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Zhu X. A linear validation method of analytical procedures based on the double logarithm function linear fitting. Anal Chim Acta 2024; 1310:342695. [PMID: 38811139 DOI: 10.1016/j.aca.2024.342695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 03/23/2024] [Accepted: 05/06/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND The ICH Q2(R1) guideline defines linearity as its ability to obtain test results which are directly proportional to the concentration of the analyte. However, the coefficient of determination typically used is limited to evaluating the response function rather than the linearity of results, the current guidelines fail to provide a method for assessing the linearity of results. RESULTS The paper presents a data analysis method to validate the linearity of results. The method demonstrates the degree of data proportionality by applying double logarithm function linear fitting and solves the problem of setting the acceptance criterion by investigating the relationship between the slope, working range ratio, and maximum error ratio. In principle, this method has advantages over the coefficient of variation and recovery rate recommended by the ICH M10 guideline. Moreover, the relative error data show that the double logarithm function is more effective in overcoming heteroscedasticity than straight-line fitting. SIGNIFICANCE This method is more consistent with the linear definition outlined in ICH Q2 guidelines and has the potential to further clarify the concept and validation method of linearity in the future.
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Li W, Wang Y, Li X, Wu H, Jia L. Dexmedetomidine hydrochloride plus sufentanil citrate inhibits glucose metabolism and epithelial‑mesenchymal transition in human esophageal squamous carcinoma KYSE30 cells by modulating the JAK/STAT3/HIF‑1α axis. Oncol Lett 2024; 27:273. [PMID: 38686357 PMCID: PMC11056934 DOI: 10.3892/ol.2024.14406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/10/2023] [Indexed: 05/02/2024] Open
Abstract
Dexmedetomidine hydrochloride (DEX-HCl) and sufentanil citrate (SFC) are commonly used anesthetic drugs for esophageal cancer (EC) surgery. The present study was performed to investigate the effect of DEX-HCl and SFC treatment on glucose metabolism and epithelial-mesenchymal transition in EC. Cell counting kit-8 (CCK8), clonogenic, wound healing and Transwell migration assays were performed to assess the effects of the DEX-HCl and SFC on KYSE30 cell proliferation, invasion and migration. Changes in lactate and glucose levels in KYSE30 cells were also detected. Western blot analysis was used to determine the protein expression levels of the JAK/STAT signaling pathway and glucose metabolism-related proteins. The results of CCK8, clonogenic and wound healing assays demonstrated that DEX-HCl and SFC inhibited KYSE30 cell proliferation, invasion and migration. Similarly, the combined DEX-HCl and SFC treatment significantly reduced lactate production, ATP production and glucose levels in KYSE30 cells. Western blotting indicated that DEX-HCl and SFC could reduce JAK/STAT and metastasis-related protein expression. Demonstrating a reduction in Hexokinase 2, matrix metallopeptidase 2 and 9, N-cadherin and lactate dehydrogenase A protein expression levels. The effects of DEX-HCl and SFC combined treatment were counteracted by the addition of JAK/STAT pathway activator RO8191, which suggested that DEX-HCl and SFC could serve a role in mediating the JAK/STAT signaling pathway in KYSE30 cells.
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Affiliation(s)
- Weijing Li
- Department of Anesthesiology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Yong Wang
- Department of Anesthesiology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Xiaolin Li
- Department of Anesthesiology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China
| | - Han Wu
- Department of Anesthesiology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Li Jia
- Department of Anesthesiology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
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Jones KL, Cunha F, Casaro S, Galvão KN. Optimization and Testing of a Commercial Viability PCR Protocol to Detect Escherichia coli in Whole Blood. Microorganisms 2024; 12:765. [PMID: 38674709 PMCID: PMC11052410 DOI: 10.3390/microorganisms12040765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Bacteremia, specifically if progressed to sepsis, poses a time-sensitive threat to human and animal health. Escherichia coli is a main causative agent of sepsis in humans. The objective was to evaluate a propidium monoazide (PMA)-based viability PCR (vPCR) protocol to detect and quantify live E. coli from whole blood. We optimized the protocol by adding a eukaryotic-specific lysis step prior to PMA exposure, then used spiking experiments to determine the lower limit of detection (LOD) and linear range of quantification. We also compared the vPCR quantification method to standard colony count of spiked inoculum. Lastly, we calculated percent viability in spiked samples containing 50% live cells or 0% live cells. The LOD was 102 CFU/mL for samples containing live cells only and samples with mixed live and heat-killed cells. The linear range of quantification was 102 CFU/mL to 108 CFU/mL (R2 of 0.997) in samples containing only live cells and 103 CFU/mL to 108 CFU/mL (R2 of 0.998) in samples containing live plus heat-killed cells. A Bland-Altman analysis showed that vPCR quantification overestimates compared to standard plate count of the spiked inoculum, with an average bias of 1.85 Log10 CFU/mL across the linear range when only live cells were present in the sample and 1.98 Log10 CFU/mL when live plus heat-killed cells were present. Lastly, percent viability calculations showed an average 89.5% viable cells for samples containing 50% live cells and an average 19.3% for samples containing 0% live cells. In summary, this optimized protocol can detect and quantify viable E. coli in blood in the presence of heat-killed cells. Additionally, the data presented here provide the groundwork for further development of vPCR to detect and quantify live bacteria in blood in clinical settings.
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Affiliation(s)
| | | | | | - Klibs N. Galvão
- Department of Large Animal Clinical Sciences, University of Florida College of Veterinary Medicine, Gainesville, FL 32608, USA
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4
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Opmeer L, Gazzoli I, Ballmann M, Willemsen M, Voshol GP, Grudniewska-Lawton M, Havenga M, Yallop C, Hamidi A, Gillissen G, Bakker WAM. High throughput AS LNA qPCR method for the detection of a specific mutation in poliovirus vaccine strains. Vaccine 2024; 42:2475-2484. [PMID: 38503660 PMCID: PMC11007389 DOI: 10.1016/j.vaccine.2024.01.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/21/2023] [Accepted: 01/30/2024] [Indexed: 03/21/2024]
Abstract
Sabin Inactivated Poliovirus Vaccine (sIPV) has become one of the preferred vaccination options for the last step in the Poliovirus eradication program. Sequencing of poliovirus samples is needed during the manufacturing of poliovirus vaccines to assure the safety and immunogenicity of these vaccines. Next-generation sequencing analysis is the current costly and time-consuming gold standard for monitoring the manufacturing processes. We developed a low-cost and quick, highly sensitive, and allele-specific locked nucleic acid-probe-based reverse transcription quantitative PCR alternative that can accurately detect mutations in poliovirus vaccine samples during process development, scaling up, and release. Using the frequently in vitro occurring and viral replication-impacting VP1-E295K mutation as a showcase, we show that this technology can accurately detect E295K mutations in poliovirus 2 samples to similar levels as NGS. The qPCR technology was developed employing a synthetic dsDNA fragment-based standard curve containing mixes of E295K-WT (wildtype) and Mut (mutant) synthetic dsDNA fragments ranging from 1 × 107 copies/µL to 1 × 102 copies/µL to achieve a linear correlation with R2 > 0.999, and PCR efficiencies of 95-105 %. Individual standard concentration levels achieved accuracies of ≥92 % (average 96 %) and precisions of ≤17 % (average 3.3 %) RSD. Specificity of locked nucleic acid (LNA)-probes was confirmed in the presence and absence of co-mutations in the probe-binding region. Application of the developed assay to Sabin Poliovirus type 2 production run samples, illustrated a linear relationship with an R2 of 0.994, and an average accuracy of 97.2 % of the variant (allele)-specific AS LNA qPCR result, compared to NGS. The assay showed good sensitivity for poliovirus samples, containing E295K mutation levels between 0 % and 95 % (quantification range). In conclusion, the developed AS LNA qPCR presents a valuable low-cost, and fast tool, suitable for the process development and quality control of polio vaccines.
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Affiliation(s)
- Lizet Opmeer
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Isabella Gazzoli
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Mónika Ballmann
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Marieke Willemsen
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Gerben P Voshol
- GenomeScan B.V., Plesmanlaan 1d, 2333 BZ Leiden, The Netherlands
| | | | - Menzo Havenga
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Christopher Yallop
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Ahd Hamidi
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Gert Gillissen
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Wilfried A M Bakker
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands.
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5
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Zang P, Xu Q, Li C, Tao M, Zhang Z, Li J, Zhang W, Li S, Li C, Yang Q, Guo Z, Yao J, Zhou L. Self-correction of cycle threshold values by a normal distribution-based process to improve accuracy of quantification in real-time digital PCR. Anal Bioanal Chem 2024:10.1007/s00216-024-05208-w. [PMID: 38400940 DOI: 10.1007/s00216-024-05208-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/29/2024] [Accepted: 02/12/2024] [Indexed: 02/26/2024]
Abstract
The digital polymerase chain reaction (dPCR) is a new and developing nucleic acid detection technology with high sensitivity that can realize the absolute quantitative analysis of samples. In order to improve the accuracy of quantitative results, real-time digital PCR emphasizes the kinetic information during amplification to identify prominent abnormal data. However, it is challenging to use a unified standard to accurately classify the amplification curve of each well as negative and positive, due to the interference caused by various factors in the experiment. In this work, a normal distribution-based cycle threshold value self-correcting model (NCSM) was established, which focused on the feature of the cycle threshold values in amplification curves and conducted continuous detection and correction on the whole. The cycle threshold value distribution was closer to the ideal normal distribution to avoid the influence of interference. Thus, the model achieves a more accurate classification between positive and negative results. The corrective process was applied to plasmid samples and resulted in an accuracy improvement from 92 to 99%. The coefficient of variation was below 5% when considering the quantitation of a range between 100 and 10,000 copies. At the same time, by utilizing this model, the distribution of cycle threshold values at the endpoint can be predicted with fewer thermal cycles, which can reduce the cycling time by around 25% while maintaining a consistency of more than 98%. Therefore, using the NCSM can effectively enhance the quantitative accuracy and increase the detection efficiency based on the real-time dPCR platform.
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Affiliation(s)
- Peilin Zang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Qi Xu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Chuanyu Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Mingli Tao
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Zhiqi Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
- Suzhou CASENS Co., Ltd, Suzhou, 215163, China
| | - Jinze Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Wei Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
- Suzhou CASENS Co., Ltd, Suzhou, 215163, China
| | - Shuli Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Chao Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Qi Yang
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Zhen Guo
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.
| | - Jia Yao
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.
| | - Lianqun Zhou
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.
- Suzhou CASENS Co., Ltd, Suzhou, 215163, China.
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6
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Hoen E, Goossens FM, Falize K, Mayerl S, van der Spek AH, Boelen A. The Differential Effect of a Shortage of Thyroid Hormone Compared with Knockout of Thyroid Hormone Transporters Mct8 and Mct10 on Murine Macrophage Polarization. Int J Mol Sci 2024; 25:2111. [PMID: 38396788 PMCID: PMC10889717 DOI: 10.3390/ijms25042111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Innate immune cells, including macrophages, are functionally affected by thyroid hormone (TH). Macrophages can undergo phenotypical alterations, shifting between proinflammatory (M1) and immunomodulatory (M2) profiles. Cellular TH concentrations are, among others, determined by TH transporters. To study the effect of TH and TH transporters on macrophage polarization, specific proinflammatory and immunomodulatory markers were analyzed in bone marrow-derived macrophages (BMDMs) depleted of triiodothyronine (T3) and BMDMs with a knockout (KO) of Mct8 and Mct10 and a double KO (dKO) of Mct10/Mct8. Our findings show that T3 is important for M1 polarization, while a lack of T3 stimulates M2 polarization. Mct8 KO BMDMs are unaffected in their T3 responsiveness, but exhibit slight alterations in M2 polarization, while Mct10 KO BMDMs show reduced T3 responsiveness, but unaltered polarization markers. KO of both the Mct8 and Mct10 transporters decreased T3 availability and, contrary to the T3-depleted BMDMs, showed partially increased M1 markers and unaltered M2 markers. These data suggest a role for TH transporters besides transport of TH in BMDMs. This study highlights the complex role of TH transporters in macrophages and provides a new angle on the interaction between the endocrine and immune systems.
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Affiliation(s)
- Esmée Hoen
- Endocrine Laboratory, Department of Laboratory Medicine, Amsterdam Gastroenterology Endocrinology & Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (E.H.); (K.F.)
| | - Franka M. Goossens
- Endocrine Laboratory, Department of Laboratory Medicine, Amsterdam Gastroenterology Endocrinology & Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (E.H.); (K.F.)
| | - Kim Falize
- Endocrine Laboratory, Department of Laboratory Medicine, Amsterdam Gastroenterology Endocrinology & Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (E.H.); (K.F.)
| | - Steffen Mayerl
- Department of Endocrinology, Diabetes & Metabolism, University Duisburg-Essen, 47057 Essen, Germany
| | - Anne H. van der Spek
- Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology & Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Anita Boelen
- Endocrine Laboratory, Department of Laboratory Medicine, Amsterdam Gastroenterology Endocrinology & Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (E.H.); (K.F.)
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Sibanda T, Marole TA, Thomashoff UL, Thantsha MS, Buys EM. Bifidobacterium species viability in dairy-based probiotic foods: challenges and innovative approaches for accurate viability determination and monitoring of probiotic functionality. Front Microbiol 2024; 15:1327010. [PMID: 38371928 PMCID: PMC10869629 DOI: 10.3389/fmicb.2024.1327010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024] Open
Abstract
Bifidobacterium species are essential members of a healthy human gut microbiota. Their presence in the gut is associated with numerous health outcomes such as protection against gastrointestinal tract infections, inflammation, and metabolic diseases. Regular intake of Bifidobacterium in foods is a sustainable way of maintaining the health benefits associated with its use as a probiotic. Owing to their global acceptance, fermented dairy products (particularly yogurt) are considered the ideal probiotic carrier foods. As envisioned in the definition of probiotics as "live organisms," the therapeutic functionalities of Bifidobacterium spp. depend on maintaining their viability in the foods up to the point of consumption. However, sustaining Bifidobacterium spp. viability during the manufacture and shelf-life of fermented dairy products remains challenging. Hence, this paper discusses the significance of viability as a prerequisite for Bifidobacterium spp. probiotic functionality. The paper focuses on the stress factors that influence Bifidobacterium spp. viability during the manufacture and shelf life of yogurt as an archetypical fermented dairy product that is widely accepted as a delivery vehicle for probiotics. It further expounds the Bifidobacterium spp. physiological and genetic stress response mechanisms as well as the methods for viability retention in yogurt, such as microencapsulation, use of oxygen scavenging lactic acid bacterial strains, and stress-protective agents. The report also explores the topic of viability determination as a critical factor in probiotic quality assurance, wherein, the limitations of culture-based enumeration methods, the challenges of species and strain resolution in the presence of lactic acid bacterial starter and probiotic species are discussed. Finally, new developments and potential applications of next-generation viability determination methods such as flow cytometry, propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR), next-generation sequencing, and single-cell Raman spectroscopy (SCRS) methods are examined.
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Affiliation(s)
- Thulani Sibanda
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
- Department of Biology, National of University of Lesotho, Maseru, Lesotho
| | - Tlaleo Azael Marole
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Mapitsi S. Thantsha
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Elna M. Buys
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
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Gerber L, Resseguier J, Helle-Valle T, Farhat E, Nilsson GE, Lefevre S. Expression of prolyl hydroxylase domains, the upstream regulators of HIF, in the brain of the anoxia-tolerant crucian carp during anoxia-reoxygenation. Am J Physiol Regul Integr Comp Physiol 2024; 326:R184-R195. [PMID: 38145292 DOI: 10.1152/ajpregu.00211.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/10/2023] [Accepted: 12/11/2023] [Indexed: 12/26/2023]
Abstract
The hypoxia-inducible factor (HIF) is considered key in the transcriptional response to low oxygen. Yet, the role of HIF in the absence of oxygen (anoxia) and in preparation for reoxygenation remains unclear. Recent studies suggest that mounting a HIF response may be counterproductive for anoxia survival. We here studied one of the champions of anoxia survival, the crucian carp (Carassius carassius), and hypothesized that expression of prolyl hydroxylase domains (PHDs; the upstream regulators of HIF) are upregulated to circumvent an energy-costly activation of HIF in anoxia and to prepare for reoxygenation. We measured whole brain mRNA and protein levels of the three isoforms PHD1, PHD2, and PHD3, coded for by multiple paralogs of the genes egln2, egln1, and egln3, using quantitative PCR and Western blotting in the brain of crucian carps exposed to 5 days normoxia or anoxia, and 5 days anoxia followed by 3 or 24 h of reoxygenation. The mRNA levels of most egln paralogs were increased in anoxia and upon reoxygenation, with egln3 showing the largest increase in mRNA level (up to 17-fold) and highest relative mRNA abundance (up to 75% of expressed egln). The protein level of all PHDs was maintained in anoxia and increased upon reoxygenation. We then explored PHD distribution in different brain regions and found PHD immunoreactivity to be associated with axonal branches and showing region-specific changes during anoxia-reoxygenation. Our results support an overall upregulation of egln under prolonged anoxia and PHDs upon reoxygenation in crucian carp, likely aimed at suppressing HIF responses, although regional differences are apparent in such a complex organ as the brain.NEW & NOTEWORTHY We report a profound upregulation of most egln paralog mRNA levels in anoxia and upon reoxygenation, with egln3ii showing the largest, a 17-fold increase, and highest relative mRNA abundance. The relative abundance of prolyl hydroxylase domain (PHD) proteins was maintained during anoxia and increased at reoxygenation. PHD immunoreactivity was localized to axonal branches with region-specific changes during anoxia-reoxygenation. These dynamic and regional changes in crucian carp, champion of anoxia tolerance, are most likely adaptive and call for further mechanistic studies.
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Affiliation(s)
- Lucie Gerber
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Julien Resseguier
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Tellef Helle-Valle
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Elie Farhat
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Göran E Nilsson
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sjannie Lefevre
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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Gamal M, Ibrahim MA. Introducing the f 0% method: a reliable and accurate approach for qPCR analysis. BMC Bioinformatics 2024; 25:17. [PMID: 38212692 PMCID: PMC10782791 DOI: 10.1186/s12859-024-05630-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND qPCR is a widely used technique in scientific research as a basic tool in gene expression analysis. Classically, the quantitative endpoint of qPCR is the threshold cycle (CT) that ignores differences in amplification efficiency among many other drawbacks. While other methods have been developed to analyze qPCR results, none has statistically proven to perform better than the CT method. Therefore, we aimed to develop a new qPCR analysis method that overcomes the limitations of the CT method. Our f0% [eff naught percent] method depends on a modified flexible sigmoid function to fit the amplification curve with a linear part to subtract the background noise. Then, the initial fluorescence is estimated and reported as a percentage of the predicted maximum fluorescence (f0%). RESULTS The performance of the new f0% method was compared against the CT method along with another two outstanding methods-LinRegPCR and Cy0. The comparison regarded absolute and relative quantifications and used 20 dilution curves obtained from 7 different datasets that utilize different DNA-binding dyes. In the case of absolute quantification, f0% reduced CV%, variance, and absolute relative error by 1.66, 2.78, and 1.8 folds relative to CT; and by 1.65, 2.61, and 1.71 folds relative to LinRegPCR, respectively. While, regarding relative quantification, f0% reduced CV% by 1.76, 1.55, and 1.25 folds and variance by 3.13, 2.31, and 1.57 folds regarding CT, LinRegPCR, and Cy0, respectively. Finally, f0% reduced the absolute relative error caused by LinRegPCR by 1.83 folds. CONCLUSIONS We recommend using the f0% method to analyze and report qPCR results based on its reported advantages. Finally, to simplify the usage of the f0% method, it was implemented in a macro-enabled Excel file with a user manual located on https://github.com/Mahmoud0Gamal/F0-perc/releases .
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Affiliation(s)
- Mahmoud Gamal
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
| | - Marwa A Ibrahim
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
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10
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Jiang X, Xie B, Li K, Zhou F. Prolonged Linear Amplification of qPCR for the Correction of Amplification Variation and the Absolute Quantification without Standard Curves. Anal Chem 2023; 95:18451-18459. [PMID: 38063082 DOI: 10.1021/acs.analchem.3c03637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The variable amplification efficiency of each thermal cycle of qPCR obeys the Poisson distribution, and the qPCR system dynamically changes, so there must be a detection error in its quantitative analysis. Here, more than 20 cycles of the linear amplification of qPCR can be produced as the BSA hydrogel is introduced to achieve the controlled release of Taq DNA polymerase. There is a significant negative correlation between the slope of linear amplification and Ct values (r = -0.9455), and it is well evident that the slope can reflect the amplification efficiency and a linear positive correlation exists between them. Through the change in the concentration of primers in the qPCR system, an exponential equation between Ct values and the slopes can be fitted (R2 = 0.9995). The slopes and Ct values of each qPCR system can be corrected by using this equation to guarantee that there will be significant consistency in their amplification efficiency because the degree of linear fitting (R2) between Ct values and the logarithm of their corresponding concentration of the DNA template increased significantly. By this time, the accurate amplification efficiency can be calculated in a known multiple of two initial concentrations of DNA templates. With the aid of the relationship between the known primer concentration and the fluorescence intensity at the end of PCR (End RFU), the initial concentrations of DNA templates can be reversely calculated in the absence of standard curves.
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Affiliation(s)
- Xinglu Jiang
- Clinical Laboratory Medicine Department, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
| | - BeiBei Xie
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
- Conservative Dentistry & Endodontics Department, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Kangjing Li
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
- Conservative Dentistry & Endodontics Department, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Fengyuan Zhou
- Clinical Laboratory Medicine Department, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction, College of Stomatology, Hospital of Stomatology, Guangxi Medical University, Nanning 530021, Guangxi, China
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11
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Tao Z, Ke K, Shi D, Zhu L. Development of a dual fluorescent reporter system to identify inhibitors of Staphylococcus aureus virulence factors. Appl Environ Microbiol 2023; 89:e0097823. [PMID: 37889047 PMCID: PMC10686081 DOI: 10.1128/aem.00978-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/15/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Staphylococcus aureus is a formidable pathogen responsible for a wide range of infections, and the emergence of antibiotic-resistant strains has posed significant challenges in treating these infections. In this study, we have established a novel dual reporter system capable of concurrently monitoring the activities of two critical virulence regulators in S. aureus. By incorporating both reporters into a single screening platform, we provide a time- and cost-efficient approach for assessing the activity of compounds against two distinct targets in a single screening round. This innovative dual reporter system presents a promising strategy for the identification of molecules capable of modulating virulence gene expression in S. aureus, potentially expediting the development of antivirulence therapies.
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Affiliation(s)
- Zhanhua Tao
- Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, China
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Nanning, China
| | - Ke Ke
- Guangxi Academy of Sciences, Nanning, China
| | | | - Libo Zhu
- Guangxi Academy of Sciences, Nanning, China
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12
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Liu L, Zou Y, Xia T, Zhang J, Xiong M, Long L, Wang K, Hao N. A double-quenching paperclip ECL biosensing platform for ultrasensitive detection of antibiotic resistance genes (mecA) based on Ti 3C 2 MXene-Au NPs as a coreactant accelerator. Biosens Bioelectron 2023; 240:115651. [PMID: 37666010 DOI: 10.1016/j.bios.2023.115651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/21/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023]
Abstract
The global spread of environmental biological pollutants, such as antibiotic-resistant bacteria and their antibiotic resistance genes (ARGs), has emerged as a critical public health concern. It is imperative to address this pressing issue due to its potential implications for public health. Herein, a DNA paperclip probe with double-quenching function of target cyclic cleavage was proposed, and an electrochemiluminescence (ECL) biosensing platform was constructed using Ti3C2 MXene in-situ reduction growth of Au NPs (TCM-Au) as a coreactant accelerator, and applied to the sensitive detection of ARGs. Thanks to the excellent catalytic performance, large surface area and Au-S affinity of TCM-Au, the ECL performance of CdS QDs have been significantly improved. By cleverly utilizing the negative charge of the paperclip nucleic acid probe and its modification group, double-quenching of the ECL signal was achieved. This innovative approach, combined with target cyclic amplification, facilitated specific and sensitive detection of the mecA gene. This biosensing platform manifested highly selective and sensitive determination of mecA genes in the range of 10 fM to 100 nM and a low detection limit of 2.7 fM. The credible detectability and anti-interference were demonstrated in Yangtze river and Aeration tank outlet, indicating its promising application toward pollution monitoring of ARGs.
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Affiliation(s)
- Liqi Liu
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Yi Zou
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Tiantian Xia
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Jiadong Zhang
- Key Laboratory for Palygorskite Science and Applied Technology of Jiangsu, National & Local Joint Engineering Research Center for Mineral Salt Deep Utilization, School of Chemical Engineering, Huaiyin Institute of Technology, Huaian, 223003, PR China
| | - Meng Xiong
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, PR China
| | - Lingliang Long
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Kun Wang
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, 212013, PR China.
| | - Nan Hao
- School of Chemistry and Materials Science, Nanjing University of Information Science & Technology, Nanjing, 210044, PR China.
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13
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Xu EY, Schneper LM, Notterman DA. A novel metric to improve mismatched primer selection and quantification accuracy in amplifying DNA repeats for quantitative polymerase chain reactions. PLoS One 2023; 18:e0292559. [PMID: 37812635 PMCID: PMC10561853 DOI: 10.1371/journal.pone.0292559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/23/2023] [Indexed: 10/11/2023] Open
Abstract
In quantitative polymerase chain reaction (qPCR) experiments, primers containing mismatches with respect to the template are widely used in measuring repetitive DNA elements. Primer-template mismatches may lead to underestimation of the input sample quantity due to inefficient annealing and amplification. But how primer-template mismatches affect quantification accuracy has not been rigorously investigated. In this study, we performed a series of qPCR experiments in which we tested three pairs of mismatched telomere primers (tel1/tel2, tel1b/tel2b and telg/telc) and two pairs of perfect-match reference gene primers (36B4-F/-R and IFNB1-F/-R) at three different primer concentrations under four cycling conditions. Templates used were genomic DNA from two human cell lines and oligo duplexes which contained telomere sequences, reference gene sequences, or both. We demonstrated that the underestimation of input sample quantity from reactions containing mismatched primers was not due to lower amplification efficiency (E), but due to ineffective usage of the input sample. We defined a novel concept of amplification efficacy (f) which quantifies the effectiveness of input sample amplification by primers. We have modified the conventional qPCR kinetic formula to include f, which corrects the effects of primer mismatches. We demonstrated that reactions containing mismatched telomere primer pairs had similar efficiency (E), but varying degrees of reduced efficacy (f) in comparison to those with the perfect-match gene primer pairs. Using the quantitative parameter f, underestimation of initial target by telomere primers can be adjusted to provide a more accurate measurement. Additionally, we found that the tel1b/tel2b primer set at concentration of 500 nM and 900 nM exhibited the best amplification efficacy f. This study provides a novel way to incorporate an evaluation of amplification efficacy into qPCR analysis. In turn, it improves mismatched primer selection and quantification accuracy in amplifying DNA repeats using qPCR methods.
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Affiliation(s)
- Eugenia Y. Xu
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Lisa M. Schneper
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Daniel A. Notterman
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
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14
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Davis G, Hameister B, Dunnum C, Vanderpas E, Carter B. Incorporating Primer Amplification Efficiencies in Quantitative Reverse Transcription Polymerase Chain Reaction Experiments; Considerations for Differential Gene Expression Analyses in Zebrafish. Zebrafish 2023; 20:189-199. [PMID: 37722027 DOI: 10.1089/zeb.2023.0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023] Open
Abstract
Quantitative reverse transcription polymerase chain reaction (RT-qPCR) is commonly used to measure the mRNA expression of target genes in zebrafish. Gene expression values from RT-qPCR are typically reported as relative fold-changes, and relative quantification of RT-qPCR data incorporates primer amplification efficiency values for each target gene. We describe the influence of the primer amplification efficiency analysis method on RT-qPCR gene expression fold-change calculations. This report describes (1) a sample analysis demonstrating incorporation of primer amplification efficiency into RT-qPCR analysis for comparing gene expression of a gene of interest between two groups when normalized to multiple reference genes, (2) the influence of differences in primer amplification efficiencies between measured genes on gene expression differences calculated from theoretical delta-Cq (dCq) values, and (3) an empirical comparison of the influence of three methods of defining primer amplification efficiency in gene expression analyses (delta-delta-Cq [ddCq], standard curve, LinRegPCR) using mRNA measurements of a set of genes in zebrafish embryonic development. Given the need to account for the influence of primer amplification efficiency along with the simplicity of using software programs (LinRegPCR) to measure primer amplification efficiency from RT-qPCR data, we encourage using empirical measurements of primer amplification efficiency for RT-qPCR analysis of differential gene expression in zebrafish.
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Affiliation(s)
- Gillian Davis
- Department of Biology, University of Wisconsin Eau Claire, Eau Claire, Wisconsin, USA
| | - Brianna Hameister
- Department of Biology, University of Wisconsin Eau Claire, Eau Claire, Wisconsin, USA
| | - Cora Dunnum
- Department of Biology, University of Wisconsin Eau Claire, Eau Claire, Wisconsin, USA
| | - Emily Vanderpas
- Department of Biology, University of Wisconsin Eau Claire, Eau Claire, Wisconsin, USA
| | - Brad Carter
- Department of Biology, University of Wisconsin Eau Claire, Eau Claire, Wisconsin, USA
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15
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Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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16
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Munguía-Ramírez B, Armenta-Leyva B, Henao-Díaz A, Cheng TY, Zhang J, Rawal G, Ye F, Giménez-Lirola L, Zimmerman JJ. Effect of extrinsic factors on the detection of PRRSV and a porcine-specific internal sample control in serum, oral fluid, and fecal specimens tested by RT-rtPCR. J Vet Diagn Invest 2023; 35:374-383. [PMID: 37166086 PMCID: PMC10331379 DOI: 10.1177/10406387231174556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
We characterized the effect of 1) temperature × time, 2) freeze-thaw cycles, and 3) high porcine reproductive and respiratory syndrome virus (PRRSV) RNA concentrations on the detection of PRRSV and a porcine-specific internal sample control (ISC) in serum, oral fluid, and fecal samples using a commercial PRRSV RT-rtPCR assay (Idexx). In study 1, the effect of temperature × time on PRRSV and ISC detection was shown to be specimen dependent. In serum stored at 4, 10, or 20°C, PRRSV detection was consistent for up to 168 h, but storage at 30°C reduced detectable PRRSV RNA. ISC RNA was stable in serum held at 4 and 10°C, but not at 20 and 30°C. In contrast, PRRSV and ISC RNAs in oral fluid and fecal samples continuously decreased at all temperature × time treatments. Based on these data, serum samples should be stored at ≤ 20°C to optimize PRRSV RNA detection. Oral fluid and fecal samples should be frozen in a non-self-defrosting freezer until tested. In study 2, freeze-thaw cycles had little impact on PRRSV and ISC detection, but more so in oral fluids than serum or fecal samples. Thus, freeze-thaw cycles in oral fluids should be minimized before RT-rtPCR testing. In study 3, the ISC was not affected by high concentrations of PRRSV RNA in serum, oral fluid, or fecal samples. It should not be assumed that data from our PRRSV study are applicable to other pathogens; additional pathogen-specific studies are required.
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Affiliation(s)
- Berenice Munguía-Ramírez
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Betsy Armenta-Leyva
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | | | - Ting-Yu Cheng
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Gaurav Rawal
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Fangshu Ye
- Department of Statistics, College of Liberal Arts and Sciences, Iowa State University, Ames, IA, USA
| | - Luis Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jeffrey J. Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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17
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Tao Z, Wang H, Ke K, Shi D, Zhu L. Flavone inhibits Staphylococcus aureus virulence via inhibiting the sae two component system. Microb Pathog 2023; 180:106128. [PMID: 37148922 DOI: 10.1016/j.micpath.2023.106128] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/08/2023] [Accepted: 04/26/2023] [Indexed: 05/08/2023]
Abstract
The rising prevalence of antibiotic resistance in Staphylococcus aureus calls for the development of innovative antimicrobial agents targeting novel pathways. S. aureus generates various virulence factors that compromise host defense mechanisms. Flavone, a core structure of flavonoids, has been shown to diminish the production of staphyloxanthin and alpha-hemolysin. Nonetheless, the influence of flavone on the majority of other virulence factors in S. aureus and its underlying molecular mechanism remain elusive. In this study, we examined the impact of flavone on the transcriptional profile of S. aureus using transcriptome sequencing. Our findings revealed that flavone substantially downregulated the expression of over 30 virulence factors implicated in immune evasion by the pathogen. Gene set enrichment analysis of the fold change-ranked gene list in relation to the Sae regulon indicated a robust association between flavone-induced downregulation and membership in the Sae regulon. Through the analysis of Sae target promoter-gfp fusion expression patterns, we observed a dose-dependent inhibition of Sae target promoter activity by flavone. Moreover, we discovered that flavone protected human neutrophils from S. aureus-mediated killing. Flavone also decreased the expression of alpha-hemolysin and other hemolytic toxins, resulting in a reduction in S. aureus' hemolytic capacity. Additionally, our data suggested that the inhibitory effect of flavone on the Sae system operates independently of its capacity to lower staphyloxanthin levels. In conclusion, our study proposes that flavone exhibits a broad inhibitory action on multiple virulence factors of S. aureus by targeting the Sae system, consequently diminishing the bacterium's pathogenicity.
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Affiliation(s)
- Zhanhua Tao
- Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530003, Guangxi, China; Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Nanning, 530003, Guangxi, China.
| | - Haoren Wang
- The First Affiliated Hospital of Jiamusi University, Jiamusi, 154002, Heilongjiang, China.
| | - Ke Ke
- Guangxi Academy of Sciences, Nanning, 530003, Guangxi, China.
| | - Deqiang Shi
- Guangxi Academy of Sciences, Nanning, 530003, Guangxi, China.
| | - Libo Zhu
- Guangxi Academy of Sciences, Nanning, 530003, Guangxi, China.
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18
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Karon BS, Donato LJ, Moyer AM, Wockenfus AM, Kelley BR, Majumdar R, Kipp BR, Yao JD. Evaluation of the analytical sensitivity of ACON and LumiraDx SARS-CoV-2 rapid antigen tests using samples with presumed Omicron variant. Diagn Microbiol Infect Dis 2023; 107:115977. [PMID: 37329875 PMCID: PMC10154058 DOI: 10.1016/j.diagmicrobio.2023.115977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/25/2023] [Accepted: 04/30/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Analytical sensitivity of 2 rapid antigen tests was evaluated for detection of presumed SARS-CoV-2 Omicron variants and earlier variants of concern. METHODS A total of 152 SARS-CoV-2 RNA positive samples (N and ORF1ab positive but S gene negative) were tested for SARS-CoV-2 antigen by ACON lateral flow and LumiraDx fluorescence immunoassays. Sensitivity within 3 viral load ranges was compared among these 152 samples and 194 similarly characterized samples collected prior to the circulation of the Delta variant (pre-Delta). RESULTS Antigen was detected in >95% of pre-Delta and presumed Omicron samples for both tests at viral loads >500,000 copies/mL, and 65 to 85% of samples with 50,000-500,000 copies/mL. At viral load <50,000 copies/mL, antigen tests showed better sensitivity in detecting pre-Delta compared to Omicron variants. LumiraDx was more sensitive than ACON at low viral load. CONCLUSIONS Antigen tests had decreased sensitivity for detecting presumed Omicron compared to pre-Delta variants at low viral load.
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Affiliation(s)
- Brad S Karon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN 55905 USA.
| | - Leslie J Donato
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN 55905 USA
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN 55905 USA
| | - Amy M Wockenfus
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN 55905 USA
| | - Brandon R Kelley
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN 55905 USA
| | - Ramanath Majumdar
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN 55905 USA
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN 55905 USA
| | - Joseph D Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN 55905 USA
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19
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Hu G, Huang K, Zhou W, Wang R, Zhao W, Zou H, Li W, Wu S, Li M, Wang G. Comparison of droplet digital PCR and real-time quantitative PCR for quantitative detection of the parasitic ciliate Ichthyophthirius multifiliis in the water environment. JOURNAL OF FISH DISEASES 2023; 46:357-367. [PMID: 36606558 DOI: 10.1111/jfd.13749] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Ichthyophthiriasis, caused by the parasitic ciliate Ichthyophthirius multifiliis (Ich), is considered one of the most harmful diseases affecting freshwater fish globally. It can cause mass mortalities of fish in intensive farming systems. In such systems, it is thus necessary to detect and quantify the number of Ich in the water so that control measures can be implemented before Ichthyophthiriasis breaks out. In recent years, molecular diagnostic methods have become increasingly important in aquaculture. Real-time quantitative polymerase chain reaction (qPCR) and droplet digital polymerase chain reaction (ddPCR) have become robust assays for detecting pathogens. In this study, a set of specific primers and a TaqMan-minor groove binder probe targeting the small-subunit rDNA (SSU rDNA) of Ich were developed. They were used in qPCR and ddPCR assays to compare the performance of these two different methods in quantitatively detecting Ich. After optimizing the reaction conditions, both qPCR and ddPCR assays were found to have high linearity and quantitative correlations for standard plasmid DNA. When used for the detection of Ich eDNA in water samples, the qPCR assay had a wider detection range, making it a suitable method to screen for the prevalence of Ichthyophthiriasis. However, the ddPCR approach had higher sensitivity, which would help provide advance notice of the disease in complex water environmental samples.
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Affiliation(s)
- Guangran Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weitian Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Runqiu Wang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Weishan Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hong Zou
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wenxiang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shangong Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guitang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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20
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Sagitov S, Ståhlberg A. Counting unique molecular identifiers in sequencing using a multi-type branching process with immigration. J Theor Biol 2023; 558:111365. [PMID: 36410451 DOI: 10.1016/j.jtbi.2022.111365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/14/2022] [Accepted: 11/16/2022] [Indexed: 11/20/2022]
Abstract
Detection of extremely rare variant alleles, such as tumor DNA, within a complex mixture of DNA molecules is experimentally challenging due to sequencing errors. Barcoding of target DNA molecules in library construction for next-generation sequencing provides a way to identify and bioinformatically remove polymerase induced errors. During the barcoding procedure involving t consecutive PCR cycles, the DNA molecules become barcoded by Unique Molecular Identifiers (UMIs). Different library construction protocols utilize different values of t. The effect of a larger t and imperfect PCR amplifications in relation to UMI cluster sizes is poorly described. This paper proposes a branching process with growing immigration as a model describing the random outcome of t cycles of PCR barcoding. Our model discriminates between five different amplification rates r1, r2, r3, r4, r for different types of molecules associated with the PCR barcoding procedure. We study this model by focussing on Ct, the number of clusters of molecules sharing the same UMI, as well as Ct(m), the number of UMI clusters of size m. Our main finding is a remarkable asymptotic pattern valid for moderately large t. It turns out that E(Ct(m))/E(Ct)≈2-m for m=1,2,…, regardless of the underlying parameters (r1,r2,r3,r4,r). The knowledge of the quantities Ct and Ct(m) as functions of the experimental parameters t and (r1,r2,r3,r4,r) will help the users to draw more adequate conclusions from the outcomes of different sequencing protocols.
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Affiliation(s)
- Serik Sagitov
- Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Sweden.
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden.
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21
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Jiménez-Zapata DL, Quiroga-Pérez M, Quiroz-Yepes M, Marulanda-Tobón A, Álvarez JC, Mosquera-López S. Development of a Method for Detecting and Estimating Moniliophthora roreri Spore Loads Based on Spore Traps and qPCR. J Fungi (Basel) 2022; 9:jof9010047. [PMID: 36675868 PMCID: PMC9862605 DOI: 10.3390/jof9010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/19/2022] [Accepted: 12/26/2022] [Indexed: 12/29/2022] Open
Abstract
Frosty pod rot, caused by Moniliophthora roreri, is the most damaging disease of cacao in Latin America and, to better comprehend its epidemiology, we must understand its dissemination and proliferation. However, we do not know how M. roreri spores loads fluctuate in time and space due to the lack of a reliable technique to quantify M. roreri spores in the fields. Therefore, we developed a method that relies on spore traps and qPCR to detect and quantify M. roreri spore loads. This study demonstrated that the qPCR protocol can detect down to 0.025 ng of M. roreri DNA and quantify between 0.006 ng and 60 ng. Moreover, it demonstrated that qPCR protocol can detect and quantify DNA extracted from spore suspension and spore traps containing at least 2.9 × 104 M. roreri spores. However, the variability of the estimates for spore samples was high. Finally, we described a spore-trap device designed to carry spore traps in the field. The qPCR protocol and spore-trap device here developed will help in the understanding of the M. roreri dissemination patterns since they can be used to assess the environmental loads of M. roreri spore in cacao fields.
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Affiliation(s)
- Diana L. Jiménez-Zapata
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
| | - Manuela Quiroga-Pérez
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
| | - Manuela Quiroz-Yepes
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- GEMA Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
| | - Alejandro Marulanda-Tobón
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- GEMA Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
| | - Javier C. Álvarez
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- Correspondence:
| | - Sandra Mosquera-López
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
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22
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Identification and Functional Characterization of CYP4D2 Putatively Associated with β-Cypermethrin Detoxification in Phortica okadai. Genes (Basel) 2022; 13:genes13122338. [PMID: 36553604 PMCID: PMC9777750 DOI: 10.3390/genes13122338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/28/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Phortica okadai, a polyphagous pest, serves as a vector for Thelazia callipaeda in China. Currently, there are no effective control strategies for this vector. Agricultural pest control may cause P. okadai to become a threat due to the development of pesticide resistance. Cytochrome P450s (CYP450) plays a significant role in detoxifying xenobiotics in insects. In this study, we performed RNA sequencing of P. okadai exposed to β-cypermethrin for 0 and 1 h and then gene cloning of the five up-regulated CYP450 genes. Three CYP450 genes were successfully cloned, and their expression patterns in different developmental stages and in different tissues were analyzed by RT-qPCR. Pocyp4d2 was observed to have the highest expression in the midgut (fold change 2.82 for Pocyp4d2, 2.62 for Pocyp49a1, and 1.77 for Pocyp28d2). Functional analysis was carried out according to overexpression in S2 cells from the pfastbac1 vector and RNAi with siRNA. The results of the CCK8 assay indicated that the overexpression of the recombinant protein PoCYP4D2 suppressed the decrease in S2 cell viability due to β-cypermethrin. The expression levels of PoCYP4D2 decreased significantly, and the mortality rates increased from 6.25% to 15.0% at 3 h and from 15.0% to 27.5% at 6 h after Pocyp4d2-siRNA injection. These results suggest that Pocyp4d2 may be an essential key gene in the metabolism of β-cypermethrin in P. okadai. This study constitutes a foundation to explore further the functions of P. okadai CYP450 genes in insecticide metabolism.
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23
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Luraschi R, Santibáñez Á, Barrera-Avalos C, Vallejos-Vidal E, Mateluna-Flores C, Alarcón J, Cayunao J, Mella-Torres A, Hernández F, Inostroza-Molina A, Valdés D, Imarai M, Acuña-Castillo C, Reyes-López FE, Sandino AM. Evaluation and comparison of the sensitivity of three commercial RT-qPCR kits used for the detection of SARS-CoV-2 in Santiago, Chile. Front Public Health 2022; 10:1010336. [PMID: 36518569 PMCID: PMC9742446 DOI: 10.3389/fpubh.2022.1010336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/08/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction The COVID-19 pandemic is still in force, causing global public health challenges and threats. Although vaccination and herd immunity have proven to be the most efficient way to control the pandemic, massive and early testing of patients using the RT-qPCR technique is crucial for constant genomic surveillance. The appearance of variants of SARS-CoV-2 with new mutations can reduce the efficiency of diagnostic detection. In this sense, several commercial RT-qPCR kits have been the target of extensive analysis because low assay performance could lead to false-negative diagnoses. Methods In this study, we evaluated the performance of three commercial RT-qPCR kits; Thermo Fisher (TaqMan 2019-nCoV Assay Kit v1), BGI and Roche (LightCycler® Multiplex RNA Virus Master) used for the diagnosis of COVID-19 throughout the pandemic in Santiago de Chile. Results Under our best assay conditions, we found significant differences in Cq amplification values for control and viral probes, against the same nasopharyngeal swab samples (NPSs). In addition, in some cases, the sensitivity of the RT-qPCR kits decreased against viral variants. Conclusion Our study suggests evaluating the RT-qPCR kits used to detect SARS-CoV-2 because variants such as Omicron, which has several mutations, can compromise their detection and underestimate viral circulation.
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Affiliation(s)
- Roberto Luraschi
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Álvaro Santibáñez
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Carlos Barrera-Avalos
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Eva Vallejos-Vidal
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile,Centro de Nanociencia y Nanotecnología CEDENNA, Universidad de Santiago de Chile, Santiago, Chile,Núcleo de Investigación Aplicada en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
| | - Carlos Mateluna-Flores
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Javiera Alarcón
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Javiera Cayunao
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Andrea Mella-Torres
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Felipe Hernández
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Ailen Inostroza-Molina
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Daniel Valdés
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile,Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Mónica Imarai
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile,Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Claudio Acuña-Castillo
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile,Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile,*Correspondence: Felipe E. Reyes-López
| | - Felipe E. Reyes-López
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile,Ana María Sandino
| | - Ana María Sandino
- Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile,Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile,Claudio Acuña-Castillo
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24
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Langan LM, O’Brien M, Rundell ZC, Back JA, Ryan BJ, Chambliss CK, Norman RS, Brooks BW. Comparative Analysis of RNA-Extraction Approaches and Associated Influences on RT-qPCR of the SARS-CoV-2 RNA in a University Residence Hall and Quarantine Location. ACS ES&T WATER 2022; 2:1929-1943. [PMID: 37552714 PMCID: PMC9063990 DOI: 10.1021/acsestwater.1c00476] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 05/09/2023]
Abstract
Wastewater-based epidemiology (WBE) provides an early warning and trend analysis approach for determining the presence of COVID-19 in a community and complements clinical testing in assessing the population level, even as viral loads fluctuate. Here, we evaluate combinations of two wastewater concentration methods (i.e., ultrafiltration and composite supernatant-solid), four pre-RNA extraction modifications, and three nucleic acid extraction kits using two different wastewater sampling locations. These consisted of a quarantine facility containing clinically confirmed COVID-19-positive inhabitants and a university residence hall. Of the combinations examined, composite supernatant-solid with pre-RNA extraction consisting of water concentration and RNA/DNA shield performed the best in terms of speed and sensitivity. Further, of the three nucleic acid extraction kits examined, the most variability was associated with the Qiagen kit. Focusing on the quarantine facility, viral concentrations measured in wastewater were generally significantly related to positive clinical cases, with the relationship dependent on method, modification, kit, target, and normalization, although results were variable-dependent on individual time points (Kendall's Tau-b (τ) = 0.17 to 0.6) or cumulatively (Kendall's Tau-b (τ) = -0.048 to 1). These observations can support laboratories establishing protocols to perform wastewater surveillance and monitoring efforts for COVID-19.
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Affiliation(s)
- Laura M. Langan
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Megan O’Brien
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Zach C. Rundell
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Jeffrey A. Back
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
| | - Benjamin J. Ryan
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
| | - C. Kevin Chambliss
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Department of Chemistry and Biochemistry,
Baylor University, One Bear Place #97348, Waco, Texas 76798,
United States
| | - R. Sean Norman
- Environmental Health Sciences, Arnold
School of Public Health, South Carolina, 921 Assembly Street, Columbia,
South Carolina 29208, United States
| | - Bryan W. Brooks
- Department of Environmental Science,
Baylor University, One Bear Place #97266, Waco, Texas 76798,
United States
- Center for Reservoir and Aquatic Systems Research,
Baylor University, One Bear Place #97178, Waco, Texas 76798,
United States
- Institute of Biomedical Studies, Baylor
University, One Bear Place #97224, Waco, Texas 76798, United
States
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25
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Crompton K, Godler DE, Ling L, Elwood N, Mechinaud-Heloury F, Soosay Raj T, Hsiao KC, Fleming J, Tiedemann K, Novak I, Fahey M, Wang X, Lee KJ, Colditz PB, Edwards P, Reddihough D. Umbilical Cord Blood Cell Clearance Post-Infusion in Immune-Competent Children with Cerebral Palsy. Cells Tissues Organs 2022; 212:546-553. [PMID: 36261026 DOI: 10.1159/000527612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
Umbilical cord blood cells have therapeutic potential for neurological disorders, through a paracrine mechanism of action. A greater understanding of the safety and immunological effects of allogeneic donor cord blood cells in the context of a healthy recipient immune system, such as in cerebral palsy, is needed. This study aimed to determine how quickly donor cord blood cells were cleared from the circulation in children with cerebral palsy who received a single intravenous infusion of 12/12 human leucocyte antigen (HLA)-matched sibling cord blood cells. Twelve participants with cerebral palsy aged 2-12 years received cord blood cell infusions as part of a phase I trial of umbilical blood infusion for cerebral palsy. Digital droplet PCR analysis of DNA copy number variants specific to donor and recipient was used to assess donor DNA clearance at five timepoints post-infusion, a surrogate measure of cell clearance. Donor cells were cleared by 3 months post-infusion in 11/12 participants. When detected, donor DNA was at a fraction of 0.01-0.31% of total DNA with no signs of graft-versus-host disease in any participant. The donor DNA clearance times provided by this study have important implications for understanding the safety of allogeneic cord blood cell infusion for cerebral palsy and translational tissue engineering or regenerative medicine research in other disorders.
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Affiliation(s)
- Kylie Crompton
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Neurodevelopment and Disability, The Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - David E Godler
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Diagnosis and Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Ling Ling
- Diagnosis and Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Ngaire Elwood
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Blood Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- The Royal Children's Hospital, Parkville, Victoria, Australia
- BMDI Cord Blood Bank, Parkville, Victoria, Australia
| | | | - Trisha Soosay Raj
- Children's Cancer Centre, The Royal Children's Hospital, Parkville, Victoria, Australia
- Oncology, Queensland Children's Hospital, South Brisbane, Queensland, Australia
| | - Kuang-Chih Hsiao
- Allergy Immunology, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Immunology, Starship Children's Hospital, Auckland, New Zealand
- Paediatrics, University of Auckland, Auckland, New Zealand
| | - Jacqueline Fleming
- Children's Cancer Centre, The Royal Children's Hospital, Parkville, Victoria, Australia
| | | | - Iona Novak
- Cerebral Palsy Alliance Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Michael Fahey
- Paediatric Neurology, Monash Children's Hospital, Clayton, Victoria, Australia
- Medicine, Monash University, Melbourne, Victoria, Australia
| | - Xiaofang Wang
- Clinical Epidemiology and Biostatistics Unit, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Katherine J Lee
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Clinical Epidemiology and Biostatistics Unit, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Paul B Colditz
- Grantley Stable Neonatal Unit, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
- Perinatal Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Priya Edwards
- Queensland Paediatric Rehabilitation Service, Queensland Children's Hospital, South Brisbane, Queensland, Australia
- Queensland Cerebral Palsy and Rehabilitation Research Centre, The Univeristy of Queensland, Brisbane, Queensland, Australia
| | - Dinah Reddihough
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Neurodevelopment and Disability, The Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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26
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Sivaganesan M, Willis JR, Karim M, Babatola A, Catoe D, Boehm AB, Wilder M, Green H, Lobos A, Harwood VJ, Hertel S, Klepikow R, Howard MF, Laksanalamai P, Roundtree A, Mattioli M, Eytcheson S, Molina M, Lane M, Rediske R, Ronan A, D'Souza N, Rose JB, Shrestha A, Hoar C, Silverman AI, Faulkner W, Wickman K, Kralj JG, Servetas SL, Hunter ME, Jackson SA, Shanks OC. Interlaboratory performance and quantitative PCR data acceptance metrics for NIST SRM® 2917. WATER RESEARCH 2022; 225:119162. [PMID: 36191524 PMCID: PMC9932931 DOI: 10.1016/j.watres.2022.119162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Surface water quality quantitative polymerase chain reaction (qPCR) technologies are expanding from a subject of research to routine environmental and public health laboratory testing. Readily available, reliable reference material is needed to interpret qPCR measurements, particularly across laboratories. Standard Reference Material® 2917 (NIST SRM® 2917) is a DNA plasmid construct that functions with multiple water quality qPCR assays allowing for estimation of total fecal pollution and identification of key fecal sources. This study investigates SRM 2917 interlaboratory performance based on repeated measures of 12 qPCR assays by 14 laboratories (n = 1008 instrument runs). Using a Bayesian approach, single-instrument run data are combined to generate assay-specific global calibration models allowing for characterization of within- and between-lab variability. Comparable data sets generated by two additional laboratories are used to assess new SRM 2917 data acceptance metrics. SRM 2917 allows for reproducible single-instrument run calibration models across laboratories, regardless of qPCR assay. In addition, global models offer multiple data acceptance metric options that future users can employ to minimize variability, improve comparability of data across laboratories, and increase confidence in qPCR measurements.
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Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Mohammad Karim
- Environmental Services Laboratory, City of Santa Cruz, Santa Cruz, CA, USA
| | - Akin Babatola
- Environmental Services Laboratory, City of Santa Cruz, Santa Cruz, CA, USA
| | - David Catoe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Maxwell Wilder
- Department of Environmental Biology, SUNY-ESF, Syracuse, NY, USA
| | - Hyatt Green
- Department of Environmental Biology, SUNY-ESF, Syracuse, NY, USA
| | - Aldo Lobos
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Stephanie Hertel
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Regina Klepikow
- U.S. Environmental Protection Agency, Region 7 Laboratory, Kansas City, KS, USA
| | | | | | - Alexis Roundtree
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mia Mattioli
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephanie Eytcheson
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Marirosa Molina
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Molly Lane
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, USA
| | - Richard Rediske
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, USA
| | - Amanda Ronan
- U.S. Environmental Protection Agency, Region 2 Laboratory, Edison, NJ, USA
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Abhilasha Shrestha
- Division of Environmental and Occupational Health Sciences, School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - Catherine Hoar
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, NY, USA
| | - Andrea I Silverman
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, NY, USA
| | | | | | - Jason G Kralj
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Stephanie L Servetas
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Monique E Hunter
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Scott A Jackson
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA.
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27
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Vera M, Zuern S, Henríquez-Valencia C, Loncoman C, Canales J, Waller F, Basoalto E, Garnica S. Exploring interactions between Beauveria and Metarhizium strains through co-inoculation and responses of perennial ryegrass in a one-year trial. PeerJ 2022; 10:e12924. [PMID: 35341038 PMCID: PMC8944343 DOI: 10.7717/peerj.12924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/20/2022] [Indexed: 01/11/2023] Open
Abstract
Perennial ryegrass (Lolium perenne L.) possesses a high level of nutritional quality and is widely used as a forage species to establish permanent pastures in southern Chile. However, the productivity of most such pastures is limited by various environmental agents, such as insect pests and drought. In this context, our work stresses the need for elucidating the ability of fungal endophytes to establish interactions with plants, and to understand how these processes contribute to plant performance and fitness. Therefore, we evaluated the colonization and impact of two native strains of the endophytic insect-pathogenic fungus (EIPF) group isolated from permanent ryegrass pastures in southern Chile. Roots and seeds of ryegrass and scarabaeid larvae were collected from nine different ryegrass pastures in the Los Ríos region of southern Chile to specifically isolate EIPFs belonging to the genera Beauveria and Metarhizium. Fungal isolations were made on 2% water agar with antibiotics, and strains were identified by analyzing the entire internal transcribed spacer (ITS) 1-5.8S-ITS2 ribosomal DNA region. Four strains of Beauveria and 33 strains of Metarhizium were isolated only in scarabaeid larvae from ryegrass pastures across four sites. Experimental mini-pastures that were either not inoculated (control) or co-inoculated with conidia of the strains Beauveria vermiconia NRRL B-67993 (P55_1) and Metarhizium aff. lepidiotae NRRL B-67994 (M25_2) under two soil humidity levels were used. Ryegrass plants were randomly collected from the mini-pastures to characterize EIPF colonization in the roots by real-time PCR and fluorescence microscopy. Aboveground biomass was measured to analyze the putative impact of colonization on the mini-pastures' aboveground phenotypic traits with R software using a linear mixed-effects model and the ANOVA statistical test. Seasonal variation in the relative abundance of EIPFs was observed, which was similar between both strains from autumn to spring, but different in summer. In summer, the relative abundance of both EIPFs decreased under normal moisture conditions, but it did not differ significantly under water stress. The aboveground biomass of ryegrass also increased from autumn to spring and decreased in summer in both the inoculated and control mini-pastures. Although differences were observed between moisture levels, they were not significant between the control and inoculated mini-pastures, except in July (fresh weight and leaf area) and October (dry weight). Our findings indicate that native strains of B. vermiconia NRRL B-67993 (P55_1) and M. aff. lepidiotae NRRL B-67994 (M25_2) colonize and co-exist in the roots of ryegrass, and these had little or no effect on the mini-pastures' aboveground biomass; however, they could have other functions, such as protection against root herbivory by insect pests.
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Affiliation(s)
- Milena Vera
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Sarah Zuern
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Carlos Henríquez-Valencia
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Carlos Loncoman
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile,ANID–Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Frank Waller
- Pharmaceutical Biology, Julius-von-Sachs Institute for Biosciences, Julius-Maximilians Universität Würzburg, Würzburg, Germany
| | - Esteban Basoalto
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Sigisfredo Garnica
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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28
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Soper DM, Villafranca N, Dieffenthaller JP, Dieffenthaller M, Tompkins H, Weglarz M, Vaughan D, Hamlyn SB, Stenesen D. Growth and Cyclin-E Expression in the Stony Coral Species Orbicella faveolata Post-Microfragmentation. THE BIOLOGICAL BULLETIN 2022; 242:40-47. [PMID: 35245162 DOI: 10.1086/717926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
AbstractCoral growth is critical to reef health, resilience under rapidly changing environmental conditions, and restoration efforts. Although fragmenting coral has been occurring for many years in an effort to restore reefs, recently it was discovered that microfragmenting, the process of cutting one piece of coral into many small pieces (about three to five polyps), induces exponential growth. Our study investigates the process by which microfragments of nine different genotypes from the stony coral species Orbicella faveolata grow and exhibit Cyclin-E expression. Microfragments were examined by using a high-powered dissecting microscope with a camera to document the precise areas of tissue exhibiting exponential growth. We found that new polyp formation occurs only on the microfragment edges and that edge polyp growth rates varied between different genotypes. We then extracted tissue from both the edge and the center of five genotypes for genetic analysis. We chose to analyze Cyclin-E expression because it is involved with stimulating mitotic division and is a conserved signaling pathway that is known to exist in Drosophila, mammals, and Cnidaria. Two primers for Cyclin-E were utilized to examine the level of expression for center and edge tissue. We found that Cyclin-E is expressed differentially between O. faveolata polyps, with a tendency for increased expression of the Cyclin-E in edge versus center tissue in each of five genotypes, although this result was not significant. Despite consistently higher levels of Cyclin-E expression within an organism's edge tissue, genotypes varied significantly in the degree of increased expression. This variation positively correlated with growth rate, suggesting the potential for molecular selection in aid of more rapid reef restoration. Future work will focus on deciphering the specific growth pathways involved in microfragmented coral growth and analyzing expression patterns in injured tissues.
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29
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Ren G, Juhl M, Peng Q, Fink T, Porsborg SR. Selection and validation of reference genes for qPCR analysis of differentiation and maturation of THP-1 cells into M1 macrophage-like cells. Immunol Cell Biol 2022; 100:822-829. [PMID: 36184577 PMCID: PMC9828170 DOI: 10.1111/imcb.12590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/19/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
For cell-based assays studying monocytes and macrophages, the immortalized monocyte cell line THP-1 is widely used and stimulated with phorbol 12-myristate 13-acetate, lipopolysaccharide (LPS) and/or interferon-γ (IFN-γ), after which it differentiates and polarizes into proinflammatory M1-like macrophages. For the quantification of this and the effect of different factors affecting these processes, the expression levels of various maturation markers are determined using reverse transcription-quantitative PCR. For this purpose, stably expressed reference genes are crucial. However, no studies evaluating the stability of reference genes in THP-1 cells stimulated with LPS and IFN-γ have been performed. Therefore, this paper describes the selection of the most used reference genes [RPL37A (ribosomal protein L37a), GAPDH (glyceraldehyde-3-phosphate dehydrogenase), UBC (ubiquitin C), B2M (0β2-microbulin), ACTB (β-actin) and PPIA (cyclophilin A)], the in silico primer design, the analysis and the validation of these in accordance with the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines and more recent recommendations for the validation of the stability of reference genes. Using the RefFinder platform, including the four most popular algorithms for reference gene validation, the Delta CT, BestKeeper, NormFinder and geNorm, we find the reference genes GAPDH and UBC to be the most stable. Furthermore, we demonstrate that the normalization of gene expression data using the least stable reference genes, ACTB and B2M, dramatically affects the interpretation of experimental data. Taken together, it is vital to validate the stability of reference genes under the specific experimental conditions used when utilizing the THP-1 monocyte model system.
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Affiliation(s)
- Guoqiang Ren
- Regenerative Medicine Group, Department of Health Science and TechnologyAalborg UniversityFredrik Bajers Vej 3B9220AalborgDenmark
| | - Morten Juhl
- Cardiology Stem Cell Centre, The Centre for Cardiac, Vascular, Pulmonary and Infectious DiseasesCopenhagen University Hospital RigshospitaletDenmark
| | - Qiuyue Peng
- Regenerative Medicine Group, Department of Health Science and TechnologyAalborg UniversityFredrik Bajers Vej 3B9220AalborgDenmark
| | - Trine Fink
- Regenerative Medicine Group, Department of Health Science and TechnologyAalborg UniversityFredrik Bajers Vej 3B9220AalborgDenmark
| | - Simone Riis Porsborg
- Regenerative Medicine Group, Department of Health Science and TechnologyAalborg UniversityFredrik Bajers Vej 3B9220AalborgDenmark
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Ruijter JM, Ruiz-Villalba A, van den Hoff MJB. Cq Values Do Not Reflect Nucleic Acid Quantity in Biological Samples. Clin Chem 2021; 68:7-9. [PMID: 34677605 DOI: 10.1093/clinchem/hvab236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 11/14/2022]
Affiliation(s)
- J M Ruijter
- Department of Medical Biology, Amsterdam University Medical Centres, Location AMC, Amsterdam, the Netherlands
| | - A Ruiz-Villalba
- Department of Animal Biology, Faculty of Sciences, Instituto Malagueño de Biomedicina (IBIMA), University of Málaga, Málaga, Spain
| | - M J B van den Hoff
- Department of Medical Biology, Amsterdam University Medical Centres, Location AMC, Amsterdam, the Netherlands
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31
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Hoorzook KB, Barnard TG. Absolute quantification of E. coli virulence and housekeeping genes to determine pathogen loads in enumerated environmental samples. PLoS One 2021; 16:e0260082. [PMID: 34843501 PMCID: PMC8629182 DOI: 10.1371/journal.pone.0260082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/02/2021] [Indexed: 11/30/2022] Open
Abstract
Quantifying pathogenic genes with q-PCR in complex samples to determine the pathogen loads is influenced by a wide range of factors, including choice of extraction method, standard curve, and the decision to use relative versus absolute quantification of the genes. The aim was to investigate the standardisation of q-PCR methods to determine enumerated E. coli gene ratios grown with the IDEXX Colilert® Quanti-Trays® using enteropathogenic E. coli as the model pathogen. q-PCR targeting the eaeA and gadAB genes was used to calculate the eaeA: gadAB ratios for clinical strains collected between [2005–2006 (n = 55)] and [2008–2009 (n = 19)] using the LinRegPCR software and Corbett Research Thermal cycler software. Both programs grouped the isolates into two distinct groups based on the gene ratios although the Corbett Research Thermal cycler software gave results one log higher than the LinRegPCR program. Although the eaeA: gadAB ratio range was determined using extracted E. coli DNA, the impact of free DNA and other bacteria present in the sample needed to be understood. Standard curve variations using serially diluted extracted E. coli DNA, serially diluted pure E. coli culture followed by DNA extraction from each dilution with or without other bacteria was tested using the eaeA q-PCR to quantify the genes. Comparison of the standard curves showed no significant difference between standard curves prepared with diluted DNA or with cells diluted before the DNA is extracted (P = 0.435). Significant differences were observed when background DNA was included in the diluent or Coliform cells added to the diluent to dilute cells before the DNA is extracted (P < 0.001). The “carrier” DNA and Coliform cells enhanced the DNA extraction results resulting in better PCR efficiency. This will have an influence on the quantification of gene ratios and pathogen load in samples containing lower numbers of E. coli.
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Affiliation(s)
- K. B. Hoorzook
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, Johannesburg, South Africa
- * E-mail:
| | - T. G. Barnard
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, Johannesburg, South Africa
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Méndez-Hernández HA, Quintana-Escobar AO, Uc-Chuc MA, Loyola-Vargas VM. Genome-Wide Analysis, Modeling, and Identification of Amino Acid Binding Motifs Suggest the Involvement of GH3 Genes during Somatic Embryogenesis of Coffea canephora. PLANTS 2021; 10:plants10102034. [PMID: 34685847 PMCID: PMC8539013 DOI: 10.3390/plants10102034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 11/23/2022]
Abstract
Auxin plays a central role in growth and plant development. To maintain auxin homeostasis, biological processes such as biosynthesis, transport, degradation, and reversible conjugation are essential. The Gretchen Hagen 3 (GH3) family genes codify for the enzymes that esterify indole-3-acetic acid (IAA) to various amino acids, which is a key process in the induction of somatic embryogenesis (SE). The GH3 family is one of the principal families of early response to auxin genes, exhibiting IAA-amido synthetase activity to maintain optimal levels of free auxin in the cell. In this study, we carried out a systematic identification of the GH3 gene family in the genome of Coffea canephora, determining a total of 18 CcGH3 genes. Analysis of the genetic structures and phylogenetic relationships of CcGH3 genes with GH3 genes from other plant species revealed that they could be clustered in two major categories with groups 1 and 2 of the GH3 family of Arabidopsis. We analyzed the transcriptome expression profiles of the 18 CcGH3 genes using RNA-Seq analysis-based data and qRT-PCR during the different points of somatic embryogenesis induction. Furthermore, the endogenous quantification of free and conjugated indole-3-acetic acid (IAA) suggests that the various members of the CcGH3 genes play a crucial role during the embryogenic process of C. canephora. Three-dimensional modeling of the selected CcGH3 proteins showed that they consist of two domains: an extensive N-terminal domain and a smaller C-terminal domain. All proteins analyzed in the present study shared a unique conserved structural topology. Additionally, we identified conserved regions that could function to bind nucleotides and specific amino acids for the conjugation of IAA during SE in C. canephora. These results provide a better understanding of the C. canephora GH3 gene family for further exploration and possible genetic manipulation.
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Lau MJ, Hoffmann AA, Endersby-Harshman NM. A diagnostic primer pair to distinguish between wMel and wAlbB Wolbachia infections. PLoS One 2021; 16:e0257781. [PMID: 34555085 PMCID: PMC8459989 DOI: 10.1371/journal.pone.0257781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/09/2021] [Indexed: 11/20/2022] Open
Abstract
Detection of the Wolbachia endosymbiont in Aedes aegypti mosquitoes through real-time polymerase chain reaction assays is widely used during and after Wolbachia releases in dengue reduction trials involving the wMel and wAlbB strains. Although several different primer pairs have been applied in current successful Wolbachia releases, they cannot be used in a single assay to distinguish between these strains. Here, we developed a new diagnostic primer pair, wMwA, which can detect the wMel or wAlbB infection in the same assay. We also tested current Wolbachia primers and show that there is variation in their performance when they are used to assess the relative density of Wolbachia. The new wMwA primers provide an accurate and efficient estimate of the presence and density of both Wolbachia infections, with practical implications for Wolbachia estimates in field collected Ae. aegypti where Wolbachia releases have taken place.
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Affiliation(s)
- Meng-Jia Lau
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
| | - Ary A. Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Nancy M. Endersby-Harshman
- Pest and Environmental Adaptation Research Group, Bio21 Institute and the School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
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Untergasser A, Ruijter JM, Benes V, van den Hoff MJB. Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data. BMC Bioinformatics 2021; 22:398. [PMID: 34433408 PMCID: PMC8386043 DOI: 10.1186/s12859-021-04306-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/22/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The analyses of amplification and melting curves have been shown to provide valuable information on the quality of the individual reactions in quantitative PCR (qPCR) experiments and to result in more reliable and reproducible quantitative results. IMPLEMENTATION The main steps in the amplification curve analysis are (1) a unique baseline subtraction, not using the ground phase cycles, (2) PCR efficiency determination from the exponential phase of the individual reactions, (3) setting a common quantification threshold and (4) calculation of the efficiency-corrected target quantity with the common threshold, efficiency per assay and Cq per reaction. The melting curve analysis encompasses smoothing of the observed fluorescence data, normalization to remove product-independent fluorescence loss, peak calling and assessment of the correct peak by comparing its melting temperature with the known melting temperature of the intended amplification product. RESULTS The LinRegPCR web application provides visualization and analysis of a single qPCR run. The user interface displays the analysis results on the amplification curve analysis and melting curve analysis in tables and graphs in which deviant reactions are highlighted. The annotated results in the tables can be exported for calculation of gene-expression ratios, fold-change between experimental conditions and further statistical analysis. Web-based LinRegPCR addresses two types of users, wet-lab scientists analyzing the amplification and melting curves of their own qPCR experiments and bioinformaticians creating pipelines for analysis of series of qPCR experiments by splitting its functionality into a stand-alone back-end RDML (Real-time PCR Data Markup Language) Python library and several companion applications for data visualization, analysis and interactive access. The use of the RDML data standard enables machine independent storage and exchange of qPCR data and the RDML-Tools assist with the import of qPCR data from the files exported by the qPCR instrument. CONCLUSIONS The combined implementation of these analyses in the newly developed web-based LinRegPCR ( https://www.gear-genomics.com/rdml-tools/ ) is platform independent and much faster than the original Windows-based versions of the LinRegPCR program. Moreover, web-based LinRegPCR includes a novel statistical outlier detection and the combination of amplification and melting curve analyses allows direct validation of the amplification product and reporting of reactions that amplify artefacts.
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Affiliation(s)
- Andreas Untergasser
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany. .,European Molecular Biology Laboratory (EMBL), Genomics Core Facility, 69117, Heidelberg, Germany.
| | - Jan M Ruijter
- Department of Medical Biology, Amsterdam University Medical Centres, Academic Medical Center, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Vladimir Benes
- European Molecular Biology Laboratory (EMBL), Genomics Core Facility, 69117, Heidelberg, Germany
| | - Maurice J B van den Hoff
- Department of Medical Biology, Amsterdam University Medical Centres, Academic Medical Center, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
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Use and Misuse of C q in qPCR Data Analysis and Reporting. Life (Basel) 2021; 11:life11060496. [PMID: 34072308 PMCID: PMC8229287 DOI: 10.3390/life11060496] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
In the analysis of quantitative PCR (qPCR) data, the quantification cycle (Cq) indicates the position of the amplification curve with respect to the cycle axis. Because Cq is directly related to the starting concentration of the target, and the difference in Cq values is related to the starting concentration ratio, the only results of qPCR analysis reported are often Cq, ΔCq or ΔΔCq values. However, reporting of Cq values ignores the fact that Cq values may differ between runs and machines, and, therefore, cannot be compared between laboratories. Moreover, Cq values are highly dependent on the PCR efficiency, which differs between assays and may differ between samples. Interpreting reported Cq values, assuming a 100% efficient PCR, may lead to assumed gene expression ratios that are 100-fold off. This review describes how differences in quantification threshold setting, PCR efficiency, starting material, PCR artefacts, pipetting errors and sampling variation are at the origin of differences and variability in Cq values and discusses the limits to the interpretation of observed Cq values. These issues can be avoided by calculating efficiency-corrected starting concentrations per reaction. The reporting of gene expression ratios and fold difference between treatments can then easily be based on these starting concentrations.
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