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Jo TS. Larger particle size distribution of environmental RNA compared to environmental DNA: a case study targeting the mitochondrial cytochrome b gene in zebrafish (Danio rerio) using experimental aquariums. Naturwissenschaften 2024; 111:18. [PMID: 38502308 DOI: 10.1007/s00114-024-01904-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
Environmental RNA (eRNA) analysis is conventionally expected to infer physiological information about organisms within their ecosystems, whereas environmental DNA (eDNA) analysis only infers their presence and abundance. Despite the promise of eRNA application, basic research on eRNA characteristics and dynamics is limited. The present study conducted aquarium experiments using zebrafish (Danio rerio) to estimate the particle size distribution (PSD) of eRNA in order to better understand the persistence state of eRNA particles. Rearing water samples were sequentially filtered using different pore-size filters, and the resulting size-fractioned mitochondrial cytochrome b (CytB) eDNA and eRNA data were modeled with the Weibull complementary cumulative distribution function (CCDF) to estimate the parameters characterizing the PSDs. It was revealed that the scale parameter (α) was significantly higher (i.e., the mean particle size was larger) for eRNA than eDNA, while the shape parameter (β) was not significantly different between them. This result supports the hypothesis that most eRNA particles are likely in a protected, intra-cellular state, which mitigates eRNA degradation in water. Moreover, these findings also imply the heterogeneous dispersion of eRNA relative to eDNA and suggest an efficient method of eRNA collection using a larger pore-size filter. Further studies on the characteristics and dynamics of eRNA particles should be pursued in the future.
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Affiliation(s)
- Toshiaki S Jo
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-Ku, Tokyo, 102-0083, Japan.
- Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
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Sun D, Rozmoš M, Kotianová M, Hršelová H, Jansa J. Arbuscular mycorrhizal fungi suppress ammonia-oxidizing bacteria but not archaea across agricultural soils. Heliyon 2024; 10:e26485. [PMID: 38444950 PMCID: PMC10912043 DOI: 10.1016/j.heliyon.2024.e26485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
Arbuscular mycorrhizal (AM) fungi are supposedly competing with ammonia-oxidizing microorganisms (AO) for soil nitrogen in form of ammonium. Despite a few studies directly addressing AM fungal and AO interactions, mostly in artificial cultivation substrates, it is not yet clear whether AM fungi can effectively suppress AO in field soils containing complex indigenous microbiomes. To fill this knowledge gap, we conducted compartmentalized pot experiments using four pairs of cropland and grassland soils with varying physicochemical properties. To exclude the interference of roots, a fine nylon mesh was used to separate the rhizosphere and mesh bags, with the latter being filled with unsterile field soils. Inoculation of plants with AM fungus Rhizophagus irregularis LPA9 suppressed AO bacteria (AOB) but not archaea (AOA) in the soils, indicating how soil nitrification could be suppressed by AM fungal presence/activity. In addition, in rhizosphere filled with artificial substrate, AM inoculation did suppress both AOB and AOA, implying more complex interactions between roots, AO, and AM fungi. Besides, we also observed that indigenous AM fungi contained in the field soils eventually did colonize the roots of plants behind the root barrier, and that the extent of such colonization was higher if the soil has previously been taken from cropland than from grassland. Despite this, the effect of experimental AM fungal inoculation on suppression of indigenous AOB in the unsterile field soils did not vanish. It seems that studying processes at a finer temporal scale, using larger buffer zones between rhizosphere and mesh bags, and/or detailed characterization of indigenous AM fungal and AO communities would be needed to uncover further details of the biotic interactions between the AM fungi and indigenous soil AO.
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Affiliation(s)
- Daquan Sun
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Martin Rozmoš
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Michala Kotianová
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Hana Hršelová
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Jan Jansa
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
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Wen D, Chen J, Lin P, Pang J, Pang Y, Chen G, He Y, Yang H. Investigation of Circular RNA Expression Profiles in Ultrasound-guided Incomplete Radiofrequency Ablation Transplanted Tumor Models of Human Liver Cancer. Mol Biotechnol 2024:10.1007/s12033-024-01075-z. [PMID: 38281266 DOI: 10.1007/s12033-024-01075-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/12/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND Abnormally expressed circular RNAs (circRNAs) are associated with many diseases and have important biological effects on the regulation of gene expression. However, the circRNA expression profile in incomplete radiofrequency ablation (RFA)-treated liver cancer (LC) patients has not been characterized. This study investigated the potential biological effects of differentially expressed (DE) circRNAs in an incomplete RFA-treated transplantation tumor model of human LC. MATERIAL/METHODS A circRNA microarray was utilized to analyze changes in the circRNA expression profiles. CircRNA host gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were also conducted using computational biology. Quantitative real-time PCR (qPCR) was also performed on the selected DE-circRNAs to verify the reliability of the microarray. The circRNA/miRNA interactions were predicted by Arraystar software and confirmed by a dual-luciferase assay. RESULTS Following RFA incomplete ablation, 76 DE-circRNAs were detected (|fold change |>1.5, P-value < 0.05), 21 of which were upregulated and 55 of which were downregulated. Computational biological analysis revealed that the T-cell receptor signaling pathway was the most significantly enriched pathway of the genes related to altered expression, as indicated by enrichment of LCK, AKT3 and DLG1. PCR results for the upregulated hsa_circRNA_103595 and downregulated hsa_circRNA_001264 indicated that the circRNA microarray sequencing results were reliable. Double luciferase reporter assays confirmed that hsa-miR-185-3p was the target miRNA of hsa_circRNA_103595. CONCLUSIONS The current study confirmed the changes in the expression profiles of circRNAs in tumor transplantation models after incomplete ablation, these changes may play a crucial role in the pathophysiological process of residual cancer transplantation tumors. These findings could lead to new directions for investigating the molecular biological mechanisms underlying RFA-treated LC as well as new ideas for treating LC by regulating circRNAs.
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Affiliation(s)
- Dongyue Wen
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, P. R. China
| | - Jiamin Chen
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, P. R. China
| | - Peng Lin
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, P. R. China
| | - Jinshu Pang
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, P. R. China
| | - Yuyan Pang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Zhuang Autonomous Region, Nanning, Guangxi, P. R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Zhuang Autonomous Region, Nanning, Guangxi, P. R. China
| | - Yun He
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, P. R. China.
| | - Hong Yang
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, P. R. China.
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Che J, Chen BH, Xu L, Gao Y, Yue MM, Chen ZM, Zhang MJ, Shao ZJ. Establishment and Modification of Ninety-seven Pneumococcal Serotyping Assays Based on Quantitative Real-time Polymerase Chain Reaction. Biomed Environ Sci 2023; 36:787-799. [PMID: 37803892 DOI: 10.3967/bes2023.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/09/2023] [Indexed: 10/08/2023]
Abstract
Objective To establish and modify quantitative real-time polymerase chain reaction (qPCR)-based serotyping assays to distinguish 97 pneumococcal serotypes. Methods A database of capsular polysaccharide ( cps) loci sequences was generated, covering 97 pneumococcal serotypes. Bioinformatics analyses were performed to identify the cps loci structure and target genes related to different pneumococcal serotypes with specific SNPs. A total of 27 novel qPCR serotyping assay primers and probes were established based on qPCR, while 27 recombinant plasmids containing serotype-specific DNA sequence fragments were constructed as reference target sequences to examine the specificity and sensitivity of the qPCR assay. A panel of pneumococcal reference strains was employed to evaluate the capability of pneumococcal serotyping. Results A total of 97 pneumococcal serotyping assays based on qPCR were established and modified, which included 64 serotypes previously reported as well as an additional 33 serotypes. Twenty-seven novel qPCR serotyping target sequences were implemented in the pneumococcal qPCR serotyping system. A total of 97 pneumococcal serotypes, which included 52 individual serotypes and 45 serotypes belonging to 20 serogroups, could not be identified as individual serotypes. The sensitivity of qPCR assays based on 27 target sequences was 1-100 copies/µL. The specificity of the qPCR assays was 100%, which were tested by a panel of 90 serotypes of the pneumococcal reference strains. Conclusion A total of 27 novel qPCR assays were established and modified to analyze 97 pneumococcal serotypes.
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Affiliation(s)
- Jie Che
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Bo Han Chen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Li Xu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yuan Gao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Meng Meng Yue
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China;School of Public Health, Nanjing Medical University, Nanjing 210029, Jiangsu China
| | - Zi Man Chen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Mao Jun Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Zhu Jun Shao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China;School of Public Health, Nanjing Medical University, Nanjing 210029, Jiangsu China
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Esfandiari Z, Vakili B, Ahangarzadeh S, Esfahani SN, Shoaei P. Impact of Selenium Nanoparticle-Enriched Lactobacilli Feeding Against Escherichia coli O157:H7 Infection of BALB/c Mice. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10081-7. [PMID: 37145299 DOI: 10.1007/s12602-023-10081-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2023] [Indexed: 05/06/2023]
Abstract
The effectiveness of selenium nanoparticle (SeNP)-enriched Lactiplantibacillus plantarum and Lactobacillus acidophilus was studied against Shiga toxin-producing Escherichia coli O157:H7 infection on the intestinal fragments and kidney tissue of BALB/c mice. Gut microbiota-targeted bacteria and E. coli O157:H7 counts were obtained by qPCR and PCR. Histology of ileum, colon, and kidney tissues and Stx secretions were analyzed until one-week post-infection. Mice fed with SeNP Lpb. plantarum in the preinfection feeding groups have lower E. coli O157:H7 counts and lower intestinal damage than those in the infected group. The lowest mean fecal probiotic counts were in the L. acidophilus group (7.61 log 10). In pretreatment groups of SeNP L. acidophilus and L. acidophilus, the mean counts of bacteria decreased to 104 CFU/g by day 7. The lowest Stx copy number was demonstrated in SeNP Lpb. plantarum feeding groups' day 7 (P < 0.05). Feeding groups with SeNP Lpb. plantarum had significantly higher members of Lactobacilli in their fecal microbiota than the control group on day 7. It was clarified that Se-enriched Lpb. plantarum and L. acidophilus can be useful as a method of preventing STEC infections. The viability of STEC infection exposure to selenium-enriched Lactobacillus spp. was decreased more than for non-Se-enriched Lactobacillus spp.
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Affiliation(s)
- Zahra Esfandiari
- Department of Food Science and Technology, Nutrition and Food Security Research Center, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bahareh Vakili
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shahrzah Ahangarzadeh
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Salar Nasr Esfahani
- Department of Pathology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Parisa Shoaei
- Nosocomial Infection Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
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Pajič T. Testing for Factor V Leiden (FVL) and Prothrombin G20210A Genetic Variants. Methods Mol Biol 2023; 2663:233-251. [PMID: 37204714 DOI: 10.1007/978-1-0716-3175-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Laboratory testing for Factor V Leiden and Prothrombin G20210A genetic variants permits defining the increased relative risk for venous thromboembolism in selected patients. Laboratory DNA testing for these variants may be undertaken by a variety of methods, including fluorescence-based quantitative real-time PCR (qPCR). This is a rapid, simple, robust, and reliable method to identify genotypes of interest. This chapter describes the method that employs PCR amplification of the patient DNA region of interest and genotyping by allele-specific discrimination technology on a quantitative real-time PCR (qPCR) instrument.
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Affiliation(s)
- Tadej Pajič
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia.
- Faculty of Medicine, University of Maribor, Maribor, Slovenia.
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Jo TS, Tsuri K, Yamanaka H. Can nuclear aquatic environmental DNA be a genetic marker for the accurate estimation of species abundance? Naturwissenschaften 2022; 109:38. [PMID: 35861927 DOI: 10.1007/s00114-022-01808-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 06/22/2022] [Accepted: 07/11/2022] [Indexed: 12/19/2022]
Abstract
Environmental DNA (eDNA) analysis is a promising tool for the sensitive and effective monitoring of species distribution and abundance. Traditional eDNA analysis has targeted mitochondrial DNA (mtDNA) fragments due to their abundance in cells; however, the quantification may vary depending on cell type and physiology. Conversely, some recent eDNA studies have targeted multi-copy nuclear DNA (nuDNA) fragments, such as ribosomal RNA genes, in water, and reported a higher detectability and more rapid degradation than mitochondrial eDNA (mt-eDNA). These properties suggest that nuclear eDNA (nu-eDNA) may be useful for the accurate estimation of species abundance relative to mt-eDNA, but which remains unclear. In this study, we compiled previous studies and re-analyzed the relationships between mt- and nu-eDNA concentration and species abundance by comparing the R2 values of the linear regression. We then performed an aquarium experiment using zebrafish (Danio rerio) to compare the relationships across genetic regions, including single-copy nuDNA. We found more accurate relationships between multi-copy nu-eDNA and species abundance than mt-eDNA in these datasets, although the difference was not significant upon weighted-averaging the R2 values. Moreover, we compared the decay rate constants of zebrafish eDNA across genetic regions and found that multi-copy nu-eDNA degraded faster than mt-eDNA under pH 7, implying a quick turnover of multi-copy nu-eDNA in the field. Although further empirical studies of nu-eDNA applications are necessary to support our findings, this study provides the groundwork for improving the estimation accuracy of species abundance via eDNA analysis.
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Sherina V, McMurray HR, Powers W, Land H, Love TMT, McCall MN. Multiple imputation and direct estimation for qPCR data with non-detects. BMC Bioinformatics 2020; 21:545. [PMID: 33243147 PMCID: PMC7693525 DOI: 10.1186/s12859-020-03807-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/13/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Quantitative real-time PCR (qPCR) is one of the most widely used methods to measure gene expression. An important aspect of qPCR data that has been largely ignored is the presence of non-detects: reactions failing to exceed the quantification threshold and therefore lacking a measurement of expression. While most current software replaces these non-detects with a value representing the limit of detection, this introduces substantial bias in the estimation of both absolute and differential expression. Single imputation procedures, while an improvement on previously used methods, underestimate residual variance, which can lead to anti-conservative inference. RESULTS We propose to treat non-detects as non-random missing data, model the missing data mechanism, and use this model to impute missing values or obtain direct estimates of model parameters. To account for the uncertainty inherent in the imputation, we propose a multiple imputation procedure, which provides a set of plausible values for each non-detect. We assess the proposed methods via simulation studies and demonstrate the applicability of these methods to three experimental data sets. We compare our methods to mean imputation, single imputation, and a penalized EM algorithm incorporating non-random missingness (PEMM). The developed methods are implemented in the R/Bioconductor package nondetects. CONCLUSIONS The statistical methods introduced here reduce discrepancies in gene expression values derived from qPCR experiments in the presence of non-detects, providing increased confidence in downstream analyses.
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Affiliation(s)
- Valeriia Sherina
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Blvd., 14642, Rochester, NY, USA
| | - Helene R McMurray
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Ave., 14642, Rochester, NY, USA
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave., 14642, Rochester, NY, USA
| | - Winslow Powers
- Department of Biomedical Engineering, University of Rochester, 201 Robert B. Goergen Hall, 14627, Rochester, NY, USA
| | - Harmut Land
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Ave., 14642, Rochester, NY, USA
| | - Tanzy M T Love
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Blvd., 14642, Rochester, NY, USA
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Blvd., 14642, Rochester, NY, USA.
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Ave., 14642, Rochester, NY, USA.
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Zhang Y, Zhang Z, Wang Z, Wang Z, Wang C, Feng C, Yuan W, Lin X, Wu S. Development of a droplet digital PCR assay for sensitive detection of porcine circovirus 3. Mol Cell Probes 2018; 43:50-57. [PMID: 30468765 DOI: 10.1016/j.mcp.2018.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 01/26/2023]
Abstract
Porcine circovirus 3 (PCV3), a newly emerged circovirus, is associated with porcine dermatitis and nephropathy syndrome, reproductive failure and multi-systemic inflammation disease, and is widely distributed in pig populations worldwide. Therefore, developing specific diagnostic assays will be important for controlling this emerging pathogen. In this study, we developed a novel droplet digital PCR (ddPCR) assay targeting the PCV3 cap gene to improve the sensitivity of PCV3 detection. The established assay is highly specific to PCV3, and does not cross react with other important swine pathogens. The assay's detection limit was 1.68 ± 0.29 copies of PCV3 DNA per reaction (n = 8), an approximately 10-fold greater sensitivity than that of our previously developed quantitative real-time PCR (qPCR) assay for the same virus. The ddPCR assay results were highly reproducible, with intra- and inter-assay coefficient of variation values of <9.0%. Of the 239 archived pig tissue and serum samples, 42 tested positive for PCV3 by the ddPCR assay. Among the 42 positive samples, 31 tested positive by the qPCR assay. Notably, PCV3 was detected in the serum samples collected from commercially imported healthy boars from the US, France and the UK during 2011-2017. The overall agreement between the two assays was 95.39% (228/239). Furthermore, the linear regression analysis showed that the ddPCR and the qPCR results were significantly correlated with an R2 value of 0.9945. Collectively, these results indicate that the ddPCR assay is a robust diagnostic tool for sensitive detection of PCV3, even in samples with low viral loads.
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Affiliation(s)
- Yongning Zhang
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
| | - Zhou Zhang
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Zhanying Wang
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Zili Wang
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Caixia Wang
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Chunyan Feng
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Wanzhe Yuan
- College of Veterinary Medicine, Agricultural University of Hebei, Baoding, 071001, China
| | - Xiangmei Lin
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Shaoqiang Wu
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
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Zhao C, Chen Q, Li C, Yang J, Li C, Zhou Y, Liao J. The association of NF2 (neurofibromin 2) gene polymorphism and the risk of medulloblastomas. Neurol Sci 2018; 39:1175-1183. [PMID: 29637450 DOI: 10.1007/s10072-018-3327-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/13/2018] [Indexed: 02/05/2023]
Abstract
To explore the relationship between NF2 promoter gene mutation and the risk of medulloblastomas (MBs). We collected tissues from 16 MB patients and 7 age-matched non-MB controls. Gene sequencing, qPCR (real-time quantitative polymerase chain reaction), IHC (immunohistochemistry), and WB (Western blot) were used to analyze the changes in the NF2 gene sequence and expression between patients and controls. We found that NF2 promoter gene mutations occurred in MB patients. The NF2 mRNA expression was higher in the controls than in patients (p = 0.03 < 0.05); however, the results of IHC and WB demonstrated that the NF2 protein expression was significantly higher in patients than in the controls (IHC: p = 0.0001; WB: p = 0.01). There was no significant difference in the CRL4 mRNA and protein levels. In addition, NF2 protein was mainly expressed in the nucleus in MB patients, while the NF2 protein was mainly expressed in the cytoplasm in the controls. NF2 promoter mutations exist in MB patients. NF2 mRNA expression was higher in controls than patients; whereas NF2 protein level was higher in patients than in controls.
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Affiliation(s)
- Cailei Zhao
- Department of Biomedical Engineering, Xi'an Jiaotong University, Xi'an, No. 277, Yantaxi Road, Xi'an, 710061, China
- Department of Radiology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, No. 277, Yantaxi Road, Xi'an, 710061, China
- Department of Radiology, Shenzhen Children's Hospital, Shenzhen, China
| | - Qian Chen
- Department of Neurosurgery, Shenzhen Children's Hospital, Shenzhen, No. 7019, Yitian Road, Shenzhen, 518038, China.
| | - Chunde Li
- Department of Pediatric Neurosurgery, Beijing Tianan Hospital, China Capital Medical University, Beijing, China.
| | - Jian Yang
- Department of Radiology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, No. 277, Yantaxi Road, Xi'an, 710061, China.
| | - Cong Li
- Department of Neurosurgery, Shenzhen Children's Hospital, Shenzhen, No. 7019, Yitian Road, Shenzhen, 518038, China
| | - Yangyang Zhou
- Department of Radiology, Shenzhen Children's Hospital, Shenzhen, China
| | - Jianxiang Liao
- Department of Neurology, Shenzhen Children's Hospital, Shenzhen, No. 7019, Yitian Road, Shenzhen, 518038, China.
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Bukovská P, Bonkowski M, Konvalinková T, Beskid O, Hujslová M, Püschel D, Řezáčová V, Gutiérrez-Núñez MS, Gryndler M, Jansa J. Utilization of organic nitrogen by arbuscular mycorrhizal fungi-is there a specific role for protists and ammonia oxidizers? Mycorrhiza 2018; 28:269-283. [PMID: 29455336 DOI: 10.1007/s00572-018-0825-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/07/2018] [Indexed: 05/14/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi can significantly contribute to plant nitrogen (N) uptake from complex organic sources, most likely in concert with activity of soil saprotrophs and other microbes releasing and transforming the N bound in organic forms. Here, we tested whether AM fungus (Rhizophagus irregularis) extraradical hyphal networks showed any preferences towards certain forms of organic N (chitin of fungal or crustacean origin, DNA, clover biomass, or albumin) administered in spatially discrete patches, and how the presence of AM fungal hyphae affected other microbes. By direct 15N labeling, we also quantified the flux of N to the plants (Andropogon gerardii) through the AM fungal hyphae from fungal chitin and from clover biomass. The AM fungal hyphae colonized patches supplemented with organic N sources significantly more than those receiving only mineral nutrients, organic carbon in form of cellulose, or nothing. Mycorrhizal plants grew 6.4-fold larger and accumulated, on average, 20.3-fold more 15N originating from the labeled organic sources than their nonmycorrhizal counterparts. Whereas the abundance of microbes (bacteria, fungi, or Acanthamoeba sp.) in the different patches was primarily driven by patch quality, we noted a consistent suppression of the microbial abundances by the presence of AM fungal hyphae. This suppression was particularly strong for ammonia oxidizing bacteria. Our results indicate that AM fungi successfully competed with the other microbes for free ammonium ions and suggest an important role for the notoriously understudied soil protists to play in recycling organic N from soil to plants via AM fungal hyphae.
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Affiliation(s)
- Petra Bukovská
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michael Bonkowski
- Cologne Biocenter, University of Cologne, Zülpicher Strasse 47b, 50674, Köln, Germany
| | - Tereza Konvalinková
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Olena Beskid
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Hujslová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - David Püschel
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Veronika Řezáčová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - María Semiramis Gutiérrez-Núñez
- Institute of Ecosystems and Sustainability Research, National Autonomous University of Mexico, Antigua Carretera a Pátzcuaro, 8701, C.P, 58190, Morelia, Michoacán, Mexico
| | - Milan Gryndler
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jan Jansa
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
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12
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Vasquez Y, Escobar MC, Saenz JS, Quiceno-Vallejo MF, Neculita CM, Arbeli Z, Roldan F. Effect of hydraulic retention time on microbial community in biochemical passive reactors during treatment of acid mine drainage. Bioresour Technol 2018; 247:624-632. [PMID: 28988048 DOI: 10.1016/j.biortech.2017.09.144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 06/07/2023]
Abstract
The effect of hydraulic retention time (HRT) on the microbial community during acid mine drainage (AMD) treatment was investigated. Physicochemical and molecular (illumina and qPCR) analyses were performed on reactive mixtures collected from seven bioreactors in three-operation period (8, 17 and 36weeks). Long HRT (4day) favored the relative abundance of SRB, causing the increase of residual sulfides and short HRT (1day) affected the anaerobic conditions of the bioreactors and favored the presence the acidophilic chemolithotrophic microorganisms. Besides qPCR indicated that genes related to cellulose degradation were present in low copy numbers and were affected by the HRT. Finally, environmental factors (pH, organic source, metal sulfides, and sulfate concentrations) had significant impact on relative abundance of the phylogenetic lineages, rather than the types of lineages present in the reactive mixture. The findings of this study indicate that HRT affects the stability of passive bioreactors and their microbial communities.
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Affiliation(s)
- Yaneth Vasquez
- Departamento de Ciencias Naturales, Facultad de Ingeniería y Ciencias Básicas, Universidad Central, Calle 21 No. 4-40, Bogota, Colombia; Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, Cra. 7 No. 40-62, Bogota, Colombia.
| | - Maria C Escobar
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, Cra. 7 No. 40-62, Bogota, Colombia
| | - Johan S Saenz
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, Cra. 7 No. 40-62, Bogota, Colombia
| | - Maria F Quiceno-Vallejo
- Departamento de Ciencias Naturales, Facultad de Ingeniería y Ciencias Básicas, Universidad Central, Calle 21 No. 4-40, Bogota, Colombia
| | - Carmen M Neculita
- Canada Research Chair in Treatment of Contaminated Mine Water, Research Institute on Mines and Environment (RIME), University of Quebec in Abitibi-Temiscamingue (UQAT), 445 Boulevard de l'Universite, Rouyn-Noranda, QC J9X 5E4, Canada
| | - Ziv Arbeli
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, Cra. 7 No. 40-62, Bogota, Colombia
| | - Fabio Roldan
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, Cra. 7 No. 40-62, Bogota, Colombia
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13
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Wang L, Chen Y, Wang S, Xue H, Su Y, Yang J, Li X. Identification of candidate genes involved in the sugar metabolism and accumulation during pear fruit post-harvest ripening of 'Red Clapp's Favorite' ( Pyrus communis L.) by transcriptome analysis. Hereditas 2017; 155:11. [PMID: 28943832 PMCID: PMC5609059 DOI: 10.1186/s41065-017-0046-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/11/2017] [Indexed: 01/08/2023] Open
Abstract
Background Pear (Pyrus spp.) is a popular fruit that is commercially cultivated in most temperate regions. In fruits, sugar metabolism and accumulation are important factors for fruit organoleptic quality. Post-harvest ripening is a special feature of ‘Red Clapp’s Favorite’. Results In this study, transcriptome sequencing based on the Illumina platform generated 23.8 - 35.8 million unigenes of nine cDNA libraries constructed using RNAs from the ‘Red Clapp’s Favorite’ pear variety with different treatments, in which 2629 new genes were discovered, and 2121 of them were annotated. A total of 2146 DEGs, 3650 DEGs, 1830 DEGs from each comparison were assembled. Moreover, the gene expression patterns of 8 unigenes related to sugar metabolism revealed by qPCR. The main constituents of soluble sugars were fructose and glucose after pear fruit post-harvest ripening, and five unigenes involved in sugar metabolism were discovered. Conclusions Our study not only provides a large-scale assessment of transcriptome resources of ‘Red Clapp’s Favorite’ but also lays the foundation for further research into genes correlated with sugar metabolism. Electronic supplementary material The online version of this article (10.1186/s41065-017-0046-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Long Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Weilai Road South End, Zhengzhou, Henan 450009 China
| | - Yun Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Weilai Road South End, Zhengzhou, Henan 450009 China
| | - Suke Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Weilai Road South End, Zhengzhou, Henan 450009 China
| | - Huabai Xue
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Weilai Road South End, Zhengzhou, Henan 450009 China
| | - Yanli Su
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Weilai Road South End, Zhengzhou, Henan 450009 China
| | - Jian Yang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Weilai Road South End, Zhengzhou, Henan 450009 China
| | - Xiugen Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Weilai Road South End, Zhengzhou, Henan 450009 China
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14
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Steinhäuser SS, Andrésson ÓS, Pálsson A, Werth S. Fungal and cyanobacterial gene expression in a lichen symbiosis: Effect of temperature and location. Fungal Biol 2016; 120:1194-208. [PMID: 27647237 DOI: 10.1016/j.funbio.2016.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 05/27/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Organisms have evolved different cellular mechanisms to deal with environmental stress, primarily through complex molecular mechanisms including protein refolding and DNA repair. As mutualistic symbioses, lichens offer the possibility of analyzing molecular stress responses in a particularly tight interspecific relationship. We study the widespread cyanolichen Peltigera membranacea, a key player in carbon and nitrogen cycling in terrestrial ecosystems at northern latitudes. We ask whether increased temperature is reflected in mRNA levels of selected damage control genes, and do the response patterns show geographical associations? Using real-time PCR quantification of 38 transcripts, differential expression was demonstrated for nine cyanobacterial and nine fungal stress response genes (plus the fungal symbiosis-related lec2 gene) when the temperature was increased from 5 °C to 15 °C and 25 °C. Principle component analysis (PCA) revealed two gene groups with different response patterns. Whereas a set of cyanobacterial DNA repair genes and the fungal lec2 (PC1 group) showed an expression drop at 15 °C vs. 5 °C, most fungal candidates (PC2 group) showed increased expression at 25 °C vs. 5 °C. PC1 responses also correlated with elevation. The correlated downregulation of lec2 and cyanobacterial DNA repair genes suggests a possible interplay between the symbionts warranting further studies.
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Affiliation(s)
- Sophie S Steinhäuser
- Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland
| | - Ólafur S Andrésson
- Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland
| | - Arnar Pálsson
- Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland
| | - Silke Werth
- Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland; Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria.
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15
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Shu D, He Y, Yue H, Wang Q. Microbial structures and community functions of anaerobic sludge in six full-scale wastewater treatment plants as revealed by 454 high-throughput pyrosequencing. Bioresour Technol 2015; 186:163-172. [PMID: 25817026 DOI: 10.1016/j.biortech.2015.03.072] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/12/2015] [Accepted: 03/14/2015] [Indexed: 05/19/2023]
Abstract
The microbial communities and abundance in anaerobic sludge from 4 industrial and 2 municipal wastewater treatment plants were investigated using 454 pyrosequencing technology in this study. A total of 5482-8692 high-quality reads of 16S rRNA V3-V5 regions were obtained. Taxonomic analysis using QIIME and RDP classifier found that Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes were the most abundant phyla in these samples. Furthermore, real-time PCR was used to validate the absolute abundance of these 16S rRNAs and some functional genes, including total bacteria, anammox bacteria, NOB (Nitrobacter, Nitrospira), AOA amoA, AOB amoA, nosZ, nirS, nirK, narG, napA, nrfA, mcrA and dsrA. Multivariate linear regression analysis indicated that AOA might be mixotrophic. Finally, redundancy analysis was used to reveal the relationships between operation parameters and microbial communities. Results showed that the coexistence of anammox, denitrification and DNRA could be useful for the simultaneous removal of nitrogen and organic matter.
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Affiliation(s)
- Duntao Shu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, 710049 Shaanxi, China
| | - Yanling He
- School of Human Settlements & Civil Engineering, Xi'an Jiaotong University, 710049 Shaanxi, China.
| | - Hong Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Qingyi Wang
- School of Chemical Engineering & Technology, Xi'an Jiaotong University, 710049 Shaanxi, China
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16
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Jang HM, Ha JH, Park JM, Kim MS, Sommer SG. Comprehensive microbial analysis of combined mesophilic anaerobic-thermophilic aerobic process treating high-strength food wastewater. Water Res 2015; 73:291-303. [PMID: 25689817 DOI: 10.1016/j.watres.2015.01.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/27/2015] [Accepted: 01/28/2015] [Indexed: 06/04/2023]
Abstract
A combined mesophilic anaerobic-thermophilic aerobic process was used to treat high-strength food wastewater in this study. During the experimental period, most of solid residue from the mesophilic anaerobic reactor (R1) was separated by centrifugation and introduced into the thermophilic aerobic reactor (R2) for further digestion. Then, thermophilic aerobically-digested sludge was reintroduced into R1 to enhance reactor performance. The combined process was operated with two different Runs: Run I with hydraulic retention time (HRT) = 40 d (corresponding OLR = 3.5 kg COD/m(3) d) and Run II with HRT = 20 d (corresponding OLR = 7 kg COD/m(3)). For a comparison, a single-stage mesophilic anaerobic reactor (R3) was operated concurrently with same OLRs and HRTs as the combined process. During the overall digestion, all reactors showed high stability without pH control. The combined process demonstrated significantly higher organic matter removal efficiencies (over 90%) of TS, VS and COD and methane production than did R3. Quantitative real-time PCR (qPCR) results indicated that higher populations of both bacteria and archaea were maintained in R1 than in R3. Pyrosequencing analysis revealed relatively high abundance of phylum Actinobacteria in both R1 and R2, and a predominance of phyla Synergistetes and Firmicutes in R3 during Run II. Furthermore, R1 and R2 shared genera (Prevotella, Aminobacterium, Geobacillus and Unclassified Actinobacteria), which suggests synergy between mesophilic anaerobic digestion and thermophilic aerobic digestion. For archaea, in R1 methanogenic archaea shifted from genus Methanosaeta to Methanosarcina, whereas genera Methanosaeta, Methanobacterium and Methanoculleus were predominant in R3. The results demonstrated dynamics of key microbial populations that were highly consistent with an enhanced reactor performance of the combined process.
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Affiliation(s)
- Hyun Min Jang
- School of Environmental Science and Engineering, Pohang University of Science and Technology, 77, Cheongam-Ro, Pohang 790-784, Republic of Korea
| | - Jeong Hyub Ha
- School of Environmental Science and Engineering, Pohang University of Science and Technology, 77, Cheongam-Ro, Pohang 790-784, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77, Cheongam-Ro, Pohang 790-784, Republic of Korea.
| | - Jong Moon Park
- School of Environmental Science and Engineering, Pohang University of Science and Technology, 77, Cheongam-Ro, Pohang 790-784, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77, Cheongam-Ro, Pohang 790-784, Republic of Korea; Division of Advanced Nuclear Engineering, Pohang University of Science and Technology, 77, Cheongam-Ro, Pohang 790-784, Republic of Korea.
| | - Mi-Sun Kim
- Biomass and Waste Energy Laboratory, Korea Institute of Energy Research, 152 Gajeong-ro, Yuseong-gu, Daejeon 305-343, Republic of Korea
| | - Sven G Sommer
- Institute of Chemical Engineering, Biotechnology and Environmental Technology, Faculty of Engineering, University of Southern Denmark, Niels Bohrs Allé 1, DK-5230 Odense M, Denmark
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17
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Jang HM, Kim JH, Ha JH, Park JM. Bacterial and methanogenic archaeal communities during the single-stage anaerobic digestion of high-strength food wastewater. Bioresour Technol 2014; 165:174-182. [PMID: 24613673 DOI: 10.1016/j.biortech.2014.02.028] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/06/2014] [Accepted: 02/09/2014] [Indexed: 05/28/2023]
Abstract
Single-stage anaerobic digestion (AD) was operated to treat high-strength food wastewater (FWW) derived from food waste recycling facilities at two different organic loading rates (OLRs) of 3.5 (Phase I) and 7 (Phase II) kgCOD/m(3)d. Changes in composition of microbial communities were investigated using quantitative real-time PCR (qPCR) and barcoded-pyrosequencing. At the high FWW loading rate, AD showed efficient performance (i.e., organic matter removal and methane production). Bacterial communities were represented by the phyla Bacteroidetes, Firmicutes, Synergistetes and Actinobacteria. During the entire digestion process, the relative abundance phylum Chloroflexi decreased significantly. The qPCR analysis demonstrated that the methanogenic communities shifted from aceticlastic (Methanosarcinales) to hydrogenotrophic methanogens (Methanobacteriales and Methanomicrobiales) with high increase in the proportion of syntrophic bacterial communities. Canonical correspondence analysis revealed a strong relationship between reactor performance and microbial community shifts.
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Affiliation(s)
- Hyun Min Jang
- School of Environmental Science and Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, South Korea
| | - Ji Hyun Kim
- School of Environmental Science and Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, South Korea
| | - Jeong Hyub Ha
- School of Environmental Science and Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, South Korea
| | - Jong Moon Park
- Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, South Korea; Division of Advanced Nuclear Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, South Korea.
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18
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Zinzow-Kramer WM, Horton BM, Maney DL. Evaluation of reference genes for quantitative real-time PCR in the brain, pituitary, and gonads of songbirds. Horm Behav 2014; 66:267-75. [PMID: 24780145 PMCID: PMC4131286 DOI: 10.1016/j.yhbeh.2014.04.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 04/01/2014] [Accepted: 04/20/2014] [Indexed: 01/18/2023]
Abstract
Quantitative real-time PCR (qPCR) is becoming a popular tool for the quantification of gene expression in the brain and endocrine tissues of songbirds. Accurate analysis of qPCR data relies on the selection of appropriate reference genes for normalization, yet few papers on songbirds contain evidence of reference gene validation. Here, we evaluated the expression of ten potential reference genes (18S, ACTB, GAPDH, HMBS, HPRT, PPIA, RPL4, RPL32, TFRC, and UBC) in brain, pituitary, ovary, and testis in two species of songbirds: zebra finch and white-throated sparrow. We used two algorithms, geNorm and NormFinder, to assess the stability of these reference genes in our samples. We found that the suitability of some of the most popular reference genes for target gene normalization in mammals, such as 18S, depended highly on tissue type. Thus, they are not the best choices for brain and gonad in these songbirds. In contrast, we identified alternative genes, such as HPRT, RPL4 and PPIA, that were highly stable in brain, pituitary, and gonad in these species. Our results suggest that the validation of reference genes in mammals does not necessarily extrapolate to other taxonomic groups. For researchers wishing to identify and evaluate suitable reference genes for qPCR in songbirds, our results should serve as a starting point and should help increase the power and utility of songbird models in behavioral neuroendocrinology.
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Affiliation(s)
| | - Brent M Horton
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Donna L Maney
- Department of Psychology, Emory University, Atlanta, GA, USA
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