frass and exuviae, in wheat germ traps are difficult to sort and taxonomically identify. Additionally, high levels of polysaccharides in wheat germ can inhibit PCR based molecular detection of this pest captured in the traps. METHODS AND RESULTS We have developed a sensitive and low-cost protocol for extracting trace levels of Khapra beetle DNA from an entire wheat germ trap. Overnight digestion of entire trap contents in 6 mL of ATL buffer, followed by a 40 min lysis step was optimal for DNA extraction. Paired with reported qPCR assays, this protocol allows the detection of a few hairs of T. granarium in a typical 2-gram wheat germ trap. CONCLUSION This DNA extraction protocol makes it possible to perform a more rapid identification of the pest following wheat germ sample collection. The protocol has potential to improve international efforts for Khapra beetle surveillance.
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Affiliation(s)
- Xiaocheng Zhu
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia.
| | - David Gopurenko
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
| | - Francesca Galea
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, 2568, Australia
| | - Ian B Marsh
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, 2568, Australia
| | - Sandra McDougall
- NSW Department of Primary Industries, Yanco Agricultural Institute, Yanco, NSW, 2703, Australia
| | - Agasthya Thotagamuwa
- School of Agriculture, Environment and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
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14
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Scholz P, Chapman KD, Ischebeck T, Guzha A. Quantification of Botrytis cinerea Growth in Arabidopsis thaliana. Bio Protoc 2023; 13:e4740. [PMID: 37638304 PMCID: PMC10450733 DOI: 10.21769/bioprotoc.4740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/06/2023] [Accepted: 06/19/2023] [Indexed: 08/29/2023] Open
Abstract
Yield losses attributed to plant pathogens pose a serious threat to plant productivity and food security. Botrytis cinerea is one of the most devastating plant pathogens, infecting a wide array of plant species; it has also been established as a model organism to study plant-pathogen interactions. In this context, development of different assays to follow the relative success of B. cinerea infections is required. Here, we describe two methods to quantify B. cinerea development in Arabidopsis thaliana genotypes through measurements of lesion development and quantification of fungal genomic DNA in infected tissues. This provides two independent techniques that are useful in assessing the susceptibility or tolerance of different Arabidopsis genotypes to B. cinerea. Key features Protocol for the propagation of the necrotrophic plant pathogen fungus Botrytis cinerea and spore production. Two methods of Arabidopsis thaliana infection with the pathogen using droplet and spray inoculation. Two readouts, either by measuring lesion size or by the quantification of fungal DNA using quantitative PCR. The two methods are applicable across plant species susceptible the B. cinerea. Graphical overview A simplified overview of the droplet and spray infection methods used for the determination of B. cinerea growth in different Arabidopsis genotypes.
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Affiliation(s)
- Patricia Scholz
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department for Plant Biochemistry, Goettingen, Germany
| | - Kent D Chapman
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Till Ischebeck
- Institute of Plant Biology and Biotechnology (IBBP), Green Biotechnology, University of Münster, Münster, Germany
| | - Athanas Guzha
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department for Plant Biochemistry, Goettingen, Germany
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15
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Monteiro S, Machado-Moreira B, Linke R, Blanch AR, Ballesté E, Méndez J, Maunula L, Oristo S, Stange C, Tiehm A, Farnleitner AH, Santos R, García-Aljaro C. Performance of bacterial and mitochondrial qPCR source tracking methods: A European multi-center study. Int J Hyg Environ Health 2023; 253:114241. [PMID: 37611533 DOI: 10.1016/j.ijheh.2023.114241] [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: 04/20/2023] [Revised: 07/07/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023]
Abstract
With the advent of molecular biology diagnostics, different quantitative PCR assays have been developed for use in Source Tracking (ST), with none of them showing 100% specificity and sensitivity. Most studies have been conducted at a regional level and mainly in fecal slurry rather than in animal wastewater. The use of a single molecular assay has most often proven to fall short in discriminating with precision the sources of fecal contamination. This work is a multicenter European ST study to compare bacterial and mitochondrial molecular assays and was set to evaluate the efficiency of nine previously described qPCR assays targeting human-, cow/ruminant-, pig-, and poultry-associated fecal contamination. The study was conducted in five European countries with seven fecal indicators and nine ST assays being evaluated in a total of 77 samples. Animal fecal slurry samples and human and non-human wastewater samples were analyzed. Fecal indicators measured by culture and qPCR were generally ubiquitous in the samples. The ST qPCR markers performed at high levels in terms of quantitative sensitivity and specificity demonstrating large geographical application. Sensitivity varied between 73% (PLBif) and 100% for the majority of the tested markers. On the other hand, specificity ranged from 53% (CWMit) and 97% (BacR). Animal-associated ST qPCR markers were generally detected in concentrations greater than those found for the respective human-associated qPCR markers, with mean concentration for the Bacteroides qPCR markers varying between 8.74 and 7.22 log10 GC/10 mL for the pig and human markers, respectively. Bacteroides spp. and mitochondrial DNA qPCR markers generally presented higher Spearman's rank coefficient in the pooled fecal samples tested, particularly the human fecal markers with a coefficient of 0.79. The evaluation of the performance of Bacteroides spp., mitochondrial DNA and Bifidobacterium spp. ST qPCR markers support advanced pollution monitoring of impaired aquatic environments, aiming to elaborate strategies for target-oriented water quality management.
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Affiliation(s)
- Sílvia Monteiro
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisboa, Portugal; CERIS, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisboa, Portugal; Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, EN. 10, 2695-066, Bobadela, Portugal.
| | - Bernardino Machado-Moreira
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisboa, Portugal
| | - Rita Linke
- Institute of Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics 166/5/3, TU Wien, Gumpendorferstr. 1a, 1060, Vienna, Austria
| | - Anicet R Blanch
- Dept. Genetics, Microbiology and Statistics, University of Barcelona, Catalonia, Spain
| | - Elisenda Ballesté
- Dept. Genetics, Microbiology and Statistics, University of Barcelona, Catalonia, Spain
| | - Javier Méndez
- Dept. Genetics, Microbiology and Statistics, University of Barcelona, Catalonia, Spain
| | - Leena Maunula
- Dept. Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Satu Oristo
- Dept. Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Claudia Stange
- Dept. Water Microbiology, DVGW-Technologiezentrum Wasser, Germany
| | - Andreas Tiehm
- Dept. Water Microbiology, DVGW-Technologiezentrum Wasser, Germany
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics 166/5/3, TU Wien, Gumpendorferstr. 1a, 1060, Vienna, Austria; Karl Landsteiner University of Health Sciences, Research Division Water Quality and Health, Dr.- Karl-Dorrek-Straße 30, 3500, Krems an der Donau, Austria
| | - Ricardo Santos
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisboa, Portugal; CERIS, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisboa, Portugal; Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, EN. 10, 2695-066, Bobadela, Portugal
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Simms LA, Davies C, Jayasundara N, Sandhu S, Pintara A, Pretorius A, Nimmo GR, Harper J, Hiskens M, Smith K, Boxall S, Lord A, Giardino R, Farlow D, Ward DM, Huygens F. Performance evaluation of InfectID-BSI: A rapid quantitative PCR assay for detecting sepsis-associated organisms directly from whole blood. J Microbiol Methods 2023:106783. [PMID: 37442279 DOI: 10.1016/j.mimet.2023.106783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/15/2023]
Abstract
BACKGROUND Bloodstream infections (BSIs) (presence of pathogenic organism in blood) that progress to sepsis (life-threatening organ dysfunction caused by the body's dysregulated response to an infection) is a major healthcare issue globally with close to 50 million cases annually and 11 million sepsis-related deaths, representing about 20% of all global deaths. A rapid diagnostic assay with accurate pathogen identification has the potential to improve antibiotic stewardship and clinical outcomes. METHODS The InfectID-Bloodstream Infection (InfectID-BSI) test is a real-time quantitative PCR assay, which detects 26 of the most prevalent BSI-causing pathogens (bacteria and yeast) directly from blood (without need for pre-culture). InfectID-BSI identifies pathogens using highly discriminatory single nucleotide polymorphisms located in conserved regions of bacterial and fungal genomes. This report details the findings of a patient study which compared InfectID-BSI with conventional blood culture at two public hospitals in Queensland, Australia, using 375 whole blood samples (from multiple anatomical sites, eg. left arm, right arm, etc.) from 203 patients that have been clinically assessed to have signs and symptoms of suspected BSI, sepsis and septic shock. FINDINGS InfectID-BSI was a more sensitive method for microorganism detection compared with blood culture (BacT/ALERT, bioMerieux) for positivity rate (102 vs 54 detections), detection of fastidious organisms (Streptococcus pneumoniae and Aerococcus viridans) (25 vs 0), detection of low bioburden infections (measured as genome copies/0.35 mL of blood), time to result (<3 h including DNA extraction for InfectID-BSI vs 16 h-48 h for blood culture), and volume of blood required for testing (0.5 mL vs 40-60 mL). InfectID-BSI is an excellent 'rule out' test for BSI, with a negative predictive value of 99.7%. InfectID-BSI's ability to detect 'difficult to culture' microorganisms re-defines the four most prevalent BSI-associated pathogens as E. coli (28.4%), S. pneumoniae (17.6%), S. aureus (13.7%), and S. epidermidis (13.7%). INTERPRETATION InfectID-BSI has the potential to alter the clinical treatment pathway for patients with BSIs that are at risk of progressing to sepsis.
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Affiliation(s)
- Lisa A Simms
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia.
| | - Corey Davies
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Nadeesha Jayasundara
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Sumeet Sandhu
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia; Queensland Health, Brisbane, Queensland, Australia
| | - Alexander Pintara
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Amorette Pretorius
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Graeme R Nimmo
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; School of Medicine, Griffith University, Gold Coast, Queensland, Australia
| | - Jacqueline Harper
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia
| | - Matthew Hiskens
- Mackay Institute of Research and Innovation, Mackay Hospital and Health Service, Mackay, Queensland 4740, Australia
| | - Karen Smith
- Mackay Institute of Research and Innovation, Mackay Hospital and Health Service, Mackay, Queensland 4740, Australia; Department of Emergency Medicine, Mackay Hospital and Health Service, Mackay, Queensland 4740, Australia
| | - Sarah Boxall
- Department of Emergency Medicine, Mackay Hospital and Health Service, Mackay, Queensland 4740, Australia
| | - Anton Lord
- Spectroscopy and Data Consultants, Brisbane, Queensland, Australia
| | - Raffaella Giardino
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - David Farlow
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia; Mackay Institute of Research and Innovation, Mackay Hospital and Health Service, Mackay, Queensland 4740, Australia
| | | | - Flavia Huygens
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia
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Manter DK, Hamm AK, Deel HL. Community structure and abundance of ACC deaminase containing bacteria in soils with 16S-PICRUSt2 inference or direct acdS gene sequencing. J Microbiol Methods 2023:106740. [PMID: 37301376 DOI: 10.1016/j.mimet.2023.106740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
Bacteria containing the enzyme 1-aminocyclopropane-1-carboxylate deaminase (ACCD+) can reduce plant ethylene levels and increase root development and elongation resulting in increased resiliency to drought and other plant stressors. Although these bacteria are ubiquitous in the soil, non-culture-based methods for their enumeration and identification are not well developed. In this study we compare two culture-independent approaches for identifying ACCD+ bacteria. First, quantitative PCR (qPCR) and direct acdS sequencing with newly designed gene-specific primers; and second, phylogenetic construction of 16S rRNA amplicon libraries with the PICRUSt2 tool. Using soils from eastern Colorado, we showed complementary yet differing results in ACCD+ abundance and community structure responding to water availability. Across all sites, gene abundances estimated from qPCR with the acdS gene-specific primers and phylogenetic reconstruction using PICRUSt2 were significantly correlated. However, PICRUSt2 identified members of the Acidobacteria, Proteobacteria, and Bacteroidetes phyla (now known as Acidobacteriota, Pseudomonadota, and Bacteroidota according to the International Code of Nomenclature of Prokaryotes) as ACCD+ bacteria, whereas the acdS primers amplified only members of the Proteobacteria phyla. Despite these differences, both measures showed that bacterial abundance of ACCD+ decreased as soil water content decreased along a potential evapotranspiration (PET) gradient at three sites in eastern Colorado. One major advantage of using 16S sequencing and PICRUSt2 in metagenomic studies is the ability to get a potential functional profile of all known KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes within the bacterial community of a single soil sample. The 16S-PICRUSt2 method paints a broader picture of the biological and biochemical function of the soil microbiome compared to direct acdS sequencing; however, phylogenetic analysis based on 16S gene relatedness may not reflect that of the functional gene of interest.
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Affiliation(s)
- Daniel K Manter
- United States Department of Agriculture, Agricultural Research Service, Soil Management and Sugarbeet Research Unit, 2150 Centre Ave Bldg D, Fort Collins, CO 80526, USA.
| | - Alison K Hamm
- United States Department of Agriculture, Agricultural Research Service, Soil Management and Sugarbeet Research Unit, 2150 Centre Ave Bldg D, Fort Collins, CO 80526, USA
| | - Heather L Deel
- United States Department of Agriculture, Agricultural Research Service, Soil Management and Sugarbeet Research Unit, 2150 Centre Ave Bldg D, Fort Collins, CO 80526, USA
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Bay H, Haghighatfard A, Karimipour M, Seyedena SY, Hashemi M. Expression alteration of Neuroligin family gene in attention deficit and hyperactivity disorder and autism spectrum disorder. Res Dev Disabil 2023; 139:104558. [PMID: 37285744 DOI: 10.1016/j.ridd.2023.104558] [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] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a complex neurodevelopment disorder with social and communicational deficiency, language impairment, and ritualistic behaviors. Attention deficit hyperactivity disorder (ADHD) is a pediatric psychiatric disorder with symptoms, including attention deficit, hyperactivity, and impulsiveness. ADHD is a childhood-onset disorder that can persist into adult life. Neuroligins are post-synaptic cell-adhesion molecules that connect neurons and have an essential role in the mediation of trans-synaptic signaling and shaping the synapse and circuits and neural network functioning. AIMS Present study aimed to shed light on the role of the Neuroligin gene family in ASD and ADHD. METHODS AND PROCEDURES mRNA levels of the Neuroligin gene family (NLGN1, NLGN2, NLGN3, and NLGN4X) were studied in the peripheral blood of 450 unrelated ASD patients, 450 unrelated ADHD patients, and the normal group included 490 unrelated non-psychiatric children by quantitative PCR. Also, clinical situations were considered. OUTCOMES AND RESULTS Results showed that mRNA levels of NLGN1, NLGN2, and NLGN3 were significantly down-regulated in the ASD group vs. control subjects. In ADHD, a significant reduction of NLGN2 and NLGN3 was detected in comparison with normal children. A comparison of ASD and ADHD subjects revealed that NLGN2 was significantly down-regulated in ASD subjects. CONCLUSIONS The Neuroligin family gene may play an essential role in the etiology of ASD and ADHD and thus be a source for a better understanding of neurodevelopment disorders. IMPLICATIONS Similar patterns of deficiency of Neuroligin family genes in ASDs and ADHDs may indicate the role of these genes in functions that have been affected in both disorders.
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Affiliation(s)
- Hanie Bay
- Department of biology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Arvin Haghighatfard
- Department of biology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | | | | | - Mehrdad Hashemi
- Department of Medical genetics, Tehran medical sciences branch, Islamic Azad University, Tehran, Iran.
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19
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Lafaurie GI, Castillo DM, Iniesta M, Sanz M, Gómez LA, Castillo Y, Pianeta R, Delgadillo NA, Neuta Y, Diaz-Báez D, Herrera D. Differential analysis of culturable and unculturable subgingival target microorganisms according to the stages of periodontitis. Clin Oral Investig 2023; 27:3029-3043. [PMID: 36806930 PMCID: PMC10264511 DOI: 10.1007/s00784-023-04907-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 09/26/2022] [Accepted: 02/03/2023] [Indexed: 02/21/2023]
Abstract
OBJECTIVES Culturable and unculturable microorganisms have been associated with periodontitis. Their differential proportions and composition have not been evaluated by their severity and complexity defined by stages in the 2018 AAP-EEP classification. METHODS One hundred eighty subgingival biofilm samples were collected in Spain and Colombia from subjects categorized as health/gingivitis: periodontitis stages I/II periodontitis stages III/IV. Target culturable microorganisms (Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Tannerella forsythia, Treponema denticola, and Eubacterium nodatum) and target unculturable microorganisms (Filifactor alocis, Eubacterium saphenum, Eubacterium brachy, Desulfobulbus oralis) were evaluated by quantitative PCR analysis. In addition, their differences and association with periodontal status were analyzed by ANCOVA and logistic regression models once adjusted to age, current smoking, and country. RESULTS P. gingivalis was significantly associated with periodontitis stages I/II, OR 2.44 (CI 95% 1.08-5.47) and stages III/V, OR 6.43 (CI 95% 2.43-16.9). T forsythia, OR 7.53 (CI 95% 2.07-27.4); D. oralis, OR 5.99 (CI 95% 2.71-13.23); F. alocis, OR 10.9 (CI 95% 4.56-23.2); E. brachy, 3.57 (CI 95% 1.40-9.11); and E. saphenum, 4.85 (CI 95% 1.99-11.7) were significantly associated only with stages III/IV periodontitis. P. gingivalis evidenced significant differences with the increase in the severity of the periodontal lesion: 2.97 colony forming unit (CFU)/μL (CI 95% 2.32-3.54) health/gingivitis, and 4.66 CFU/μL (CI 95% 4.03-5.30) and 5.90 CFU/μL (CI 95% 5.20-6.48) in stages I/II and III/IV respectively (p < 0.0001). Unculturable microorganisms only evidenced differences in concentration in stages III/IV compared with health-gingivitis (p ≤ 0.001). CONCLUSION Culturable and unculturable are strongly associated with stages III/IV periodontitis. Classic culturable microorganisms are more sensitive to differentiate between stages of periodontitis in the quantitative analysis. CLINICAL RELEVANCE Future interventional studies of periodontal disease should include Filifactor alocis, Eubacterium saphenum, Eubacterium brachy, and Desulfobulbus oralis as possible markers of therapy response and as indicators of progressive disease.
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Affiliation(s)
- Gloria Inés Lafaurie
- Unit of Basic Oral Investigation (UIBO), School of Dentistry, Universidad El Bosque, Ak. 9 #13, 1a-20 Bogotá, Colombia
| | - Diana Marcela Castillo
- Unit of Basic Oral Investigation (UIBO), School of Dentistry, Universidad El Bosque, Ak. 9 #13, 1a-20 Bogotá, Colombia
| | - Margarita Iniesta
- ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, University Complutense of Madrid (UCM), Madrid, Spain
| | - Mariano Sanz
- ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, University Complutense of Madrid (UCM), Madrid, Spain
| | - Luz Amparo Gómez
- Unit of Basic Oral Investigation (UIBO), School of Dentistry, Universidad El Bosque, Ak. 9 #13, 1a-20 Bogotá, Colombia
| | - Yormaris Castillo
- Unit of Basic Oral Investigation (UIBO), School of Dentistry, Universidad El Bosque, Ak. 9 #13, 1a-20 Bogotá, Colombia
| | - Roquelina Pianeta
- ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, University Complutense of Madrid (UCM), Madrid, Spain
- School of Dentistry, Corporación Universitaria Rafael Núñez, Cartagena, Colombia
| | - Nathaly Andrea Delgadillo
- Unit of Basic Oral Investigation (UIBO), School of Dentistry, Universidad El Bosque, Ak. 9 #13, 1a-20 Bogotá, Colombia
| | - Yineth Neuta
- Unit of Basic Oral Investigation (UIBO), School of Dentistry, Universidad El Bosque, Ak. 9 #13, 1a-20 Bogotá, Colombia
| | - David Diaz-Báez
- Unit of Basic Oral Investigation (UIBO), School of Dentistry, Universidad El Bosque, Ak. 9 #13, 1a-20 Bogotá, Colombia
| | - David Herrera
- ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, University Complutense of Madrid (UCM), Madrid, Spain
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Erratt KJ, Creed IF, Favot EJ, Smol JP, Vinebrooke RD, Lobb DA, Trick CG. Reconstructing historical time-series of cyanobacteria in lake sediments: Integrating technological innovation to enhance cyanobacterial management. J Environ Manage 2023; 343:118162. [PMID: 37224685 DOI: 10.1016/j.jenvman.2023.118162] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023]
Abstract
The global rise of cyanobacterial blooms emphasizes the need to develop tools to manage water bodies prone to cyanobacterial dominance. Reconstructing cyanobacterial baselines and identifying environmental drivers that favour cyanobacterial dominance are important to guide management decisions. Conventional techniques for estimating cyanobacteria in lake sediments require considerable resources, creating a barrier to routine reconstructions of cyanobacterial time-series. Here, we compare a relatively simple technique based on spectral inferences of cyanobacteria using visible near-infrared reflectance spectroscopy (VNIRS) with a molecular technique based on real-time PCR quantification (qPCR) of the 16S rRNA gene conserved in cyanobacteria in 30 lakes across a broad geographic gradient. We examined the sedimentary record from two perspectives: 1) relationships throughout the entire core (without radiometric dating); 2) relationships post-1900s with the aid of radiometric dating (i.e., 210Pb). Our findings suggest that the VNIRS-based cyanobacteria technique is best suited for reconstructing cyanobacterial abundance in recent decades (i.e., circa 1990 onwards). The VNIRS-based cyanobacteria technique showed agreement with those generated using qPCR, with 23 (76%) lakes showing a strong or very strong positive relationship between the results of the two techniques. However, five (17%) lakes showed negligible relationships, suggesting cyanobacteria VNIRS requires further refinement to understand where VNIRS is unsuitable. This knowledge will help scientists and lake managers select alternative cyanobacterial diagnostics where appropriate. These findings demonstrate the utility of VNIRS, in most instances, as a valuable tool for reconstructing past cyanobacterial prevalence.
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Affiliation(s)
- Kevin J Erratt
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada.
| | - Irena F Creed
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5E2, Canada; Department of Physical and Environmental Sciences, University of Toronto, Toronto, ON, Canada, M1C 1A4, Canada.
| | - Elizabeth J Favot
- Paleoecological Environmental Assessment and Research Lab, Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada.
| | - John P Smol
- Paleoecological Environmental Assessment and Research Lab, Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada.
| | - Rolf D Vinebrooke
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
| | - David A Lobb
- Department of Soil Science, University of Manitoba, Winnipeg, MB, Canada.
| | - Charles G Trick
- Department of Health and Society, University of Toronto, Toronto, ON, M1C 1A4, Canada.
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21
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Pinho SCM, Faria MA, Alves R, Cabrita ARJ, Fonseca AJM, M P L V O Ferreira I. Gastric epithelial response to milk fat using the semi-dynamic INFOGEST digestion model coupled with NCI-N87 cells. Food Res Int 2023; 166:112576. [PMID: 36914314 DOI: 10.1016/j.foodres.2023.112576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/21/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023]
Abstract
The stomach is a relevant spot of lipolysis for milk fat, but research on the effect of digested milk fat in the gastric epithelium is scarce and difficult to evaluate. In the present study, we implemented the semi-dynamic in vitro digestion model of INFOGEST, combined with gastric NCI-N87 cells, to study the effect of fat-free, whole conventional, and whole pasture-based milk on gastric epithelium. Cellular messenger ribonucleic acid (mRNA) expression of membrane fatty acids receptors (GPR41, GPR84), antioxidant enzymes (CAT, SOD, GPX), and inflammatory molecules (NF-κB p65, IL-1β, IL-6, IL-8 and TNF-α) was assessed. No significant differences were observed in mRNA expression of GPR41, GPR84, SOD, GPX, IL-6, IL-8, and TNF-α, after exposure of the NCI-N87 cells to milk digesta samples (p > 0.05). An increase of CAT mRNA expression was observed (p < 0.05), at a similar level, for all milk types. Whole milk digested samples induced higher mRNA expression of NF-κB p65 and IL-1β than fat-free milk (p < 0.05); while no differences were observed between whole conventional and whole pasture-based milk (p > 0.05). Moreover, the effect of milk digesta on gastric mRNA expression was studied in a scenario of subsequent stimulation of NCI-N87 monolayer with the pro-inflammatory cytokine IFN-γ. In these conditions, milk digesta samples increased CAT mRNA expression (p < 0.05), but had no effect in the expression of NF-κB p65 and IL-1β (p > 0.05). The increase of CAT mRNA expression suggests that milk fatty acids are used for energy production by gastric epithelial cells. Cellular antioxidant response to higher milk fatty acids availability could be associated to gastric epithelial inflammation, but did not contribute to increased inflammation in case of an external contact with IFN-γ. Besides, a conventional or a pasture-based origin did not affect the impact of whole milk in the NCI-N87 monolayer. The combined model responded to differences in milk fat content, which indicates its usefulness to study effects of foods at the gastric level.
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Affiliation(s)
- Susana C M Pinho
- LAQV/REQUIMTE, Department of Chemical Sciences, Laboratory of Food Science and Hydrology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; LAQV/REQUIMTE, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo, Ferreira 228, 4050-313 Porto, Portugal
| | - Miguel A Faria
- LAQV/REQUIMTE, Department of Chemical Sciences, Laboratory of Food Science and Hydrology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Rui Alves
- SORGAL, Sociedade de Óleos e Rações S.A., Estrada Nacional 109, Lugar da Pardala, 3880-728 S. João Ovar, Portugal
| | - Ana R J Cabrita
- LAQV/REQUIMTE, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo, Ferreira 228, 4050-313 Porto, Portugal
| | - António J M Fonseca
- LAQV/REQUIMTE, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo, Ferreira 228, 4050-313 Porto, Portugal
| | - Isabel M P L V O Ferreira
- LAQV/REQUIMTE, Department of Chemical Sciences, Laboratory of Food Science and Hydrology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
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Ahlstrom CA, Scott LC, Woksepp H, Bonnedahl J, Ramey AM. Environmental antimicrobial resistance gene detection from wild bird habitats using two methods: a commercially available culture-independent qPCR assay and culture of indicator bacteria followed by whole genome sequencing. J Glob Antimicrob Resist 2023; 33:186-193. [PMID: 36972752 DOI: 10.1016/j.jgar.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
OBJECTIVES A variety of methods have been developed to detect antimicrobial resistance (AMR) in different environments to better understand the evolution and dissemination of this public health threat. Comparison of results generated using different AMR detection methods, such as qPCR and whole genome sequencing (WGS), is often imperfect and few studies have analyzed samples in parallel to evaluate differences. In this study, we compared bacterial culture and WGS to a culture-independent commercially available qPCR assay to evaluate the concordance between methods and utility of each in answering research questions regarding presence and epidemiology of AMR in wild bird habitats. METHODS We first assessed AMR gene detection in 45 bacterial isolates using qPCR from which we had existing WGS data. We then analyzed 52 wild bird fecal samples and nine spatiotemporally collected water samples using culture-independent qPCR and WGS of phenotypically resistant indicator bacterial isolates. RESULTS Overall concordance was strong between qPCR and WGS of bacterial isolates, though concordance differed among antibiotic classes. Analysis of wild bird fecal and water samples revealed more samples to be positive for AMR using qPCR than culture and WGS of bacterial isolates, though qPCR did not detect AMR genes in two samples from which phenotypically resistant isolates were found. CONCLUSIONS Based on our results, both qPCR and culture followed by sequencing may be effective approaches for characterizing AMR harbored by wild birds, though data streams produced using these different tools may have advantages and disadvantages that should be considered given the application and sample matrix.
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Affiliation(s)
- Christina A Ahlstrom
- Alaska Science Center, U.S. Geological Survey, 4210 University Drive, Anchorage, AK, 99508 USA.
| | - Laura C Scott
- Alaska Science Center, U.S. Geological Survey, 4210 University Drive, Anchorage, AK, 99508 USA
| | - Hanna Woksepp
- Department of Research, Region Kalmar County, Kalmar, 391 85, Sweden and Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Jonas Bonnedahl
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, 581 83, Sweden; Department of Infectious Diseases, Region Kalmar County, Kalmar, 391 85, Sweden
| | - Andrew M Ramey
- Alaska Science Center, U.S. Geological Survey, 4210 University Drive, Anchorage, AK, 99508 USA
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23
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Zoghroban HS, Elmansory BM, Issa YA, Eltokhy AK, Abo Safia HS, El Maghraby GM, Salama AM. Novel insights on the therapeutic effect of levamisole on the chronic toxoplasmosis in mice model. Exp Parasitol 2023; 248:108515. [PMID: 36958594 DOI: 10.1016/j.exppara.2023.108515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/02/2023] [Accepted: 03/20/2023] [Indexed: 03/25/2023]
Abstract
Latent toxoplasmosis mostly reactivates which could result in acute encephalitis. Chronic toxoplasmosis treatments are severely constrained by Toxoplasma cyst resistance. Novel therapeutic approaches are therefore becoming more essential. In this study, the effects of levamisole (LEVA) and spiramycin on the early and late stages of experimental toxoplasmosis are investigated. MATERIALS AND METHODS Seventy-five Me49 Toxoplasma gondii infected Swiss albino mice were divided into five groups; (GI): noninfected control group; (GII): infected untreated control group; (GIII): infected- LEVA treated group; (GIV): infected and received combination of spiramycin and LEVA and (GV): infected-spiramycin treated group. The impact was assessed through brain cyst count by Quantitative Real-Time Polymerase Chain Reaction (PCR), interferon gamma (IFN-γ) assay, histopathological study, and total blood counts. RESULTS The progression of chronic toxoplasmosis could only be partially controlled by using either levamisole or spiramycin as a separate drug. The combined spiramycin and levamisole treatment significantly decreased the burden of Toxoplasma brain cyst, increased IFN-γ level, total blood parameters and improved the histopathological features especially at the late stage of infection. IN CONCLUSION Levamisole effectively modulated Toxoplasma-induced immune responses, resulting in chronic toxoplasmosis remission. Further clinical trials will be needed to study the effect of these combination in HIV/AIDS (human immunodeficiency virus) patients with toxoplasmosis.
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Affiliation(s)
- Hager S Zoghroban
- Department of Medical Parasitology, Faculty of Medicine, Tanta University, Tanta, Egypt.
| | - Basma M Elmansory
- Department of Medical Parasitology, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Yasmine Amr Issa
- Department of Medical Biochemistry, Faculty of Medicine, Alexandria University, Alexandria, Egypt; Medical Biochemistry, College of Medicine, Arab Academy for Science, Technology and Maritime Transport, New Alamein, Egypt
| | - Amira K Eltokhy
- Department of Medical Biochemistry, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Hend S Abo Safia
- Department of Medical Pathology, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Gamal M El Maghraby
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Amina M Salama
- Department of Medical Parasitology, Faculty of Medicine, Tanta University, Tanta, Egypt
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Galeotti M, Orioles M, Saccà E, Byadgi O, Pesaro S, Di Cerbo A, Magi GE. Understanding the Pathogenesis of Red Mark Syndrome in Rainbow Trout ( Oncorhynchus mykiss) through an Integrated Morphological and Molecular Approach. Animals (Basel) 2023; 13:ani13061103. [PMID: 36978643 PMCID: PMC10044500 DOI: 10.3390/ani13061103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Red mark syndrome (RMS) is a widespread skin disorder of rainbow trout in freshwater aquaculture, believed to be caused by a Midichloria-like organism (MLO). Here, we aimed to study the pathologic mechanisms at the origin of RMS by analyzing field samples from a recent outbreak through gene expression, MLO PCR, quantitative PCR, and a histopathological scoring system proposed for RMS lesions. Statistical analyses included a One-Way Analysis of Variance (ANOVA) with a Dunnett's multiple comparisons test to assess differences among gene expression groups and a nonparametric Spearman correlation between various categories of skin lesions and PCR results. In short, the results confirmed the presence of a high quantity of 16S gene copy numbers of Midichloria-like organisms in diseased skin tissues. However, the number of Midichloria-like organisms detected was not correlated to the degree of severity of skin disease. Midichloria-like organism DNA was found in the spleen and head kidney. The spleen showed pathologic changes mainly of hyperplastic type, reflecting its direct involvement during infection. The most severe skin lesions were characterized by a high level of inflammatory cytokines sustaining and modulating the severe inflammatory process. IL-1 β, IL-6, IL-10, MHC-II, and TCR were upregulated in severe skin lesions, while IL-10 was highly expressed in moderate to severe ones. In the moderate form, the response was driven to produce immunoglobulins, which appeared crucial in controlling the skin disease's severity. Altogether our results illustrated a complex immune interaction between the host and Midichloria-like organism.
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Affiliation(s)
- Marco Galeotti
- Department of Agricultural, Food, Environmental and Animal Sciences, DI4A, University of Udine, 33100 Udine, Italy
| | - Massimo Orioles
- Department of Agricultural, Food, Environmental and Animal Sciences, DI4A, University of Udine, 33100 Udine, Italy
| | - Elena Saccà
- Department of Agricultural, Food, Environmental and Animal Sciences, DI4A, University of Udine, 33100 Udine, Italy
| | - Omkar Byadgi
- International Program in Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan
| | - Stefano Pesaro
- Department of Agricultural, Food, Environmental and Animal Sciences, DI4A, University of Udine, 33100 Udine, Italy
| | - Alessandro Di Cerbo
- School of Biosciences and Veterinary Medicine, University of Camerino, 62024 Matelica, Italy
| | - Gian Enrico Magi
- School of Biosciences and Veterinary Medicine, University of Camerino, 62024 Matelica, Italy
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Boezen D, Johnson ML, Grum-Grzhimaylo AA, van der Vlugt RA, Zwart MP. Evaluation of sequencing and PCR-based methods for the quantification of the viral genome formula. Virus Res 2023; 326:199064. [PMID: 36746340 DOI: 10.1016/j.virusres.2023.199064] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023]
Abstract
Viruses show great diversity in their genome organization. Multipartite viruses package their genome segments into separate particles, most or all of which are required to initiate infection in the host cell. The benefits of such seemingly inefficient genome organization are not well understood. One hypothesised benefit of multipartition is that it allows for flexible changes in gene expression by altering the frequency of each genome segment in different environments, such as encountering different host species. The ratio of the frequency of segments is termed the genome formula (GF). Thus far, formal studies quantifying the GF have been performed for well-characterised virus-host systems in experimental settings using RT-qPCR. However, to understand GF variation in natural populations or novel virus-host systems, a comparison of several methods for GF estimation including high-throughput sequencing (HTS) based methods is needed. Currently, it is unclear how HTS-methods compare a golden standard, such as RT-qPCR. Here we show a comparison of multiple GF quantification methods (RT-qPCR, RT-digital PCR, Illumina RNAseq and Nanopore direct RNA sequencing) using three host plants (Nicotiana tabacum, Nicotiana benthamiana, and Chenopodium quinoa) infected with cucumber mosaic virus (CMV), a tripartite RNA virus. Our results show that all methods give roughly similar results, though there is a significant method effect on genome formula estimates. While the RT-qPCR and RT-dPCR GF estimates are congruent, the GF estimates from HTS methods deviate from those found with PCR. Our findings emphasize the need to tailor the GF quantification method to the experimental aim, and highlight that it may not be possible to compare HTS and PCR-based methods directly. The difference in results between PCR-based methods and HTS highlights that the choice of quantification technique is not trivial.
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Affiliation(s)
- Dieke Boezen
- Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708PB, The Netherlands; Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands.
| | - Marcelle L Johnson
- Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708PB, The Netherlands; Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Alexey A Grum-Grzhimaylo
- Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708PB, The Netherlands; Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht 3584CT, The Netherlands
| | - René Aa van der Vlugt
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Mark P Zwart
- Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708PB, The Netherlands
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Zsurka G, Trombly G, Schöler S, Blei D, Kunz WS. Functional Assessment of Mitochondrial DNA Maintenance by Depletion and Repopulation Using 2',3'-Dideoxycytidine in Cultured Cells. Methods Mol Biol 2023; 2615:229-40. [PMID: 36807796 DOI: 10.1007/978-1-0716-2922-2_17] [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: 02/23/2023]
Abstract
The manipulation of mitochondrial DNA (mtDNA) copy number in cultured cells, using substances that interfere with DNA replication, is a useful tool to investigate various aspects of mtDNA maintenance. Here we describe the use of 2',3'-dideoxycytidine (ddC) to induce a reversible reduction of mtDNA copy number in human primary fibroblasts and human embryonic kidney (HEK293) cells. Once the application of ddC is stopped, cells depleted for mtDNA attempt to recover normal mtDNA copy numbers. The dynamics of repopulation of mtDNA provide a valuable measure for the enzymatic activity of the mtDNA replication machinery.
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Wei Y, Liu Y, Li L, Xiang S, Zhang H, Shang Y. Identification of s9ap used as an endogenous reference gene in qualitative and real-time quantitative PCR detection of Pleurotus eryngii. Mol Biol Rep 2023; 50:621-9. [PMID: 36370299 DOI: 10.1007/s11033-022-07562-3] [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] [Received: 02/17/2022] [Revised: 04/25/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Pleurotus eryngii is a kind of edible fungi with good quality, and it is popular among consumers. At present, some adulterated edible fungi are available in the market. The rights and interests of consumers can be ensured by establishing a practical edible fungi detection system. Among the existing methods for detecting food adulteration, endogenous reference gene amplification is convenient and reliable. However, no ideal endogenous reference gene is available for P. eryngii. METHODS AND RESULTS In this study, s9ap was screened as an endogenous reference gene through sequence alignment. Qualitative and quantitative PCR analysis of this gene was carried out in one P. eryngii variety and 18 other species. The detection limit of quantitative PCR was 400 pg, and no s9ap amplification products were detected in the 18 other species. CONCLUSIONS This study confirmed that s9ap was an ideal endogenous reference gene for the detection of P. eryngii. This method was also suitable for processed food products.
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Laveroni SL, Parks VR. Quantitative PCR of Alu Repeats Using PowerUp™ SYBR ® Green Master Mix. Methods Mol Biol 2023; 2685:149-174. [PMID: 37439981 DOI: 10.1007/978-1-0716-3295-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Quantitative PCR is one of the fundamental steps performed when processing routine casework in a forensic laboratory. Quantitative PCR of Alu repeats using a SYBR® Green master mix can produce calculated estimates of how much DNA was extracted from a sample. This process offers more efficiency, human specificity, and can be performed faster than other outdated quantification methods, such as slot blot or yield gel. A qPCR master mix is prepared and consists of Alu-F primers, Alu-R primers, water, and SYBR® Green master mix. The Alu-F and Alu-R primers target Alu sequences that are present hundreds of thousands of times throughout the human genome and are effective markers for human DNA quantification. During qPCR, the 7500 system facilitates the amplification of target Alu repeats. The SYBR® Green I fluorescent dye intercalates between the amplified dsDNA targets. During each amplification cycle, the 7500 system agitates the SYBR® Green I dye, resulting in a fluorescence signal that is recorded when it passes a specified Ct value. After qPCR amplification is complete, a standard curve is created and used to determine how much DNA a sample contains. This chapter provides instructions on how to accurately prepare a 96-well plate for qPCR, use the 7500 system and associated software to set up the qPCR amplification, and interpret the corresponding results produced.
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Affiliation(s)
- Sierra L Laveroni
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA.
| | - Victoria R Parks
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
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Jammes M, Urbino C, Diouf MB, Peterschmitt M. Refining the emergence scenario of the invasive recombinant Tomato yellow leaf curl virus -IS76. Virology 2023; 578:71-80. [PMID: 36473279 DOI: 10.1016/j.virol.2022.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/02/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]
Abstract
TYLCV-IS76, a unique recombinant between tomato yellow leaf curl virus (TYLCV) and tomato yellow leaf curl Sardinia virus (TYLCSV), has replaced its parental viruses in southern Morocco. To refine its emergence scenario, its fitness was monitored experimentally in conditions aiming at reproducing natural situations, i.e. superinfection of plants already infected with parental viruses and competition with other TYLCV/TYLCSV recombinants (LSRec) automatically generated in plants coinfected with TYLCV and TYLCSV. TYLCV-IS76 accumulated significantly more than parental viruses regardless of plant age and superinfection delay. Although TYLCV-IS76 and LSRec both accumulated more than parental viruses in laboratory conditions, LSRec were displaced by TYLCV-IS76 in nature like parental viruses were. TYLCV-IS76 did not exhibit any vector transmission advantage over LSRec and TYLCV the most competitive parental virus. Thus, it is apparently only in the plant compartment that the recombination event that generated TYLCV-IS76, induced the competitiveness advantage by which the last became first.
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Affiliation(s)
- Margaux Jammes
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Cica Urbino
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Mame Boucar Diouf
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Michel Peterschmitt
- CIRAD, UMR PHIM, F-34398, Montpellier, France; PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
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Schvartz G, Karniely S, Azar R, Kabat A, Steinman A, Erster O. Detection and Analysis of West Nile Virus Structural Protein Genes in Animal or Bird Samples. Methods Mol Biol 2023; 2585:127-143. [PMID: 36331771 DOI: 10.1007/978-1-0716-2760-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
West Nile virus (WNV) is an important zoonotic pathogen, which is detected mainly by identification of its RNA using PCR. Genetic differentiation between WNV lineages is usually performed by complete genome sequencing, which is not available in many research and diagnostic laboratories. In this chapter, we describe a protocol for detection and analysis of WNV samples by sequencing the entire region of their structural genes capsid (C), preM/membrane, and envelope. The primary step is the detection of WNV RNA by quantitative PCR of the NS2A gene or the C gene regions. Next, the entire region containing the structural protein genes is amplified by PCR. The primary PCR product is then amplified again in parallel reactions, and these secondary PCR products are sequenced. Finally, bioinformatic analysis enables detection of mutations and classification of the samples of interest. This protocol is designed to be used by any laboratory equipped for endpoint and quantitative PCR. The sequencing can be performed either in-house or outsourced to a third-party service provider. This protocol may therefore be useful for rapid and affordable classification of WNV samples, obviating the need for complete genome sequencing.
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Affiliation(s)
- Gili Schvartz
- Kimron Veterinary Institute, Israel Ministry of Agriculture, Bet Dagan, Israel
- Koret School of Veterinary Medicine, The Robert H. Smith, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Sharon Karniely
- Kimron Veterinary Institute, Israel Ministry of Agriculture, Bet Dagan, Israel
| | - Roberto Azar
- Central Virology Laboratory of Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Areej Kabat
- Central Virology Laboratory of Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Amir Steinman
- Koret School of Veterinary Medicine, The Robert H. Smith, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- Veterinary Teaching Hospital, Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Oran Erster
- Central Virology Laboratory of Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel.
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Megarani DV, Al-Hussinee L, Subramaniam K, Sriwanayos P, Imnoi K, Keleher B, Nicholson P, Surachetpong W, Tattiyapong P, Hick P, Gustafson LL, Waltzek TB. Development of a TaqMan quantitative reverse transcription PCR assay to detect tilapia lake virus. Dis Aquat Organ 2022; 152:147-158. [PMID: 36546687 DOI: 10.3354/dao03700] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Tilapia lake virus disease (TiLVD) is an emerging viral disease associated with high morbidity and mortality in cultured tilapia worldwide. In this study, we have developed and validated a TaqMan quantitative reverse transcription PCR (RT-qPCR) assay for TiLV, targeting a conserved region within segment 10 of the genome. The RT-qPCR assay was efficient (mean ± SD: 96.71 ± 3.20%), sensitive with a limit of detection of 10 RNA viral copies per reaction, and detected TiLV strains from different geographic regions including North America, South America, Africa, and Asia. The intra- and inter-assay variability ranged over 0.18-1.41% and 0.21-2.21%, respectively. The TaqMan RT-qPCR assay did not cross-react with other RNA viruses of fish, including an orthomyxovirus, a betanodavirus, a picornavirus, and a rhabdovirus. Analysis of 91 proven-positive and 185 proven-negative samples yielded a diagnostic sensitivity of 96.7% and a diagnostic specificity of 100%. The TaqMan RT-qPCR assay also detected TiLV RNA in infected Nile tilapia liver tissue extracts following an experimental challenge study, and it successfully detected TiLV RNA in SSN-1 (E-11 clone) cell cultures displaying cytopathic effects following their inoculation with TiLV-infected tissue homogenates. Thus, the validated TaqMan RT-qPCR assay should be useful for both research and diagnostic purposes. Additionally, the TiLV qPCR assay returns the clinically relevant viral load of a sample which can assist health professionals in determining the role of TiLV during disease investigations. This RT-qPCR assay could be integrated into surveillance programs aimed at mitigating the effects of TiLVD on global tilapia production.
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Affiliation(s)
- Dorothea V Megarani
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32610, USA
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Beheshti Zadeh R, Safaeian S, Moslemi E, Mosavi Nadushen R, Esfahani K. Monitoring of Infant Formula and Baby Food for the Pat and NOS Terminator of Genetically Modified Maize and Soybean by Real-time PCR in Iran. Iran J Pharm Res 2022; 21:e126921. [PMID: 36060903 PMCID: PMC9420218 DOI: 10.5812/ijpr-126921] [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] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/10/2022] [Accepted: 04/03/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Soybean and maize are the most cultivated genetically modified (GM) plants. Because of the increase in the imports of GM products to Iran, infant formula and baby food, which is consumed by babies during their first month of life, can also contain soybean and maize. It has become fundamental to screen these types of products. OBJECTIVES The present study aimed to investigate the GM corn and soybean in baby food and infant formula using real-time polymerase chain reaction (PCR). METHODS A total of 60 baby food and infant formulas were collected randomly from the local drugstores in Tehran. Genomic DNA was extracted from all samples, then by real-time PCR detection, tested Pat/NOS. Internal control genes zein and lectin were used for maize and soybean, respectively. RESULTS Results showed that 5% of infant formulas and 5% of baby food, two Iranian and one imported baby food, and two imported and one Iranian infant formula were positive for pat. However, NOS was detected in none of the samples. The results showed positive results for the presence of the pat gene in the products without an appropriate label. CONCLUSIONS This article provides evidence of GM maize and soybean presence in baby food and infant formula in Iran.
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Affiliation(s)
- Ramin Beheshti Zadeh
- Department of Food Science, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Shila Safaeian
- Department of Food Science, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Elham Moslemi
- Department of Biology, East Tehran Branch, Islamic Azad University, Tehran, Iran
| | | | - Kasra Esfahani
- Department of Plant Bioproducts, Institute of Agricultural Biotechnology (IAB), National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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Almendras K, Iannuzzi S, Carú M, Orlando J. Diversity of Microbial Functional Genes Should Be Considered During the Interpretation of the qPCR Melting Curves. Microb Ecol 2022; 84:935-940. [PMID: 34599356 DOI: 10.1007/s00248-021-01883-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Soil microorganisms play an essential role in biogeochemical cycles. One approach to study these microbial communities is quantifying functional genes by quantitative PCR (qPCR), in which a melting curve analysis is usually assessed to confirm that a single PCR product is being quantified. However, the high diversity of functional genes in environmental samples could generate more than one peak in those curves, so the presence of two or multiple peaks does not always indicate nonspecific amplification. Here, we analyzed the taxonomic diversity of soil microorganisms harboring functional genes involved in nitrogen (N) and phosphorus (P) cycles, based on a database of genomes and metagenomes, and predicted the melting curve profiles of these genes. These functional genes were spread across many bacterial phyla, but mainly Proteobacteria and Actinobacteria. In general, the melting curves exhibited more than one peak or peaks with shoulders, mainly related to the variation of the nucleotide composition of the genes and the expected size of the amplicons. These results indicate that the melting curves of functional genes from environmental samples should be carefully evaluated, being in silico analyses a cost-effective way to identify inherent sequence diversity and avoid interpreting multiple peaks always as unspecific amplifications.
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Affiliation(s)
- Katerin Almendras
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, 7800003, Santiago, Chile
| | - Stefania Iannuzzi
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, 7800003, Santiago, Chile
| | - Margarita Carú
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, 7800003, Santiago, Chile
| | - Julieta Orlando
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, 7800003, Santiago, Chile.
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Wang WJ, Feng SQ, He F, Du HJ, Feng M, Wang RF, Mei GY, Liu M, Liu R, Yao HL, Han J. The Viral Load of Epstein-Barr Virus in Blood of Children after Hematopoietic Stem Cell Transplantation. Biomed Environ Sci 2022; 35:804-810. [PMID: 36189995 DOI: 10.3967/bes2022.052] [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] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/31/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVE To detect the Epstein-Barr virus (EBV) viral load of children after hematopoietic stem cell transplantation (HSCT) using chip digital PCR (cdPCR). METHODS The sensitivity of cdPCR was determined using EBV plasmids and the EBV B95-8 strain. The specificity of EBV cdPCR was evaluated using the EBV B95-8 strain and other herpesviruses (herpes simplex virus 1, herpes simplex virus 2, varicella zoster virus, human cytomegalovirus, human herpesvirus 6, and human herpesvirus 7). From May 2019 to September 2020, 64 serum samples of children following HSCT were collected. EBV infection and the viral load of serum samples were detected by cdPCR. The epidemiological characteristics of EBV infections were analyzed in HSCT patients. RESULTS The limit of detection of EBV cdPCR was 110 copies/mL, and the limit of detection of EBV quantitative PCR was 327 copies/mL for the pUC57-BALF5 plasmid. The result of EBV cdPCR was up to 121 copies/mL in the EBV B95-8 strain, and both were more sensitive than that of quantitative PCR. Using cdPCR, the incidence of EBV infection was 18.75% in 64 children after HSCT. The minimum EBV viral load was 140 copies/mL, and the maximum viral load was 3,209 copies/mL using cdPCR. The average hospital stay of children with EBV infection (184 ± 91 days) was longer than that of children without EBV infection (125 ± 79 days), P = 0.026. CONCLUSION EBV cdPCR had good sensitivity and specificity. The incidence of EBV infection was 18.75% in 64 children after HSCT from May 2019 to September 2020. EBV cdPCR could therefore be a novel method to detect EBV viral load in children after HSCT.
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Affiliation(s)
- Wen Jun Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shun Qiao Feng
- Department of Hematology, Children's Hospital of Capital Institute of Pediatrics, Beijing 100020, China
| | - Feng He
- Department of Biochemistry & Immunology, Capital Institute of Pediatrics, Beijing 100020, China
| | - Hai Jun Du
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Miao Feng
- Department of Biochemistry & Immunology, Capital Institute of Pediatrics, Beijing 100020, China
| | - Rui Fang Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Guo Yong Mei
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Mi Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Rong Liu
- Department of Hematology, Children's Hospital of Capital Institute of Pediatrics, Beijing 100020, China
| | - Hai Lan Yao
- Department of Biochemistry & Immunology, Capital Institute of Pediatrics, Beijing 100020, China
| | - Jun Han
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Fujii K, Mita Y, Watahiki H, Fukagawa T, Kitayama T, Mizuno N, Nakahara H, Sekiguchi K. Development and validation of a SYBR green-based mitochondrial DNA quantification method by following the MIQE and other guidelines. Leg Med (Tokyo) 2022; 58:102096. [PMID: 35689884 DOI: 10.1016/j.legalmed.2022.102096] [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] [Received: 01/30/2022] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 01/28/2023]
Abstract
In forensic mitochondrial DNA (mtDNA) analysis, quantitative PCR (qPCR) is usually performed to obtain high-quality sequence data for subsequent Sanger or massively parallel sequencing. Unlike methods for nuclear DNA quantification using qPCR, a calibrator is necessary to obtain mtDNA concentrations (i.e., copies/µL). Herein, we developed and validated a mtDNA quantification method based on a SYBR Green assay by following MIQE [Bustin et al., Clin. Chem. 55 (2009) 611-22] and other guidelines. Primers were designed to amplify nucleotide positions 16,190-16,420 in hypervariable region 1 for qPCR using PowerUp SYBR Green and QuantStudio 5. The optimized conditions were 0.3 µM each primer and an annealing temperature of 60 °C under a 2-step cycling protocol. K562 DNA at 100 pg/µL was converted into a mtDNA concentration of 16,400 copies/µL using linearized plasmid DNA. This mtDNA calibrator was obtained by cloning the synthesized DNA fragments of mtDNA (positions 16,140-16,470) containing a 100-bp inversion. The linear dynamic range of the K562 standard curve was 10,000-0.1 pg/µL (r2 ≥ 0.999). The accuracy was examined using NIST SRM 2372a, and its components A, B, and C were quantified with differences of -29.4%, -35.0%, and -22.0%, respectively, against the mtDNA concentrations calculated from published NIST data. We also examined the specificity of the primers, stability of the reaction mix, precision, tolerance against PCR inhibitors, and cross-reactivity against DNA from various animal taxa. Our newly developed mtDNA quantification method is expected to be useful for forensic mtDNA analysis.
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Wu Y, Li Y, Niu L, Zhang W, Wang L, Zhang H. Nutrient status of integrated rice-crayfish system impacts the microbial nitrogen-transformation processes in paddy fields and rice yields. Sci Total Environ 2022; 836:155706. [PMID: 35526617 DOI: 10.1016/j.scitotenv.2022.155706] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/30/2022] [Accepted: 05/01/2022] [Indexed: 06/14/2023]
Abstract
Increasing rice yield is essential for alleviating global food crisis. High soil nutrient level guarantees high rice yields in conventional rice monoculture (RM) systems, but excessive unconsumed nutrients act as pollutants and can even threaten rice growth. The integrated rice-crayfish (IRC) system aims to transfer the excess nutrients from crayfish to paddy fields to improve the comprehensive utilization rate of nutrients and create additional profits, while the responding characteristics of IRC microbial communities in paddy fields and rice yields to the nutrient status remain unclear. Considering the crucial roles of microbiomes in promoting nutrient cycling for crop absorption in rice production progresses, the composition and functional characteristics of soil microbial communities from six IRC farms with variant nutrient statuses in the Yangtze River Delta were surveyed in this study. Compared with RM systems, IRC systems with appropriately improved (p < 0.05) soil quality created favorable nutrient (FN) status accompanied by 15% rice yields increase, while IRC systems with extremely high nutrients (HN) status (p < 0.01) accompanied by 14% rice yields reduction. Soil microbial diversity and network complexity were maintained in FN-IRC systems, but declined in HN-IRC systems, with the Shannon index significantly decreased by 9.2% and network density decreased from 0.135 (in RM) to 0.062. In the FN-IRC systems, the keystone taxa identified by co-occurrence networks displayed inextricably positive correlations with soil nitrification potential (calculated by normalization of amoA gene abundance) and rice yields. While in HN-IRC systems, the large loss of keystone taxa might limit soil nitrogen fixation potential (calculated by normalization of nifH gene abundance), and further rice yields. Our study indicates that soil nutrient management in IRC systems claim attention, and the improvement of nitrogen metabolism is the key to realize agricultural cleaner production.
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Affiliation(s)
- Yunyu Wu
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, PR China
| | - Yi Li
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
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Kyslík J, Vancová M, Bartošová-Sojková P, Lövy A, Holzer AS, Fiala I. Expression profiling and cellular localization of myxozoan minicollagens during nematocyst formation and sporogenesis. Int J Parasitol 2022:S0020-7519(22)00104-7. [PMID: 35970383 DOI: 10.1016/j.ijpara.2022.07.002] [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] [Received: 04/27/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 11/20/2022]
Abstract
In free-living cnidarians, minicollagens are major structural components in the biogenesis of nematocysts. Recent sequence mining and proteomic analysis demonstrate that minicollagens are also expressed by myxozoans, a group of evolutionarily ancient cnidarian endoparasites. Nonetheless, the presence and abundance of nematocyst-associated genes/proteins in nematocyst morphogenesis have never been studied in Myxozoa. Here, we report the gene expression profiles of three myxozoan minicollagens, ncol-1, ncol-3, and the recently identified noncanonical ncol-5, during the intrapiscine development of Myxidium lieberkuehni, the myxozoan parasite of the northern pike, Esox lucius. Moreover, we localized the myxozoan-specific minicollagen Ncol-5 in the developing myxosporean stages by Western blotting, immunofluorescence, and immunogold electron microscopy. We found that expression of minicollagens was spatiotemporally restricted to developing nematocysts within the myxospores during sporogenesis. Intriguingly, Ncol-5 is localized in the walls of nematocysts and predominantly in nematocyst tubules. Overall, we demonstrate that despite being significantly reduced in morphology, myxozoans retain structural components associated with nematocyst development in free-living cnidarians. Furthermore, our findings have practical implications for future functional and comparative studies as minicollagens are useful markers of the developmental phase of myxozoan parasites.
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Nash MT, Quijada-Rodriguez AR, Allen GJP, Wilson JM, Weihrauch D. Characterization of 3 different types of aquaporins in Carcinus maenas and their potential role in osmoregulation. Comp Biochem Physiol A Mol Integr Physiol 2022; 272:111281. [PMID: 35902004 DOI: 10.1016/j.cbpa.2022.111281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/18/2022]
Abstract
Intertidal crustaceans like Carcinus maenas shift between an osmoconforming and osmoregulating state when inhabiting full-strength seawater and dilute environments, respectively. While the bodily fluids and environment of marine osmoconformers are approximately isosmotic, osmoregulating crabs inhabiting dilute environments maintain their bodily fluid osmolality above that of their environment by actively absorbing and retaining osmolytes (e.g., Na+, Cl-, urea) while eliminating excess water. Few studies have investigated the role of aquaporins (AQPs) in the osmoregulatory organs of crustaceans, especially within brachyuran species. In the current study, three different aquaporins were identified within a transcriptome of C. maenas, including a classical AQP (CmAQP1), an aquaglyceroporin (CmGLP1), and a big-brain protein (CmBIB1), all of which are expressed in the gills and the antennal glands. Functional expression of these aquaporins confirmed water transport capabilities for CmAQP1, CmGLP1, but not for CmBIB1, while CmGLP1 also transported urea. Higher relative CmAQP1 mRNA expression within tissues of osmoconforming crabs suggests the apical/sub-apically localized channel attenuates osmotic gradients created by non-osmoregulatory processes while its downregulation in dilute media reduces the water permeability of tissues to facilitate osmoregulation. Although hemolymph urea concentrations rose upon exposure to brackish water, urea was not detected in the final urine. Due to its urea-transport capabilities, CmGLP1 is hypothesized to be involved in a urea retention mechanism believed to be involved in the production of diluted urine. Overall, these results suggest that AQPs are involved in osmoregulation and provide a basis for future mechanistic studies investigating the role of AQPs in volume regulation in crustaceans.
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Affiliation(s)
- M T Nash
- Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | | | - G J P Allen
- Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - J M Wilson
- Biology, Wilfrid Laurier University, Waterloo, Canada
| | - D Weihrauch
- Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada.
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da Cunha ET, Pedrolo AM, Bueno JCF, Pereira TP, Soares CRFS, Arisi ACM. Inoculation of Herbaspirillum seropedicae strain SmR1 increases biomass in maize roots DKB 390 variety in the early stages of plant development. Arch Microbiol 2022; 204:373. [PMID: 35672591 DOI: 10.1007/s00203-022-02986-8] [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: 12/10/2021] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 11/26/2022]
Abstract
Herbaspirillum seropedicae is a plant growth-promoting bacteria isolated from diverse plant species. In this work, the main objective was to investigate the efficiency of H. seropedicae strain SmR1 in colonizing and increasing maize growth (DKB 390 variety) in the early stages of development under greenhouse conditions. Inoculation with H. seropedicae resulted in 19.43 % (regarding High and Low N controls) and 10.51% (regarding Low N control) in mean of increase of root biomass, for 1st and 2nd greenhouse experiments, respectively, mainly in the initial stages of plant development, at 21 days after emergence (DAE). Quantification of H. seropedicae in roots and leaves was performed by quantitative PCR. H. seropedicae was detected only in maize inoculated roots by qPCR, and a slight decrease in DNA copy number g-1 of fresh root weight was observed from 7 to 21 DAE, suggesting that there was initial effective colonization on maize plants. H. seropedicae strain SmR1 efficiently increased maize root biomass exhibiting its potential to be used as inoculant in agricultures systems.
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Affiliation(s)
- Elisandra Triches da Cunha
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil
| | - Ana Marina Pedrolo
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil
| | - Jessica Cavalheiro Ferreira Bueno
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil
| | - Tomás Pelizzaro Pereira
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil
- Public Policy Coordination Department, EPAGRI, Santa Catarina Agricultural Research and Rural Extension Company, Rio do Sul, SC, Brazil
| | - Cláudio Roberto Fônseca Sousa Soares
- Microbiology, Immunology and Parasitology Department, MIP CCB UFSC, Federal University of Santa Catarina, Av Prof Henrique da Silva Fontes, 2754, Florianópolis, SC, 88040-900, Brazil
| | - Ana Carolina Maisonnave Arisi
- Food Science and Technology Department, CAL CCA UFSC, Federal University of Santa Catarina, Rod Admar Gonzaga, 1346, Florianópolis, SC, 88034-001, Brazil.
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Deepti P, Pasha A, Kumbhakar DV, Doneti R, Heena SK, Bhanoth S, Poleboyina PK, Yadala R, S D A, Pawar SC. Overexpression of Secreted Phosphoprotein 1 (SPP1) predicts poor survival in HPV positive cervical cancer. Gene X 2022; 824:146381. [PMID: 35271951 DOI: 10.1016/j.gene.2022.146381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/24/2022] [Accepted: 02/24/2022] [Indexed: 12/24/2022] Open
Abstract
Cervical cancer (CC) is the most prevalent malignant gynecological tumor with limited treatments. The present study describes the role of SPP1 in cancer progression, SPP1 emerged as one of the most overexpressed genes identified through clariom D transcriptome microarray. This investigation aims towards identifying a potential gene with significant prognostic value for detection and early diagnosis of cervical cancer. The elevated expression of SPP1 in cervical squamous cell carcinoma tissue was validated across GEO (Gene Expression Omnibus) microarray data sets, TCGA (The Cancer Genome Atlas), and Oncomine databases. SPP1 expression was found to be prognostically significant, showing association with poor survival rate of the patients. Our study intended to assess the expression of secreted phosphoprotein (SPP1) gene at mRNA and protein levels, and to explore the association of single nucleotide polymorphisms of SPP1 with risk of CC. Further, receiver operating characteristics (ROC) curve was plotted to determine the levels of SPP1 to differentiate CC against control. Results revealed significant (p < 0.01) stage-wise upregulation of SPP1 in CC compared to the normal cervical tissue and this was further confirmed using Immunohistochemistry and real-time PCR. The ROC for SPP1 demonstrated good selective power to differentiate malignant CC and non-malignant cervical tissues. The SPP1 gene -443 T > C promoter polymorphisms are found to be significantly predominant in the disease group and Insilico analysis by the TRANSFAC software confirms its association with loss of STAT6 transcription factor binding site leading to overexpression of the SPP1.
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Affiliation(s)
- Pasumarthi Deepti
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad 500007, Telangana, India
| | - Akbar Pasha
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad 500007, Telangana, India
| | - Divya Vishambhar Kumbhakar
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad 500007, Telangana, India
| | - Ravinder Doneti
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad 500007, Telangana, India
| | - S K Heena
- Department of Pathology, Osmania Medical College, Hyderabad, 500095 Telangana, India
| | - Shivaji Bhanoth
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad 500007, Telangana, India
| | - Pavan Kumar Poleboyina
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad 500007, Telangana, India
| | - Rajesh Yadala
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad 500007, Telangana, India
| | - Annapurna S D
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad 500007, Telangana, India
| | - Smita C Pawar
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad 500007, Telangana, India.
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Knudsen SW, Hesselsøe M, Thaulow J, Agersnap S, Hansen BK, Jacobsen MW, Bekkevold D, Jensen SKS, Møller PR, Andersen JH. Monitoring of environmental DNA from nonindigenous species of algae, dinoflagellates and animals in the North East Atlantic. Sci Total Environ 2022; 821:153093. [PMID: 35038516 DOI: 10.1016/j.scitotenv.2022.153093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/04/2021] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
Monitoring the distribution of marine nonindigenous species is a challenging task. To support this monitoring, we developed and validated the specificity of 12 primer-probe assays for detection of environmental DNA (eDNA) from marine species, all nonindigenous to Europe. The species include sturgeons, a Pacific red algae, oyster thief, a freshwater hydroid from the Black Sea, Chinese mitten crab, Pacific oyster, warty comb jelly, sand gaper, round goby, pink salmon, rainbow trout and North American mud crab. We tested all assays in the laboratory, on DNA extracted from both the target and non-target species to ensure that they only amplified DNA from the intended species. Subsequently, all assays were used to analyse water samples collected at 16 different harbours across two different seasons during 2017. We also included six previously published assays targeting eDNA from goldfish, European carp, two species of dinoflagellates of the genera Karenia and Prorocentrum, two species of the heterokont flagellate genus Pseudochattonella. Conventional monitoring was carried out alongside eDNA sampling but with only one sampling event over the one year. Because eDNA was relatively fast and easy to collect compared to conventional sampling, we sampled eDNA twice during 2017, which showed seasonal changes in the distribution of nonindigenous species. Comparing eDNA levels with salinity gradients did not show any correlation. A significant correlation was observed between number of species detected with conventional monitoring methods and number of species found using eDNA at each location. This supports the use of eDNA for surveillance of the distribution of marine nonindigenous species, where the speed and relative easy sampling in the field combined with fast molecular analysis may provide advantages compared to conventional monitoring methods. Prior validation of assays increases taxonomic precision, and laboratorial setup facilitates analysis of multiple samples simultaneously. The specific eDNA assays presented here can be implemented directly in monitoring programmes across Europe and potentially worldwide to infer a more precise picture of the dynamics in the distribution of marine nonindigenous species.
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Affiliation(s)
- Steen Wilhelm Knudsen
- NIVA Denmark Water Research, Njalsgade 76, DK-2300 Copenhagen, Denmark; Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
| | | | - Jens Thaulow
- NIVA Denmark Water Research, Njalsgade 76, DK-2300 Copenhagen, Denmark
| | - Sune Agersnap
- Department of Bioscience, Aarhus University, Ny Munkegade 116, Building 1540, DK-8000 Aarhus, Denmark
| | - Brian Klitgaard Hansen
- Danish Technical University of Denmark, Section for Marine Living Resources, Vejlsøvej 39, DK-8600 Silkeborg, Denmark
| | - Magnus Wulff Jacobsen
- Danish Technical University of Denmark, Section for Marine Living Resources, Vejlsøvej 39, DK-8600 Silkeborg, Denmark
| | - Dorte Bekkevold
- Danish Technical University of Denmark, Section for Marine Living Resources, Vejlsøvej 39, DK-8600 Silkeborg, Denmark
| | | | - Peter Rask Møller
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark; Norwegian College of Fishery Science, UiT Norwegian Arctic University, Tromsø, Norway
| | - Jesper H Andersen
- NIVA Denmark Water Research, Njalsgade 76, DK-2300 Copenhagen, Denmark
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Gruneck L, Gentekaki E, Kespechara K, Denny J, Sharpton TJ, Marriott LK, Shannon J, Popluechai S. The fecal microbiota of Thai school-aged children associated with demographic factors and diet. PeerJ 2022; 10:e13325. [PMID: 35469202 PMCID: PMC9034706 DOI: 10.7717/peerj.13325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 04/01/2022] [Indexed: 01/13/2023] Open
Abstract
Background Birth delivery method and breastfeeding practices contribute to microbiota colonization. Other factors including diet and demographic factors structure the gut microbiome assembly and diversity through childhood development. The exploration of these factors, especially in Southeast Asian children, remains limited. Methods We investigated the fecal microbiota of 127 school-aged children in Thailand using quantitative PCR (qPCR) to assess the influence of diet and demographic factors on the gut microbiota. Multivariate analysis (multiple factor analysis (MFA) and Partial Least Squares Discriminant Analysis (PLS-DA)) were used to link particular gut microbes to diet and demographic factors. Results Diet and demographic factors were associated with variation among gut microbiota. The abundance of Gammaproteobacteria increased in children with infrequent intake of high fat foods. Obese children possessed a lower level of Firmicutes and Ruminococcus. Bifidobacterium was enriched in pre-teen aged children and detected at lower levels among formula-fed children. Prevotella was more abundant in children who were delivered vaginally. While ethnicity explained a small amount of variation in the gut microbiota, it nonetheless was found to be significantly associated with microbiome composition. Conclusions Exogenous and demographic factors associate with, and possibly drive, the assembly of the gut microbiome of an understudied population of school-aged children in Thailand.
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Affiliation(s)
- Lucsame Gruneck
- Gut Microbiome Research Group, Mae Fah Luang University, Muang, Chiang Rai, Thailand
| | - Eleni Gentekaki
- Gut Microbiome Research Group, Mae Fah Luang University, Muang, Chiang Rai, Thailand,School of Science, Mae Fah Luang University, Muang, Chiang Rai, Thailand
| | | | - Justin Denny
- OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, OR, United States of America
| | - Thomas J. Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, United States of America,Department of Statistics, Oregon State University, Corvallis, OR, United States of America
| | - Lisa K. Marriott
- OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, OR, United States of America
| | - Jackilen Shannon
- OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, OR, United States of America
| | - Siam Popluechai
- Gut Microbiome Research Group, Mae Fah Luang University, Muang, Chiang Rai, Thailand,School of Science, Mae Fah Luang University, Muang, Chiang Rai, Thailand
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Geraci-Yee S, Allam B, Collier JL. Keeping up with advances in qPCR pathogen detection: an example for QPX disease in hard clams. Dis Aquat Organ 2022; 148:127-144. [PMID: 35356896 DOI: 10.3354/dao03648] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
With marine diseases on the rise and increased reliance on molecular tools for disease surveillance, validated pathogen detection capabilities are important for effective management, mitigation, and response to disease outbreaks. At the same time, in an era of continual evolution and advancement of molecular tools for pathogen detection, it is critical to regularly reassess previously established assays to incorporate improvements of common practices and procedures, such as the minimum information for publication of quantitative real-time PCR experiments (MIQE) guidelines. Here, we reassessed, re-optimized, and improved the quantitative PCR (qPCR) assay routinely used for Quahog Parasite Unknown (QPX) disease monitoring. We made 19 significant changes to the qPCR assay, including improvements to PCR amplification efficiency, DNA extraction efficiency, inhibition testing, incorporation of linearized standards for absolute quantification, an inter-plate calibration technique, and improved conversion from copy number to number of cells. These changes made the assay a more effective and efficient tool for disease monitoring and pathogen detection, with an improved linear relationship with histopathology compared to the previous version of the assay. To support the wide adoption of validated qPCR assays for marine pathogens, we provide a simple workflow that can be applied to the development of new assays, re-optimization of old or suboptimal assays, or assay validation after changes to the protocol and a MIQE-compliant checklist that should accompany any published qPCR diagnostic assay to increase experimental transparency and reproducibility amongst laboratories.
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Affiliation(s)
- Sabrina Geraci-Yee
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, USA
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Zhang X, Tian Y, Xu L, Fan Z, Cao Y, Ma Y, Li H, Ren F. CRISPR/Cas13-assisted hepatitis B virus covalently closed circular DNA detection. Hepatol Int 2022; 16:306-315. [PMID: 35298777 PMCID: PMC9013339 DOI: 10.1007/s12072-022-10311-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/06/2022] [Indexed: 11/10/2022]
Abstract
Background and aims The formation of an intranuclear pool of covalently closed circular DNA (cccDNA) in the liver is the main cause of persistent hepatitis B virus (HBV) infection. Here, we established highly sensitive and specific methods to detect cccDNA based on CRISPR-Cas13a technology. Methods We used plasmid-safe ATP-dependent DNase (PSAD) enzymes and HindIII to digest loose circle rcDNA and double-stranded linear DNA, amplify specific HBV cccDNA fragments by rolling circle amplification (RCA) and PCR, and detect the target gene using CRISPR-Cas13a technology. The CRISPR-Cas13a-based assay for the detection of cccDNA was further clinically validated using HBV-related liver tissues, plasma, whole blood and peripheral blood mononuclear cells (PBMCs). Results Based on the sample pretreatment step, the amplification step and the detection step, we established a new CRISPR-Cas13a-based assay for the detection of cccDNA. After the amplification of RCA and PCR, 1 copy/μl HBV cccDNA could be detected by CRISPR/Cas13-assisted fluorescence readout. We used ddPCR, qPCR, RCA-qPCR, PCR-CRISPR and RCA-PCR-CRISPR methods to detect 20, 4, 18, 14 and 29 positive samples in liver tissue samples from 40 HBV-related patients, respectively. HBV cccDNA was almost completely undetected in the 20 blood samples of HBV patients (including plasma, whole blood and PBMCs) by the above 5 methods. Conclusions We developed a novel CRISPR-based assay for the highly sensitive and specific detection of HBV cccDNA, presenting a promising alternative for accurate detection of HBV infection, antiviral therapy evaluation and treatment guidance. Supplementary Information The online version contains supplementary material available at 10.1007/s12072-022-10311-0.
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Affiliation(s)
- Xiangying Zhang
- Beijing Youan Hospital, Capital Medical University, No. 8, XitouTiao Road, Youwai Street, Fengtai District, Beijing, 100069, China
| | - Yuan Tian
- Beijing Youan Hospital, Capital Medical University, No. 8, XitouTiao Road, Youwai Street, Fengtai District, Beijing, 100069, China
| | - Ling Xu
- Beijing Youan Hospital, Capital Medical University, No. 8, XitouTiao Road, Youwai Street, Fengtai District, Beijing, 100069, China
| | - Zihao Fan
- Beijing Youan Hospital, Capital Medical University, No. 8, XitouTiao Road, Youwai Street, Fengtai District, Beijing, 100069, China
| | - Yaling Cao
- Beijing Youan Hospital, Capital Medical University, No. 8, XitouTiao Road, Youwai Street, Fengtai District, Beijing, 100069, China
| | - Yingmin Ma
- Beijing Youan Hospital, Capital Medical University, No. 8, XitouTiao Road, Youwai Street, Fengtai District, Beijing, 100069, China.
| | - Hao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Feng Ren
- Beijing Youan Hospital, Capital Medical University, No. 8, XitouTiao Road, Youwai Street, Fengtai District, Beijing, 100069, China.
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Smith AJ, Adams MB, Crosbie PBB, Nowak BF, Bridle AR. Size-dependent resistance to amoebic gill disease in naïve Atlantic salmon (Salmo salar). Fish Shellfish Immunol 2022; 122:437-445. [PMID: 35189323 DOI: 10.1016/j.fsi.2022.02.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Amoebic gill disease, caused by the protozoan ectoparasite Neoparamoeba perurans, remains a significant threat to commercial Atlantic salmon aquaculture operations worldwide, despite partial control afforded by selective breeding and therapeutic intervention. Anecdotal reports from commercial producers suggest that historically, smaller Atlantic salmon smolts are more susceptible to AGD than larger smolts. Here, large (>350 g) and small (<200 g) commercially sourced, AGD-naïve Atlantic salmon cohorts were experimentally exposed to 50 N. perurans trophozoites L-1 without intervention. Progression and severity of AGD in challenged cohorts was evaluated through gill pathology, using gill score and histological examination, and quantification of gill-associated amoebae burden using qPCR. To determine the potential basis for differences in AGD susceptibility between cohorts, transcriptome analysis was conducted using RNA extracted from whole gill arches. Overall, the large Atlantic salmon cohort had significantly lower gill parasite burdens and reduced AGD-related gross pathology compared to the small cohort. Relative gill load of N. perurans appeared to be proportional to gill score in both size classes, with larger smolts typically observed to have comparatively reduced parasite burdens at a given gill score. Moreover, comparison between gene expression profiles of large and small smolts highlighted upregulation of genes consistent with elevated immune activity in large smolts. Combined, the results presented here provide strong evidence of size-dependent resistance to AGD in AGD-naïve Atlantic salmon.
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Affiliation(s)
- Aaron J Smith
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, Tasmania, Australia.
| | - Mark B Adams
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, Tasmania, Australia
| | - Philip B B Crosbie
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, Tasmania, Australia
| | - Barbara F Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, Tasmania, Australia
| | - Andrew R Bridle
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, Tasmania, Australia
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Mancusi A, Giordano A, Bosco A, Girardi S, Proroga YTR, Morena L, Pinto R, Sarnelli P, Cringoli G, Rinaldi L, Capuano F, Maurelli MP. Development of a droplet digital polymerase chain reaction tool for the detection of Toxoplasma gondii in meat samples. Parasitol Res 2022; 121:1467-1473. [PMID: 35230549 PMCID: PMC8993784 DOI: 10.1007/s00436-022-07477-9] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/22/2022] [Indexed: 12/14/2022]
Abstract
Toxoplasmosis is a zoonotic disease caused by the protozoan parasite Toxoplasma gondii. Infection in humans has usually been related to the consumption of raw, undercooked or cured meat. The aim of this study was to develop a droplet digital polymerase chain reaction (ddPCR)-based assay for the detection and quantification of T. gondii in meat samples. To optimize the ddPCR, T.gondii reference DNA aliquots at five known concentrations: 8000 cg/µl, 800 cg/µl, 80 cg/µl, 8 cg/µl were used. Moreover, results obtained by ddPCR and quantitative PCR (qPCR) were compared using 80 known samples (40 positive and 40 negative), as well as 171 unknown diaphragm tissue samples collected at slaughterhouses. The ddPCR showed a sensitivity of 97.5% and a specificity of 100%, with a detection limit of 8 genomic copy/µl of T. gondii. A nearly perfect agreement (κ = 0.85) was found between results obtained by ddPCR and qPCR for both positive and negative known samples analysed. On the 171 diaphragm tissue samples from field, 7.6% resulted positive by ddPCR and only 1.2% by qPCR. Therefore, this innovative method could be very useful for the detection of T. gondii in meat samples, aiming to prevent human infections.
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Affiliation(s)
- Andrea Mancusi
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA), Italy
| | - Angela Giordano
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA), Italy
| | - Antonio Bosco
- Unit of Parasitology and Parasitic Diseases, Department of Veterinary Medicine and Animal Production, University of Naples Federico II, CREMOPAR, Naples, Italy
| | - Santa Girardi
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA), Italy
| | | | - Luigi Morena
- Centro Di Riferimento Regionale Sanità Animale (CReSan), Salerno, Italy
| | - Renato Pinto
- UOD Prevenzione E Sanità Pubblica Veterinaria Regione Campania, Naples, Italy
| | - Paolo Sarnelli
- UOD Prevenzione E Sanità Pubblica Veterinaria Regione Campania, Naples, Italy
| | - Giuseppe Cringoli
- Unit of Parasitology and Parasitic Diseases, Department of Veterinary Medicine and Animal Production, University of Naples Federico II, CREMOPAR, Naples, Italy
- Centro Di Riferimento Regionale Sanità Animale (CReSan), Salerno, Italy
| | - Laura Rinaldi
- Unit of Parasitology and Parasitic Diseases, Department of Veterinary Medicine and Animal Production, University of Naples Federico II, CREMOPAR, Naples, Italy
- Centro Di Riferimento Regionale Sanità Animale (CReSan), Salerno, Italy
| | - Federico Capuano
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA), Italy
| | - Maria Paola Maurelli
- Unit of Parasitology and Parasitic Diseases, Department of Veterinary Medicine and Animal Production, University of Naples Federico II, CREMOPAR, Naples, Italy.
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Garcia A, Le T, Jankowski P, Yanaç K, Yuan Q, Uyaguari-Diaz MI. Quantification of human enteric viruses as alternative indicators of fecal pollution to evaluate wastewater treatment processes. PeerJ 2022; 10:e12957. [PMID: 35186509 PMCID: PMC8852272 DOI: 10.7717/peerj.12957] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/27/2022] [Indexed: 01/11/2023] Open
Abstract
We investigated the potential use and quantification of human enteric viruses in municipal wastewater samples of Winnipeg (Manitoba, Canada) as alternative indicators of contamination and evaluated the processing stages of the wastewater treatment plant. During the fall 2019 and winter 2020 seasons, samples of raw sewage, activated sludge, effluents, and biosolids (sludge cake) were collected from the North End Sewage Treatment Plant (NESTP), which is the largest wastewater treatment plant in the City of Winnipeg. DNA (Adenovirus and crAssphage) and RNA enteric viruses (Pepper mild mottle virus, Norovirus genogroups GI and GII, Rotavirus Astrovirus, and Sapovirus) as well as the uidA gene found in Escherichia coli were targeted in the samples collected from the NESTP. Total nucleic acids from each wastewater treatment sample were extracted using a commercial spin-column kit. Enteric viruses were quantified in the extracted samples via quantitative PCR using TaqMan assays. Overall, the average gene copies assessed in the raw sewage were not significantly different (p-values ranged between 0.1023 and 0.9921) than the average gene copies assessed in the effluents for DNA and RNA viruses and uidA in terms of both volume and biomass. A significant reduction (p-value ≤ 0.0438) of Adenovirus and Noroviruses genogroups GI and GII was observed in activated sludge samples compared with those for raw sewage per volume. Higher GCNs of enteric viruses were observed in dewatered sludge samples compared to liquid samples in terms of volume (g of sample) and biomass (ng of nucleic acids). Enteric viruses found in gene copy numbers were at least one order of magnitude higher than the E. coli marker uidA, indicating that enteric viruses may survive the wastewater treatment process and viral-like particles are being released into the aquatic environment. Viruses such as Noroviruses genogroups GI and GII, and Rotavirus were detected during colder months. Our results suggest that Adenovirus, crAssphage, and Pepper mild mottle virus can be used confidently as complementary viral indicators of human fecal pollution.
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Affiliation(s)
- Audrey Garcia
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Tri Le
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Paul Jankowski
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kadir Yanaç
- Department of Civil Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Qiuyan Yuan
- Department of Civil Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
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Ade J, Stadler J, Ritzmann M, Zübert C, Hoelzle K, Hoelzle LE. Occurrence of 'Candidatus Mycoplasma haemosuis' in fattening pigs, sows and piglets in Germany using a novel gap-based quantitative real-time PCR assay. BMC Vet Res 2022; 18:40. [PMID: 35039068 PMCID: PMC8762947 DOI: 10.1186/s12917-022-03147-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background The appearance of the novel porcine haemotrophic mycoplasma (HM) species ‘Candidatus Mycoplasma haemosuis’ was reported in apparently healthy but also in clinically sick animals in China, Korea and in a case report from Germany. Outside of Asia, however, nothing further is known about the frequency of ‘Ca. M. haemosuis’ in pigs to date. To investigate the distribution of this novel HM species in Germany, fattening pigs, sows and pre-suckling piglets were examined using a herein developed quantitative real-time PCR assay (qPCR). Because the piglets were sampled before the first colostrum uptake, additional information on a possible vertical transmission from dams to their offspring was obtained. Results Our novel qPCR assay successfully detected ‘Ca. M. haemosuis’ in all blood samples from the ‘Ca. M. haemosuis’-infected pigs. No cross-reactivity was detected when DNA from non-target Mycoplasma spp. and other bacterial species representing 105 bacteria/reaction were used as a template. The lower limit of detection of the qPCR was thus 10 gap gene copies per reaction and 2.5 x 103 genome equivalents (GE) per mL blood. ‘Candidatus M. haemosuis’ was detected by this qPCR in blood samples from a total out of 6.25% sows (13/208), 4.50% pre-suckling piglets (28/622) and 17.50% fattening pigs (35/200). On farm level, 3 out of 21 piglet producing farms (14.28%) and 9 out of 20 fattening farms (45.00%) were positive for ‘Ca. M. haemosuis’. Co-infections with M. suis were evident in all age groups. Conclusion ‘Candidatus M. haemosuis’ infection is present in German pig farms and the detection of the novel porcine HM species in piglets immediately after birth before colostrum intake indicates vertical transmission. The novel qPCR assay specific for ‘Ca. M. haemosuis’ described herein will be a prerequisite for future studies on the prevalence, epidemiology as well as the clinical and economic impact of ‘Ca. M. haemosuis’ infections. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03147-1.
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Affiliation(s)
- Julia Ade
- Institute of Animal Science, Department of Livestock Infectiology and Environmental Hygiene, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Julia Stadler
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität Munich, Sonnenstrasse 16, 85764, Oberschleissheim, Germany
| | - Mathias Ritzmann
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität Munich, Sonnenstrasse 16, 85764, Oberschleissheim, Germany
| | - Christina Zübert
- Institute of Animal Science, Department of Livestock Infectiology and Environmental Hygiene, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Katharina Hoelzle
- Institute of Animal Science, Department of Livestock Infectiology and Environmental Hygiene, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Ludwig E Hoelzle
- Institute of Animal Science, Department of Livestock Infectiology and Environmental Hygiene, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany.
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Veryaskina YA, Titov SE, Zhimulev IF. Reference Genes for qPCR-Based miRNA Expression Profiling in 14 Human Tissues. Med Princ Pract 2022; 31:322-332. [PMID: 35354155 PMCID: PMC9485981 DOI: 10.1159/000524283] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/22/2022] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are promising biomarkers for the diagnosis and prognosis of various diseases. Quantitative PCR is the most frequently used method of measuring expression levels of miRNA. However, the lack of validated reference genes represents the main source of potential bias in results. It is normal practice to use small nuclear RNAs as reference genes; however, they often have variable expression. Researchers tend to prefer the most stable reference genes in each experiment. The review includes reference genes for the following tissue types: gliomas, lung cancer, melanoma, gastric cancer, liver cancer, prostate cancer, breast cancer, thyroid cancer, ovarian cancer, cervical cancer, endometrial cancer, rectal cancer, blood tumors, and placental tissues.
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Affiliation(s)
- Yulia Andreevna Veryaskina
- Laboratory of Gene Engineering, Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russian Federation
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russian Federation
- *Yulia Andreevna Veryaskina,
| | - Sergei Evgenievich Titov
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russian Federation
- AO Vector-Best, Novosibirsk, Russian Federation
| | - Igor Fyodorovich Zhimulev
- Department of the Structure and Function of Chromosomes, Laboratory of Molecular Genetics Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russian Federation
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Erdiansyah M, Meryandini A, Wijaya M, Suwanto A. Microbiological quality of tempeh with different wraps: banana leaf versus plastic. J Food Sci Technol 2022; 59:300-7. [PMID: 35068574 DOI: 10.1007/s13197-021-05014-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 12/30/2020] [Accepted: 01/29/2021] [Indexed: 01/03/2023]
Abstract
Tempeh is a traditional Indonesian fermented food widely consumed and became staple food in some Indonesian diet. Commercially, tempeh is available in banana leaf or plastic wraps. The wraps are not only important for fermentation and giving final form of tempeh, but also potential source of food microbiome. This study aimed to investigate the effect of different packaging materials on the lactic acid bacteria (LAB) quantity and community composition of tempeh from three manufacturers with different production environments. Each tempeh wrapped with banana leaf or plastic during the fermentation process and then LAB from every tempeh sample were quantified using qPCR and plate count method. Terminal Restriction Fragment Length Polymorphism analysis was carried out to assign bacterial community composition from these samples. The LAB population quantity of fresh tempeh from three manufacturers were essentially similar around 10 log CFU/g. However, there is a difference in the proportion of cultured and uncultured bacteria. Principal Coordinate Analyses based on Bray-Curtis similarity matrices showed an apparent clustering pattern for tempeh samples according to tempeh manufacturers. Meanwhile, packaging materials did not significantly influence changes in bacterial community composition. The result of this work could be used for determination, authentication, and improvement of tempeh quality.
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