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Wu Y, Li H, Miao Y, Peng J, Wei H. Effects of Methionine Restriction from Different Sources on Sperm Quality in Aging Mice. Nutrients 2023; 15:4782. [PMID: 38004176 PMCID: PMC10675477 DOI: 10.3390/nu15224782] [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: 09/05/2023] [Revised: 11/07/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Decreased sperm quality causing poor pregnancy outcomes in aging males is a common problem. The aim of this study was to investigate the ameliorative effect of methionine restriction on sperm quality in aging mice, using methionine or 2-hydroxy-4-(methylthio)butanoate (HMTBA) as the methionine source, with a view to providing nutritional strategies to mitigate the decline in sperm quality in aging livestock. Fifty-one 6-week-old male mice were randomly divided into four groups: the non-aging group (NA, 0.86% methionine), the control diet group (CD, 0.86% methionine), the methionine-restricted group (MR, 0.17% methionine) and the HMTBA-restricted group (HR, 0.17% methionine). The mice in the CD, MR and HR groups were injected with a daily dose of 0.25 mL/20 g body weight of 10% D-galactose to establish an aging model. The test period was 42 days. The results showed that aging mice in the CD group had impaired testicular morphology and significantly decreased sperm quality compared to those in the NA group. Aging mice in the MR and HR groups showed attenuated impaired testicular morphology and improved sperm quality, especially sperm acrosomal integrity and membrane integrity, compared to mice in the CD group. In addition, mice in the MR and HR groups had reduced testicular inflammation and oxidative stress, increased spermidine levels, and reduced sperm RNA N6-methyladenosine (m6A) and DNA 5-methylcytosine (5mC) levels. Spermidine levels were positively correlated, whereas sperm RNA m6A and DNA 5mC levels were negatively correlated with sperm quality parameters. Our study suggests that methionine restriction alleviates the decline in sperm quality in aging mice, which may be related to changes in methionine metabolism and inhibition of sperm DNA and RNA methylation.
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Affiliation(s)
- Yinghui Wu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.W.); (Y.M.); (J.P.)
| | - Hao Li
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.W.); (Y.M.); (J.P.)
| | - Yueyue Miao
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.W.); (Y.M.); (J.P.)
| | - Jian Peng
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.W.); (Y.M.); (J.P.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China
| | - Hongkui Wei
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.W.); (Y.M.); (J.P.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China
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2
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da Silva LAGA, Piacentini KC, Caramês ETDS, Silva NCC, Wawroszová S, Běláková S, Rocha LDO. Quantitative PCR (qPCR) for estimating the presence of Fusarium and its mycotoxins in barley grains. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2023; 40:1369-1387. [PMID: 37640447 DOI: 10.1080/19440049.2023.2250474] [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: 06/23/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Members within the Fusarium sambucinum species complex (FSAMSC) are able to produce mycotoxins, such as deoxynivalenol (DON), nivalenol (NIV), zearalenone (ZEN) and enniatins (ENNs) in food products. Consequently, alternative methods for assessing the levels of these mycotoxins are relevant for quick decision-making. In this context, qPCR based on key mycotoxin biosynthetic genes could aid in determining the toxigenic fungal biomass, and could therefore infer mycotoxin content. The aim of this study was to verify the use of qPCR as a technique for estimating DON, NIV, ENNs and ZEN, as well as Fusarium graminearum sensu lato (s.l.) and F. poae in barley grains. For this purpose, 53 barley samples were selected for mycobiota, mycotoxin and qPCR analyses. ENNs were the most frequent mycotoxins, followed by DON, ZEN and NIV. 83% of the samples were contaminated by F. graminearum s.l. and 51% by F. poae. Pearson correlation analysis showed significant correlations for TRI12/15-ADON with DON, ESYN1 with ENNs, TRI12/15-ADON and ZEB1 with F. graminearum s.l., as well as ESYN1 and TRI12/NIV with F. poae. Based on the results, qPCR could be useful for the assessment of Fusarium presence, and therefore, provide an estimation of its mycotoxins' levels from the same sample.
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Affiliation(s)
| | - Karim Cristina Piacentini
- Department of Food Science and Nutrition (DECAN), State University of Campinas (UNICAMP), Campinas, Brazil
| | | | | | - Simona Wawroszová
- Regional Department Brno, Central Institute for Supervising and Testing in Agriculture, National Reference Laboratory, Brno, Czech Republic
| | - Sylvie Běláková
- Malting Institute Brno, Research Institute of Brewing and Malting, Brno, Czech Republic
| | - Liliana de Oliveira Rocha
- Department of Food Science and Nutrition (DECAN), State University of Campinas (UNICAMP), Campinas, Brazil
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3
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Ulluwishewa D, Mullaney J, Adam K, Claycomb R, Anderson RC. A bioactive bovine whey protein extract improves intestinal barrier function in vitro. JDS COMMUNICATIONS 2022; 3:387-392. [PMID: 36465501 PMCID: PMC9709612 DOI: 10.3168/jdsc.2022-0245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/30/2022] [Indexed: 06/17/2023]
Abstract
The human intestine plays an important role as a barrier against the ingress of pathogens and other harmful antigens. Accordingly, proper regulation of the intestinal barrier is essential for optimal health. Intestinal barrier function is regulated in part by the interactions between dietary compounds and the intestinal immune system. Bioactive whey proteins from bovine milk (such as lactoferrin, lactoperoxidase, and immunoglobulins) are known to exert a range of physiological functions, including modulation of the immune system, and thus have the potential to regulate intestinal barrier function. While the effects of individual whey proteins on intestinal barrier function have been studied to some extent, less is known about the potentially synergistic properties of whey protein mixtures. Here we investigated the effects of a bioactive bovine whey protein (BWP) extract containing all whey proteins with an isoelectric point >6.8 on intestinal barrier function in vitro. Intestinal epithelial cell (Caco-2) monolayers were treated with BWP before measuring the barrier integrity over 48 h by means of trans-epithelial electrical resistance (TEER). Treatment of epithelial monolayers with 1 mg/mL BWP resulted in an increase in TEER compared with untreated epithelial monolayers. To determine whether BWP could mitigate immune-mediated intestinal barrier dysfunction, we challenged differentiated Caco-2 cell monolayers with tumor necrosis factor α (TNFα) to obtain an in vitro model of a "leaky" intestinal epithelium. The TNFα challenge led to a decrease in TEER over time across untreated control monolayers, indicating a loss of barrier function. This loss of barrier function was mitigated in monolayers treated with 1 mg/mL BWP, but not monolayers treated with the equivalent amount of lactoferrin present in 1 mg/mL BWP. These data suggest that naturally co-occurring bioactive proteins together may enhance intestinal barrier integrity and protect against inflammation-induced barrier dysfunction to a greater extent than lactoferrin alone. Further work is required to determine the key proteins and protein combinations within BWP, and the mechanisms through which BWP modulates intestinal barrier function.
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Affiliation(s)
- Dulantha Ulluwishewa
- AgResearch Ltd., Te Ohu Rangahau Kai, Palmerston North 4474, New Zealand
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand
| | - Jane Mullaney
- AgResearch Ltd., Te Ohu Rangahau Kai, Palmerston North 4474, New Zealand
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand
- High-Value Nutrition National Science Challenge, Auckland 1142, New Zealand
| | | | | | - Rachel C. Anderson
- AgResearch Ltd., Te Ohu Rangahau Kai, Palmerston North 4474, New Zealand
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4
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Characterization of a GH5 endoxylanase from Penicillium funiculosum and its synergism with GH16 endo-1,3(4)-glucanase in saccharification of sugarcane bagasse. Sci Rep 2022; 12:17219. [PMID: 36241677 PMCID: PMC9568505 DOI: 10.1038/s41598-022-21529-1] [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: 07/02/2022] [Accepted: 09/28/2022] [Indexed: 01/06/2023] Open
Abstract
The production of second-generation fuels from lignocellulosic residues such as sugarcane bagasse (SCB) requires the synergistic interaction of key cellulose-degrading enzymes and accessory proteins for their complete deconstruction to useful monomeric sugars. Here, we recombinantly expressed and characterized unknown GH5 xylanase from P. funiculosum (PfXyn5) in Pichia pastoris, which was earlier found in our study to be highly implicated in SCB saccharification. The PfXyn5 has a molecular mass of ~ 55 kDa and showed broad activity against a range of substrates like xylan, xyloglucan, laminarin and p-nitrophenyl-β-D-xylopyranoside, with the highest specific activity of 0.7 U/mg against xylan at pH 4.5 and 50 °C. Analysis of the degradation products of xylan and SCB by PfXyn5 showed significant production of xylooligosaccharides (XOS) with a degree of polymerization (DP) ranging from two (DP2) to six (DP6), thus, suggesting that the PfXyn5 is an endo-acting enzyme. The enzyme synergistically improved the saccharification of SCB when combined with the crude cellulase cocktail of P. funiculosum with a degree of synergism up to 1.32. The PfXyn5 was further expressed individually and simultaneously with a notable GH16 endoglucanase (PfEgl16) in a catabolite-derepressed strain of P. funiculosum, PfMig188, and the saccharification efficiency of the secretomes from the resulting transformants were investigated on SCB. The secretome of PfMig188 overexpressing Xyn5 or Egl16 increased the saccharification of SCB by 9% or 7%, respectively, over the secretome of PfMig188, while the secretome of dual transformant increased SCB saccharification by ~ 15% at the same minimal protein concentration.
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Huwait E, Awaji SM, Kumosani TA, Barbour EK, Abulnaja KO, Moselhy SS. Ruthana date extract inhibited proliferation of human hepatocellular carcinoma (HepG2) cells by modulation of BAX gene. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:63369-63378. [PMID: 35459999 DOI: 10.1007/s11356-022-20240-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/09/2022] [Indexed: 06/14/2023]
Abstract
Cancer response to chemotherapeutic agents and its side effects remain a challenge for the development of new anticancer compounds. Dates are consumed worldwide due to their high nutritional value. We investigated the cytotoxicity and expression of the proapoptotic BAX gene in human hepatocellular carcinoma (HepG2) cells treated with Ruthana date ethanolic extract (RDE). The RDE ingredients analyzed by GC/MS and HepG2 cells were treated with different concentrations of RDE for 24, 48, and 72 h. Cytotoxicity, cell viability, DNA fragmentation, and BAX expression were determined. The GC/MS analysis of RDE showed its high content of quercetin, myricetin kaempferol, thymine, and catechol as the most active ingredients. HepG2 treated with RDE showed a significant change in morphological characteristics related to cell death. The antiproliferative activity determined by WST-1 demonstrated that RDE significantly reduced cell viability. Cells treated with RDE (10-60 mg) showed gradual DNA fragmentation in a dose-dependent manner. Gene expression analysis showed upregulation of BAX at 30 mg/ml of RDE (p < 0.001). However, it showed downregulation at (40-60 mg/ml) as compared to control. Our findings indicated that RDE exert cytotoxicity against HepG2 cells due to its high content of flavonoids. This effect through DNA fragmentation and activation of the proapoptotic BAX gene.
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Affiliation(s)
- Etimad Huwait
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Seham M Awaji
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Taha A Kumosani
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Production of Natural Products For Industrial Purposes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
- Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Elie K Barbour
- Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- R and D Department, Opticon Hygiene Consulting, 78807, Oechsli, Switzerland
| | - Khalid O Abulnaja
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Bioactive Natural Products Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Said S Moselhy
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt.
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6
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Swamy G, Salo P, Duncan N, Jirik F, Matyas J. IL‐1Ra
deficiency accelerates intervertebral disc degeneration in
C57BL6J
mice. JOR Spine 2022; 5:e1201. [PMID: 35783913 PMCID: PMC9238285 DOI: 10.1002/jsp2.1201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/24/2022] [Accepted: 03/29/2022] [Indexed: 11/26/2022] Open
Abstract
The expression of Interleukin‐1ß (IL‐1ß) and its antagonist and Interleukin‐1 receptor antagonist (IL‐1Ra) are correlated with greater human intervertebral disc (IVD) degeneration, suggesting that elevated IL‐1β activity promotes disc degeneration. Many in vitro studies support such a mechanistic relationship, whereas few in vivo investigations have been reported. The present study tests the effect of increased IL‐1β activity on intervertebral disc in mice with an IL‐1Ra gene deletion. IL‐1Ra−/− mice and wild‐type (WT) C57Bl6J mice were examined at 3 and 12 months of age. Caudal IVD segments were evaluated for disc degeneration by histopathology, functional testing, and inflammatory gene expression relevant to IL‐1β pathways. To test differences in injury response, pinprick annular puncture was performed on IL‐1Ra−/− and WT mice and evaluated similarly. IL‐1Ra−/− IVDs had significantly worse histopathology at 3 months compared to WT controls, but not at 12 months. IL‐1Ra−/− IVDs exhibited significantly more viscous mechanical properties than WT IVDs. qPCR revealed downregulation of inflammatory genes at 3 and 12 months in IL‐1Ra−/− IVDs, with concomitant downregulation of anabolic and catabolic genes. Annular puncture yielded no appreciable differences between 2‐week and 6‐week post‐injured WT and IL1‐Ra−/− IVDs in histopathology or biomechanics, but inflammatory gene expression was sharply downregulated in IL‐1Ra−/− mice at 2 weeks, returning by 6 weeks post injury. In the present study, IL‐1Ra deletion resulted in increased IVD histopathology, inferior biomechanics, and transiently decreased pro‐inflammatory cytokine gene expression. The histopathology of IL‐1Ra−/− IVDs on a C57BL/6J background is less severe than a previous report of IL1Ra−/− on a BALB/c background, yet both strains exhibit IVD degeneration, reinforcing a mechanistic role of IL‐1β signaling in IVD pathobiology. Despite a pro‐inflammatory environment, the annular puncture was no worse in IL‐1Ra−/− mice, suggesting that response to injury involves pathways other than inflammation. Overall, this study supports the hypothesis that IL‐1β‐driven inflammation is important in IVD degeneration.
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Affiliation(s)
- Ganesh Swamy
- Cumming School of Medicine McCaig Institute of Bone and Joint Health University of Calgary Calgary Alberta Canada
| | - Paul Salo
- Department of Surgery Cumming School of Medicine Calgary Alberta Canada
| | - Neil Duncan
- Department of Civil Engineering Schulich School of Engineering Calgary Alberta Canada
| | - Frank Jirik
- Department of Medicine Health Research Innovation Centre Calgary Alberta Canada
| | - John Matyas
- Department of Comparative Biology & Experimental Medicine Faculty of Veterinary Medicine University of Calgary Calgary Alberta Canada
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7
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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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Fackler N, Heffernan J, Juminaga A, Doser D, Nagaraju S, Gonzalez-Garcia RA, Simpson SD, Marcellin E, Köpke M. Transcriptional control of Clostridium autoethanogenum using CRISPRi. Synth Biol (Oxf) 2021; 6:ysab008. [PMID: 33928195 PMCID: PMC8062849 DOI: 10.1093/synbio/ysab008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/15/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
Gas fermentation by Clostridium autoethanogenum is a commercial process for the sustainable biomanufacturing of fuels and valuable chemicals using abundant, low-cost C1 feedstocks (CO and CO2) from sources such as inedible biomass, unsorted and nonrecyclable municipal solid waste, and industrial emissions. Efforts toward pathway engineering and elucidation of gene function in this microbe have been limited by a lack of genetic tools to control gene expression and arduous genome engineering methods. To increase the pace of progress, here we developed an inducible CRISPR interference (CRISPRi) system for C. autoethanogenum and applied that system toward transcriptional repression of genes with ostensibly crucial functions in metabolism.
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Affiliation(s)
| | - James Heffernan
- Australian Institute for Bioengineering and Nanotechnology, ARC Centre of Excellence in Synthetic Biology & Metabolomics Australia, The University of Queensland, Brisbane, Queensland, 4072 Australia
| | | | | | | | - R Axayacatl Gonzalez-Garcia
- Australian Institute for Bioengineering and Nanotechnology, ARC Centre of Excellence in Synthetic Biology & Metabolomics Australia, The University of Queensland, Brisbane, Queensland, 4072 Australia
| | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, ARC Centre of Excellence in Synthetic Biology & Metabolomics Australia, The University of Queensland, Brisbane, Queensland, 4072 Australia
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Unger L, Abril C, Gerber V, Jagannathan V, Koch C, Hamza E. Diagnostic potential of three serum microRNAs as biomarkers for equine sarcoid disease in horses and donkeys. J Vet Intern Med 2021; 35:610-619. [PMID: 33415768 PMCID: PMC7848377 DOI: 10.1111/jvim.16027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are potential biomarkers for equine sarcoids (ES). OBJECTIVES To assess eca-miR-331, eca-miR-100, and eca-miR-1 as serum biomarkers for ES disease. ANIMALS Sixty-eight ES cases (56 horses, 12 donkeys), 69 tumor-free controls (60 horses, 9 donkeys), and 20 horses with other skin tumors. METHODS For this case-control study, expression of serum eca-miR-331, eca-miR-100, and eca-miR-1 in ES-affected equids was compared to tumor-free age-, sex-, and breed-matched control horses and donkeys with other skin tumors using reverse transcription quantitative PCR (polymerase chain reaction) for relative miRNA quantification. Biological, preanalytical, and clinical variable influences on miRNA expression were examined. Receiver operator characteristic (ROC) curve analyses were used to determine differences in miRNA expression between groups. RESULTS The expression of eca-miR-100 was affected by age (P = .003) and expression of eca-miR-100 and eca-miR-1 were affected by hemolysis (both P < .001). Eca-miR-331 was unaffected by biological variation, hemolysis, ES type, and disease severity. Eca-miR-331 concentrations were higher in ES-affected compared to tumor-free controls (P = .002). The ROC curve analysis indicated an area under the curve of 0.65 (P = .002) with a sensitivity of 60%, specificity of 71%, and positive and negative likelihood ratios of 2.1 and 0.56, respectively, to diagnose ES. Eca-miR-331 expression did not discriminate between horses with ES and other skin tumors. Expression of eca-miR-100 and eca-miR-1 was not different between groups. CONCLUSIONS AND CLINICAL IMPORTANCE Serum eca-miR-331 expression is neither sensitive nor specific enough as a single ES biomarker. If combined with other miRNAs, it may be helpful for ES diagnosis.
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Affiliation(s)
- Lucia Unger
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine (ISME), Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
| | - Carlos Abril
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
| | - Vinzenz Gerber
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine (ISME), Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Christoph Koch
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine (ISME), Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
| | - Eman Hamza
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine (ISME), Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
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10
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Synergistic Action of a Lytic Polysaccharide Monooxygenase and a Cellobiohydrolase from Penicillium funiculosum in Cellulose Saccharification under High-Level Substrate Loading. Appl Environ Microbiol 2020; 86:AEM.01769-20. [PMID: 32978122 DOI: 10.1128/aem.01769-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/15/2020] [Indexed: 12/25/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are crucial industrial enzymes required in the biorefinery industry as well as in the natural carbon cycle. These enzymes, known to catalyze the oxidative cleavage of glycosidic bonds, are produced by numerous bacterial and fungal species to assist in the degradation of cellulosic biomass. In this study, we annotated and performed structural analysis of an uncharacterized LPMO from Penicillium funiculosum (PfLPMO9) based on computational methods in an attempt to understand the behavior of this enzyme in biomass degradation. PfLPMO9 exhibited 75% and 36% sequence identities with LPMOs from Thermoascus aurantiacus (TaLPMO9A) and Lentinus similis (LsLPMO9A), respectively. Furthermore, multiple fungal genetic manipulation tools were employed to simultaneously overexpress LPMO and cellobiohydrolase I (CBH1) in a catabolite-derepressed strain of Penicillium funiculosum, PfMig188 (an engineered variant of P. funiculosum), to improve its saccharification performance toward acid-pretreated wheat straw (PWS) at 20% substrate loading. The resulting transformants showed improved LPMO and CBH1 expression at both the transcriptional and translational levels, with ∼200% and ∼66% increases in ascorbate-induced LPMO and Avicelase activities, respectively. While the secretome of PfMig88 overexpressing LPMO or CBH1 increased the saccharification of PWS by 6% or 13%, respectively, over the secretome of PfMig188 at the same protein concentration, the simultaneous overexpression of these two genes led to a 20% increase in saccharification efficiency over that observed with PfMig188, which accounted for 82% saccharification of PWS under 20% substrate loading.IMPORTANCE The enzymatic hydrolysis of cellulosic biomass by cellulases continues to be a significant bottleneck in the development of second-generation biobased industries. While increasing efforts are being made to obtain indigenous cellulases for biomass hydrolysis, the high production cost of this enzyme remains a crucial challenge affecting its wide availability for the efficient utilization of cellulosic materials. This is because it is challenging to obtain an enzymatic cocktail with balanced activity from a single host. This report describes the annotation and structural analysis of an uncharacterized lytic polysaccharide monooxygenase (LPMO) gene in Penicillium funiculosum and its impact on biomass deconstruction upon overexpression in a catabolite-derepressed strain of P. funiculosum Cellobiohydrolase I (CBH1), which is the most important enzyme produced by many cellulolytic fungi for the saccharification of crystalline cellulose, was further overexpressed simultaneously with LPMO. The resulting secretome was analyzed for enhanced LPMO and exocellulase activities and the corresponding improvement in saccharification performance (by ∼20%) under high-level substrate loading using a minimal amount of protein.
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11
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Edmunds RC, Burrows D. Got Glycogen?: Development and Multispecies Validation of the Novel Preserve, Precipitate, Lyse, Precipitate, Purify (PPLPP) Workflow for Environmental DNA Extraction from Longmire's Preserved Water Samples. J Biomol Tech 2020; 31:125-150. [PMID: 33100918 DOI: 10.7171/jbt.20-3104-003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Unfiltered and filtered water samples can be used to collect environmental DNA (eDNA). We developed the novel "Preserve, Precipitate, Lyse, Precipitate, Purify" (PPLPP) workflow to efficiently extract eDNA from Longmire's preserved unfiltered and filtered water samples (44-100% recovery). The PPLPP workflow includes initial glycogen-aided isopropanol precipitation, guanidium hypochlorite and Triton X-100-based lysis, terminal glycogen-aided polyethylene glycol precipitation, and inhibitor purification. Three novel eDNA assays that exclusively target species invasive to Australia were also developed: Tilapia_v2_16S concurrently targets Oreochromis mossambicus (Mozambique tilapia) and Tilapia mariae (spotted tilapia) while R.marina_16S and C.caroliniana_matK discretely target Rhinella marina (cane toad) and Cabomba caroliniana (fanwort), respectively. All 3 assays were validated in silico before in vitro and in situ validations using PPLPP workflow extracted samples. PPLPP workflow was concurrently validated in vitro and in situ using all 3 assays. In vitro validations demonstrated that 1) glycogen inclusion increased extracellular DNA recovery by ∼48-fold compared with glycogen exclusion, 2) swinging-bucket centrifugation for 90 min at 3270 g is equivalent to fixed-angle centrifugation for 5-20 min at 6750 g, and 3) Zymo OneStep Inhibitor Removal Kit, Qiagen DNeasy PowerClean Pro Cleanup Kit, and silica-Zymo double purification provide effective inhibitor removal. In situ validation demonstrated 95.8 ± 2.8% (mean ± SEM) detectability across all 3 target species in Longmire's preserved unfiltered and filtered water samples extracted using the PPLPP workflow (without phenol:chloroform:isoamyl alcohol purification) after 39 d of incubation at room temperature and 50°C. PPLPP workflow is recommended for future temperate and tropical eDNA studies that use Longmire's to preserve unfiltered or filtered water samples.
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Affiliation(s)
- Richard C Edmunds
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), James Cook University, Townsville 4811, Queensland, Australia
| | - Damien Burrows
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), James Cook University, Townsville 4811, Queensland, Australia
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12
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Grembi JA, Mayer-Blackwell K, Luby SP, Spormann AM. High-Throughput Multiparallel Enteropathogen Detection via Nano-Liter qPCR. Front Cell Infect Microbiol 2020; 10:351. [PMID: 32766166 PMCID: PMC7381150 DOI: 10.3389/fcimb.2020.00351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/08/2020] [Indexed: 11/13/2022] Open
Abstract
Quantitative molecular diagnostic methods can effectively detect pathogen-specific nucleic acid sequences, but costs associated with multi-pathogen panels hinder their widespread use in research trials. Nano-liter qPCR (nL-qPCR) is a miniaturized tool for quantification of multiple targets in large numbers of samples based on assay parallelization on a single chip, with potentially significant cost-savings due to rapid throughput and reduced reagent volumes. We evaluated a suite of novel and published assays to detect 17 enteric pathogens using a commercially available nL-qPCR technology. Amplification efficiencies ranged from 88 to 98% (mean 91%) and were reproducible across four operators at two separate facilities. When applied to fecal material, assays were sensitive and selective (99.8% of DNA amplified were genes from the target organism). Due to nanofluidic volumes, detection limits were 1-2 orders of magnitude less sensitive for nL-qPCR than an enteric TaqMan Array Card (TAC). However, higher detection limits do not hinder detection of diarrhea-causing pathogen concentrations. Compared to TAC, nL-qPCR displayed 99% (95% CI 0.98, 0.99) negative percent agreement and 62% (95% CI 0.59, 0.65) overall positive percent agreement for presence of pathogens across diarrheal and non-diarrheal fecal samples. Positive percent agreement was 89% among samples with concentrations above the nL-qPCR detection limits. nL-qPCR assays showed an underestimation bias of 0.34 log10 copies/gram of stool [IQR -0.40, -0.28] compared with TAC. With 12 times higher throughput for a sixth of the per-sample cost of the enteric TAC, the nL-qPCR chip is a viable alternative for enteropathogen quantification for studies where other technologies are cost-prohibitive.
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Affiliation(s)
- Jessica A Grembi
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States
| | - Koshlan Mayer-Blackwell
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States
| | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, United States
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States.,Department of Chemical Engineering, Stanford University, Stanford, CA, United States
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13
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Circulating miR-181a-5p as a new biomarker for acute cellular rejection in heart transplantation. J Heart Lung Transplant 2020; 39:1100-1108. [PMID: 32654912 DOI: 10.1016/j.healun.2020.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/28/2020] [Accepted: 05/31/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Acute cellular rejection (ACR) is a major complication in heart transplantation (HTx). Endomyocardial biopsy is the reference method for early detection of ACR, but a new non-invasive approach is needed. Tentative candidates could be circulating microRNAs. This study aimed to discover and validate microRNAs in serum for ACR detection after HTx. METHODS This prospective, observational, single-center study included 121 HTx patients. ACR was graded according to International Society of Heart and Lung Transplantation classification (0R-3R). First, in the discovery phase, microRNA expression profile was carried out in serum samples from patients at pre-rejection, during, and post-rejection time (0RS1 → 2RS2` → 0RS3). Relative expression (2-∆Cq) of 179 microRNAs per sample was analyzed by reverse transcription quantitative polymerase chain reaction. Second, a microRNA with a significant rise and fall pattern during ACR was selected for the next validation phase, where it was analyzed (reverse transcription quantitative polymerase chain reaction) in serum samples from 2 groups of patients: the no-ACR group (0R grade) and the ACR group (≥2R grade). Finally, a sensitivity analysis (receiver operating characteristic curve) was done to assess microRNA accuracy for ACR detection in HTx. RESULTS A total of 21 ACR episodes (0RS1 → 2RS2 → 0RS3) with their respective serum samples (n = 63) were included in the discovery phase. Among the 179 microRNAs analyzed, only miR-181a-5p met the rise and fall criteria. In the validation phase, miR-181a-5p relative expression (2-∆Cq) in the ACR group (n = 45) was significantly overexpressed (p < 0.0001) vs the no-ACR group (n = 45). miR-181a-5p showed an area under the curve of 0.804 (95% confidence interval: 0.707-0.880); sensitivity and specificity of 78% and 76%, respectively; and a negative predicted value of 98%. CONCLUSIONS miR-185a-5p in serum is a candidate as a non-invasive ACR biomarker (area under the curve = 0.80 and negative predicted value = 98%). Thus, this biomarker could reduce the need for endomyocardial biopsies and the associated risks and costs of this invasive procedure.
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14
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Hiller CX, Hübner U, Fajnorova S, Schwartz T, Drewes JE. Antibiotic microbial resistance (AMR) removal efficiencies by conventional and advanced wastewater treatment processes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 685:596-608. [PMID: 31195321 DOI: 10.1016/j.scitotenv.2019.05.315] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/27/2023]
Abstract
The World Health Organization (WHO) has identified the spread of antibiotic resistance as one of the major risks to global public health. An important transfer route into the aquatic environment is the urban water cycle. In this paper the occurrence and transport of antibiotic microbial resistance in the urban water cycle are critically reviewed. The presence of antibiotic resistance in low impacted surface water is being discussed to determine background antibiotic resistance levels, which might serve as a reference for treatment targets in the absence of health-based threshold levels. Different biological, physical and disinfection/oxidation processes employed in wastewater treatment and their efficacy regarding their removal of antibiotic resistant bacteria and antibiotic resistance geness (ARGs) were evaluated. A more efficient removal of antibiotic microbial resistance abundances from wastewater effluents can be achieved by advanced treatment processes, including membrane filtration, ozonation, UV-irradiation or chlorination, to levels typically observed in urban surface water or low impacted surface water.
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Affiliation(s)
- C X Hiller
- Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany
| | - U Hübner
- Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany
| | - S Fajnorova
- Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany; Department of Water Technology and Environmental Engineering, University of Chemistry and Technology, Prague, Technická 5, 166 28 Praha, Czech Republic
| | - T Schwartz
- Karlsruhe Institute of Technology (KIT) - Campus North, Institute of Functional Interfaces (IFG), Microbiology at Natural and Technical Interfaces Department, 76021 Karlsruhe, Germany
| | - J E Drewes
- Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany.
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15
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Morenikeji OB, Akinyemi MO, Wheto M, Ogunshola OJ, Badejo AA, Chineke CA. Transcriptome profiling of four candidate milk genes in milk and tissue samples of temperate and tropical cattle. J Genet 2019. [DOI: 10.1007/s12041-019-1060-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Taylor SC, Nadeau K, Abbasi M, Lachance C, Nguyen M, Fenrich J. The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time. Trends Biotechnol 2019; 37:761-774. [PMID: 30654913 DOI: 10.1016/j.tibtech.2018.12.002] [Citation(s) in RCA: 352] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/30/2018] [Accepted: 12/07/2018] [Indexed: 12/20/2022]
Abstract
Quantitative PCR (qPCR) is one of the most common techniques for quantification of nucleic acid molecules in biological and environmental samples. Although the methodology is perceived to be relatively simple, there are a number of steps and reagents that require optimization and validation to ensure reproducible data that accurately reflect the biological question(s) being posed. This review article describes and illustrates the critical pitfalls and sources of error in qPCR experiments, along with a rigorous, stepwise process to minimize variability, time, and cost in generating reproducible, publication quality data every time. Finally, an approach to make an informed choice between qPCR and digital PCR technologies is described.
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Affiliation(s)
- Sean C Taylor
- Bio-Rad Laboratories Canada Inc., 1329 Meyerside Drive, Mississauga, Ontario L5T1C9, Canada.
| | - Katia Nadeau
- Bio-Rad Laboratories Canada Inc., 1329 Meyerside Drive, Mississauga, Ontario L5T1C9, Canada
| | - Meysam Abbasi
- Bio-Rad Laboratories Canada Inc., 1329 Meyerside Drive, Mississauga, Ontario L5T1C9, Canada
| | - Claude Lachance
- Bio-Rad Laboratories Canada Inc., 1329 Meyerside Drive, Mississauga, Ontario L5T1C9, Canada
| | - Marie Nguyen
- Bio-Rad Laboratories, 255 Linus Pauling Drive, Hercules, CA 94547, USA
| | - Joshua Fenrich
- Bio-Rad Laboratories, 255 Linus Pauling Drive, Hercules, CA 94547, USA
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17
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de Ronde MWJ, Ruijter JM, Moerland PD, Creemers EE, Pinto-Sietsma SJ. Study Design and qPCR Data Analysis Guidelines for Reliable Circulating miRNA Biomarker Experiments: A Review. Clin Chem 2018; 64:1308-1318. [PMID: 29903876 DOI: 10.1373/clinchem.2017.285288] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/08/2018] [Indexed: 01/07/2023]
Abstract
BACKGROUND In the past decade, the search for circulating microRNA (miRNA) biomarkers has yielded numerous associations between miRNAs and different types of disease. However, many of these relations could not be replicated in subsequent studies under similar experimental conditions. Although this lack of replicability may be explained by the variation in experimental design and analysis methods, guidelines on the most appropriate design and analysis methods to study circulating miRNAs are scarce. CONTENT miRNA biomarker experiments generally consist of a discovery phase and a validation phase. In the discovery phase, typically hundreds of miRNAs are measured in parallel to identify candidate biomarkers. Because of the costs of such high-throughput experiments, the number of individuals included in those studies is often too small, which can easily lead to false positives and false negatives. In the validation phase, a small number of identified biomarker candidates are measured in a large cohort of cases and controls, generally by quantitative PCR (qPCR). Although qPCR is a sensitive method to measure miRNAs in the circulation, experimental design and qPCR data analysis remain challenging. Omitting some crucial steps in the design and analysis of the qPCR experiment or performing them incorrectly can cause serious biases, ultimately leading to false conclusions. SUMMARY In this review, we aim to expose and discuss the most common sources of interstudy variation in miRNA research from a methodological point of view and to provide guidelines on how to perform these steps correctly to increase replicability of studies on circulating miRNAs.
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Affiliation(s)
- Maurice W J de Ronde
- Departments of Vascular Medicine.,Clinical Epidemiology, Biostatistics and Bioinformatics
| | | | | | - Esther E Creemers
- Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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18
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Grinstein M, Dingwall HL, Shah RR, Capellini TD, Galloway JL. A robust method for RNA extraction and purification from a single adult mouse tendon. PeerJ 2018; 6:e4664. [PMID: 29707433 PMCID: PMC5922231 DOI: 10.7717/peerj.4664] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/03/2018] [Indexed: 11/30/2022] Open
Abstract
Background Mechanistic understanding of tendon molecular and cellular biology is crucial toward furthering our abilities to design new therapies for tendon and ligament injuries and disease. Recent transcriptomic and epigenomic studies in the field have harnessed the power of mouse genetics to reveal new insights into tendon biology. However, many mouse studies pool tendon tissues or use amplification methods to perform RNA analysis, which can significantly increase the experimental costs and limit the ability to detect changes in expression of low copy transcripts. Methods Single Achilles tendons were harvested from uninjured, contralateral injured, and wild type mice between three and five months of age, and RNA was extracted. RNA Integrity Number (RIN) and concentration were determined, and RT-qPCR gene expression analysis was performed. Results After testing several RNA extraction approaches on single adult mouse Achilles tendons, we developed a protocol that was successful at obtaining high RIN and sufficient concentrations suitable for RNA analysis. We found that the RNA quality was sensitive to the time between tendon harvest and homogenization, and the RNA quality and concentration was dependent on the duration of homogenization. Using this method, we demonstrate that analysis of Scx gene expression in single mouse tendons reduces the biological variation caused by pooling tendons from multiple mice. We also show successful use of this approach to analyze Sox9 and Col1a2 gene expression changes in injured compared with uninjured control tendons. Discussion Our work presents a robust, cost-effective, and straightforward method to extract high quality RNA from a single adult mouse Achilles tendon at sufficient amounts for RT-qPCR as well as RNA-seq. We show this can reduce variation and decrease the overall costs associated with experiments. This approach can also be applied to other skeletal tissues, as well as precious human samples.
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Affiliation(s)
- Mor Grinstein
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Heather L Dingwall
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Rishita R Shah
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jenna L Galloway
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
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19
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Joshi R, Fuller B, Li J, Tavana H. Statistical analysis of multi-dimensional, temporal gene expression of stem cells to elucidate colony size-dependent neural differentiation. Mol Omics 2018; 14:109-120. [PMID: 29659650 DOI: 10.1039/c8mo00011e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High throughput gene expression analysis using qPCR is commonly used to identify molecular markers of complex cellular processes. However, statistical analysis of multi-dimensional, temporal gene expression data is complicated by limited biological replicates and large number of measurements. Moreover, many available statistical tools for analysis of time series data assume that the data sequence is static and does not evolve over time. With this assumption, the parameters used to model the time series are fixed and thus, can be estimated by pooling data together. However, in many cases, dynamic processes of biological systems involve abrupt changes at unknown time points, making the assumption of stationary time series break down. We addressed this problem using a combination of statistical methods including hierarchical clustering, change point detection, and multiple testing. We applied this multi-step method to multi-dimensional, temporal gene expression data that resulted from our study of colony size-dependent neural cell differentiation of stem cells. The gene expression data were time series as the observations were recorded sequentially over time. Hierarchical clustering segregated the genes into three distinct clusters based on their temporal expression profiles; change point detection identified specific time points at which the entire dataset was divided into several homogenous subsets to allow a separate analysis of each subset; and multiple testing procedure identified the differentially expressed genes in each cluster within each subset of data. We established that our multi-step approach pinpoints specific sets of genes that underlie colony size-mediated neural differentiation of stem cells and demonstrated its advantages over conventional parametric and non-parametric tests that do not take into account temporal dynamics of the data. Importantly, our proposed approach is broadly applicable to any multivariate data sets of limited sample size from high throughput and high content screening such as in drug and biomarker discovery studies.
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Affiliation(s)
- Ramila Joshi
- Department of Biomedical Engineering, The University of Akron, 260 S. Forge St., Akron, Ohio 44325, USA.
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20
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Randhawa A, Ogunyewo OA, Eqbal D, Gupta M, Yazdani SS. Disruption of zinc finger DNA binding domain in catabolite repressor Mig1 increases growth rate, hyphal branching, and cellulase expression in hypercellulolytic fungus Penicillium funiculosum NCIM1228. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:15. [PMID: 29416560 PMCID: PMC5784589 DOI: 10.1186/s13068-018-1011-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 01/08/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND There is an urgent requirement for second-generation bio-based industries for economical yet efficient enzymatic cocktail to convert diverse cellulosic biomass into fermentable sugars. In our previous study, secretome of Penicillium funiculosum NCIM1228 showed high commercial potential by exhibiting high biomass hydrolyzing efficiency. To develop NCIM1228 further as an industrial workhorse, one of the major genetic interventions needed is global deregulation of cellulolytic genes to achieve higher enzyme production. Mig1 orthologs found in all yeast and filamentous fungi are transcriptional regulators that maintain carbon homeostasis by negatively regulating genes of secondary carbon source utilization. Their disruption has long been known to be beneficial for increasing the production of secreted enzymes for alternate carbon source utilization. RESULTS Upon detailed genotypic and phenotypic analysis, we observed that NCIM1228 harbors a truncated yet functional allele of homolog of a well-known catabolite repressor, Mig1. Alleviation of carbon repression in NCIM1228 was attained by replacing functional Mig1134 allele with null allele Mig188. P. funiculosum having Mig188 null allele showed better growth characteristics and 1.75-fold better glucose utilization than parent strain. We also showed that visibly small colony size, one of the major characteristics of CCR disruptant strains in filamentous fungi, was not due to retarded growth, but altered hyphal morphology. CCR-disrupted strain PfMig188 showed profuse branching pattern in terminal hyphae resulting in small and compact colonies with compromised filamentous proliferation. We further observed that basal level expression of two major classes of cellulases, namely, cellobiohydrolase and endoglucanase, was regulated by Mig1134 in NCIM1228, whereas other two major classes, namely, xylanases and β-glucosidase, were only marginally regulated. Finally, CCR disruption in P. funiculosum NCIM1228 led to prolonged cellulase induction in production medium resulting in twofold increased cellulase activity than the parent strain with maximum secreted protein titer being > 14 g/l. CONCLUSIONS CCR-disrupted P. funiculosum showed better growth, enhanced carbon source utilization, profuse branching pattern in terminal hyphae, and higher cellulase activity than parent strain. Our findings are particularly important in shedding light on important functions performed by Mig1 in addition to its role as negative regulator of alternate carbon source utilization in filamentous fungi.
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Affiliation(s)
- Anmoldeep Randhawa
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Olusola A. Ogunyewo
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Danish Eqbal
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Mayank Gupta
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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21
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Plasmodium Detection and Differentiation by Direct-on-Blood PCR Nucleic Acid Lateral Flow Immunoassay. J Mol Diagn 2018; 20:78-86. [DOI: 10.1016/j.jmoldx.2017.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 09/07/2017] [Accepted: 09/25/2017] [Indexed: 12/13/2022] Open
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22
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Juhlin A, Svensson S, Thomsen P, Trobos M. Staphylococcal biofilm gene expression on biomaterials - A methodological study. J Biomed Mater Res A 2017; 105:3400-3412. [PMID: 28782178 DOI: 10.1002/jbm.a.36171] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/01/2017] [Indexed: 01/02/2023]
Abstract
The combination of increased healthcare access, universal aging, and infallible therapy demands, synergistically drive the need for the development of biomaterial technologies that mitigate the challenge of biomaterial-associated infections (BAI). Staphylococcus epidermidis and Staphylococcus aureus account for the majority of BAI due to their ability to accumulate in adherent multilayered biofilm. This investigation details the development of gene expression assays to evaluate the genetic processes of attachment, accumulation, maturation, and dispersal phases of biofilms on biomaterials in vitro, while abiding by the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines. The biofilm formation of S. epidermidis on polyurethane (PU) central venous catheters and S. aureus on machined titanium (Ti) was examined in terms of gene expression at early and late time points. The results provided insight into how each stage of biofilm formation is orchestrated over time on these biomaterials in vitro. Furthermore, the results suggested that mechanical RNA extraction, organic solvents, elimination of genomic DNA, and preamplification are advisable strategies to implement for biofilm gene expression analysis. It is concluded that this method can be employed for the assessment of biofilm-biomaterial interactions at the molecular level. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 3400-3412, 2017.
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Affiliation(s)
- Annika Juhlin
- Department of Biomaterials, Sahlgrenska Academy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden.,BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden
| | - Sara Svensson
- Department of Biomaterials, Sahlgrenska Academy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden.,BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden
| | - Peter Thomsen
- Department of Biomaterials, Sahlgrenska Academy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden.,BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden
| | - Margarita Trobos
- Department of Biomaterials, Sahlgrenska Academy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden.,BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, University of Gothenburg, P.O. Box 412, 40530, Gothenburg, Sweden
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23
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de Ronde MWJ, Ruijter JM, Lanfear D, Bayes-Genis A, Kok MGM, Creemers EE, Pinto YM, Pinto-Sietsma SJ. Practical data handling pipeline improves performance of qPCR-based circulating miRNA measurements. RNA (NEW YORK, N.Y.) 2017; 23:811-821. [PMID: 28202710 PMCID: PMC5393188 DOI: 10.1261/rna.059063.116] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/27/2017] [Indexed: 05/21/2023]
Abstract
Since numerous miRNAs have been shown to be present in circulation, these so-called circulating miRNAs have emerged as potential biomarkers for disease. However, results of qPCR studies on circulating miRNA biomarkers vary greatly and many experiments cannot be reproduced. Missing data in qPCR experiments often occur due to off-target amplification, nonanalyzable qPCR curves and discordance between replicates. The low concentration of most miRNAs leads to most, but not all missing data. Therefore, failure to distinguish between missing data due to a low concentration and missing data due to randomly occurring technical errors partly explains the variation within and between otherwise similar studies. Based on qPCR kinetics, an analysis pipeline was developed to distinguish missing data due to technical errors from missing data due to a low concentration of the miRNA-equivalent cDNA in the PCR reaction. Furthermore, this pipeline incorporates a method to statistically decide whether concentrations from replicates are sufficiently concordant, which improves stability of results and avoids unnecessary data loss. By going through the pipeline's steps, the result of each measurement is categorized as "valid, invalid, or undetectable." Together with a set of imputation rules, the pipeline leads to more robust and reproducible data as was confirmed experimentally. Using two validation approaches, in two cohorts totaling 2214 heart failure patients, we showed that this pipeline increases both the accuracy and precision of qPCR measurements. In conclusion, this statistical data handling pipeline improves the performance of qPCR studies on low-expressed targets such as circulating miRNAs.
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Affiliation(s)
- Maurice W J de Ronde
- Department of Vascular Medicine
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics
| | - Jan M Ruijter
- Department of Anatomy, Embryology and Physiology, Academic Medical Center, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - David Lanfear
- Henry Ford Hospital, Heart and Vascular Institute, Detroit, Michigan 48202, USA
| | - Antoni Bayes-Genis
- Heart Failure Unit, Germans Trias i Pujol Hospital, 08916 Badalona, Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | | | - Esther E Creemers
- Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Yigal M Pinto
- Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Sara-Joan Pinto-Sietsma
- Department of Vascular Medicine
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics
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Ghosh N, Dutta M, Singh B, Banerjee R, Bhattacharyya P, Chaudhury K. Transcriptomics, proteomics and metabolomics driven biomarker discovery in COPD: an update. Expert Rev Mol Diagn 2016; 16:897-913. [PMID: 27267972 DOI: 10.1080/14737159.2016.1198258] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Diagnosis of chronic obstructive pulmonary disease (COPD), characterized by progressive irreversible airflow limitation, remains a challenge. Lack of sensitive diagnostic markers and alternative treatments have limited patients' survival rate. Herein, we provide for clinicians and scientists a comprehensive review on the various omics platforms used to investigate COPD. AREAS COVERED This review consists of articles from PubMed (2009-2016) as well as views of the contributing authors. The review highlights the need for COPD biomarker identification and also provides an update on promising candidate markers identified in various biological fluids using omics technologies. Expert commentary: The multi-omics approach holds promise for the development of robust early stage COPD diagnostic markers, screening of high-risk population, and also improved prognosis which could lead to personalized medicine in future. Various factors regulating an omics study including sample size, control selection, disease phenotyping, usage of complementary techniques and result replication in omics-based research are outlined.
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Affiliation(s)
- Nilanjana Ghosh
- a School of Medical Science and Technology , Indian Institute of Technology Kharagpur , Kharagpur , India
| | - Mainak Dutta
- a School of Medical Science and Technology , Indian Institute of Technology Kharagpur , Kharagpur , India
| | - Brajesh Singh
- a School of Medical Science and Technology , Indian Institute of Technology Kharagpur , Kharagpur , India
| | - Rintu Banerjee
- b Department of Agricultural & Food Engineering , Indian Institute of Technology Kharagpur , Kharagpur , India
| | | | - Koel Chaudhury
- a School of Medical Science and Technology , Indian Institute of Technology Kharagpur , Kharagpur , India
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Die JV, Roman B, Flores F, Rowland LJ. Design and Sampling Plan Optimization for RT-qPCR Experiments in Plants: A Case Study in Blueberry. FRONTIERS IN PLANT SCIENCE 2016; 7:271. [PMID: 27014296 PMCID: PMC4779984 DOI: 10.3389/fpls.2016.00271] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/21/2016] [Indexed: 06/05/2023]
Abstract
The qPCR assay has become a routine technology in plant biotechnology and agricultural research. It is unlikely to be technically improved, but there are still challenges which center around minimizing the variability in results and transparency when reporting technical data in support of the conclusions of a study. There are a number of aspects of the pre- and post-assay workflow that contribute to variability of results. Here, through the study of the introduction of error in qPCR measurements at different stages of the workflow, we describe the most important causes of technical variability in a case study using blueberry. In this study, we found that the stage for which increasing the number of replicates would be the most beneficial depends on the tissue used. For example, we would recommend the use of more RT replicates when working with leaf tissue, while the use of more sampling (RNA extraction) replicates would be recommended when working with stems or fruits to obtain the most optimal results. The use of more qPCR replicates provides the least benefit as it is the most reproducible step. By knowing the distribution of error over an entire experiment and the costs at each step, we have developed a script to identify the optimal sampling plan within the limits of a given budget. These findings should help plant scientists improve the design of qPCR experiments and refine their laboratory practices in order to conduct qPCR assays in a more reliable-manner to produce more consistent and reproducible data.
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Affiliation(s)
- Jose V. Die
- U.S. Department of Agriculture, Agricultural Research ServiceBeltsville, MD, USA
| | - Belen Roman
- Area Mejora y Biotecnologia, IFAPA Centro Alameda del ObispoCordoba, Spain
| | - Fernando Flores
- Departamento Ciencias Agroforestales, Universidad de HuelvaHuelva, Spain
| | - Lisa J. Rowland
- U.S. Department of Agriculture, Agricultural Research ServiceBeltsville, MD, USA
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Wadle S, Lehnert M, Rubenwolf S, Zengerle R, von Stetten F. Real-time PCR probe optimization using design of experiments approach. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 7:1-8. [PMID: 27077046 PMCID: PMC4827641 DOI: 10.1016/j.bdq.2015.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/16/2015] [Accepted: 12/16/2015] [Indexed: 12/28/2022]
Abstract
Primer and probe sequence designs are among the most critical input factors in real-time polymerase chain reaction (PCR) assay optimization. In this study, we present the use of statistical design of experiments (DOE) approach as a general guideline for probe optimization and more specifically focus on design optimization of label-free hydrolysis probes that are designated as mediator probes (MPs), which are used in reverse transcription MP PCR (RT-MP PCR). The effect of three input factors on assay performance was investigated: distance between primer and mediator probe cleavage site; dimer stability of MP and target sequence (influenza B virus); and dimer stability of the mediator and universal reporter (UR). The results indicated that the latter dimer stability had the greatest influence on assay performance, with RT-MP PCR efficiency increased by up to 10% with changes to this input factor. With an optimal design configuration, a detection limit of 3-14 target copies/10 μl reaction could be achieved. This improved detection limit was confirmed for another UR design and for a second target sequence, human metapneumovirus, with 7-11 copies/10 μl reaction detected in an optimum case. The DOE approach for improving oligonucleotide designs for real-time PCR not only produces excellent results but may also reduce the number of experiments that need to be performed, thus reducing costs and experimental times.
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Affiliation(s)
- S. Wadle
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard Institut für Mikro-und Informationstechnik, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - M. Lehnert
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - S. Rubenwolf
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - R. Zengerle
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard Institut für Mikro-und Informationstechnik, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- BIOSS—Centre for Biological Signalling Studies, University of Freiburg, 79110 Freiburg, Germany
| | - F. von Stetten
- Laboratory for MEMS Applications, IMTEK—Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Hahn-Schickard Institut für Mikro-und Informationstechnik, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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27
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Evrony GD, Lee E, Park PJ, Walsh CA. Resolving rates of mutation in the brain using single-neuron genomics. eLife 2016; 5. [PMID: 26901440 PMCID: PMC4805530 DOI: 10.7554/elife.12966] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/01/2016] [Indexed: 12/28/2022] Open
Abstract
Whether somatic mutations contribute functional diversity to brain cells is a long-standing question. Single-neuron genomics enables direct measurement of somatic mutation rates in human brain and promises to answer this question. A recent study (Upton et al., 2015) reported high rates of somatic LINE-1 element (L1) retrotransposition in the hippocampus and cerebral cortex that would have major implications for normal brain function, and suggested that these events preferentially impact genes important for neuronal function. We identify aspects of the single-cell sequencing approach, bioinformatic analysis, and validation methods that led to thousands of artifacts being interpreted as somatic mutation events. Our reanalysis supports a mutation frequency of approximately 0.2 events per cell, which is about fifty-fold lower than reported, confirming that L1 elements mobilize in some human neurons but indicating that L1 mosaicism is not ubiquitous. Through consideration of the challenges identified, we provide a foundation and framework for designing single-cell genomics studies.
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Affiliation(s)
- Gilad D Evrony
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, United States.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, United States.,Department of Neurology, Harvard Medical School, Boston, United States.,Department of Pediatrics, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Eunjung Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, United States.,Division of Genetics, Brigham and Women's Hospital, Boston, United States
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, United States.,Division of Genetics, Brigham and Women's Hospital, Boston, United States
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, United States.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, United States.,Department of Neurology, Harvard Medical School, Boston, United States.,Department of Pediatrics, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
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28
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Masur F, Benesch F, Pfannkuche H, Fuhrmann H, Gäbel G. Conjugated linoleic acids influence fatty acid metabolism in ovine ruminal epithelial cells. J Dairy Sci 2016; 99:3081-3095. [PMID: 26830749 DOI: 10.3168/jds.2015-10042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 12/11/2015] [Indexed: 12/31/2022]
Abstract
Conjugated linoleic acids (CLA), particularly cis-9,trans-11 (c9t11) and trans-10,cis-12 (t10c12), are used as feed additives to adapt to constantly increasing demands on the performance of lactating cows. Under these feeding conditions, the rumen wall, and the rumen epithelial cells (REC) in particular, are directly exposed to high amounts of CLA. This study determined the effect of CLA on the fatty acid (FA) metabolism of REC and expression of genes known to be modulated by FA. Cultured REC were incubated with c9t11, t10c12, and the structurally similar FA linoleic acid (LA), oleic acid (OA), and trans-vaccenic acid (TVA) for 48 h at a concentration of 100 µM. Cellular FA levels were determined by gas chromatography. Messenger RNA expression levels of stearoyl-CoA desaturase (SCD) and monocarboxylate transporter (MCT) 1 and 4 were quantified by reverse transcription-quantitative PCR. Fatty acid evaluation revealed significant effects of CLA, LA, OA, and TVA on the amount of FA metabolites of β-oxidation and elongation and of metabolites related to desaturation by SCD. The observed changes in FA content point (among others) to the ability of REC to synthesize c9t11 from TVA endogenously. The mRNA expression levels of SCD identified a decrease after CLA, LA, OA, or TVA treatment. In line with the changes in mRNA expression, we found reduced amounts of C16:1n-7 cis-9 and C18:1n-9 cis-9, the main products of SCD. The expression of MCT1 mRNA increased after c9t11 and t10c12 treatment, and CLA c9t11 induced an upregulation of MCT4. Application of peroxisome proliferator-activated receptor (PPAR) α antagonist suggested that activation of PPARα is involved in the changes of MCT1, MCT4, and SCD mRNA expression induced by c9t11. Participation of PPARγ in the changes of MCT1 and SCD mRNA expression was shown by the application of the respective antagonist. The study demonstrates that exposure to CLA affects both FA metabolism and regulatory pathways within REC.
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Affiliation(s)
- F Masur
- Institute of Veterinary Physiology, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, 04103, Germany.
| | - F Benesch
- Institute of Veterinary Physiology, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, 04103, Germany
| | - H Pfannkuche
- Institute of Veterinary Physiology, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, 04103, Germany
| | - H Fuhrmann
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, 04103, Germany
| | - G Gäbel
- Institute of Veterinary Physiology, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, 04103, Germany
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Weikl F, Radl V, Munch JC, Pritsch K. Targeting allergenic fungi in agricultural environments aids the identification of major sources and potential risks for human health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 529:223-30. [PMID: 26022406 DOI: 10.1016/j.scitotenv.2015.05.056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 04/30/2015] [Accepted: 05/15/2015] [Indexed: 05/20/2023]
Abstract
Fungi are, after pollen, the second most important producers of outdoor airborne allergens. To identify sources of airborne fungal allergens, a workflow for qPCR quantification from environmental samples was developed, thoroughly tested, and finally applied. We concentrated on determining the levels of allergenic fungi belonging to Alternaria, Cladosporium, Fusarium, and Trichoderma in plant and soil samples from agricultural fields in which cereals were grown. Our aims were to identify the major sources of allergenic fungi and factors potentially influencing their occurrence. Plant materials were the main source of the tested fungi at and after harvest. Amounts of A. alternata and C. cladosporioides varied significantly in fields under different management conditions, but absolute levels were very high in all cases. This finding suggests that high numbers of allergenic fungi may be an inevitable side effect of farming in several crops. Applied in large-scale studies, the concept described here may help to explain the high number of sensitization to airborne fungal allergens.
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Affiliation(s)
- F Weikl
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Biochemical Plant Pathology, Neuherberg, Germany.
| | - V Radl
- Helmholtz Zentrum München - German Research Center for Environmental Health, Research Unit Environmental Genomics, Neuherberg, Germany.
| | - J C Munch
- Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.
| | - K Pritsch
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Biochemical Plant Pathology, Neuherberg, Germany.
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30
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Dai Y, Xia Y, Chen HB, Li N, Chen G, Zhang FM, Gu N. Optimization of sterilization methods for electrospun poly(ε-caprolactone) to enhance pre-osteoblast cell behaviors for guided bone regeneration. J BIOACT COMPAT POL 2015. [DOI: 10.1177/0883911515598795] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The aim of this study was to determine the optimal sterilization procedure for biodegradable polyester-based guided bone regeneration membranes. The effects of sterilization using low-temperature hydrogen peroxide gas plasma, 75% ethanol (EtOH; two soaking times), and ultraviolet radiation on the structure and biological properties of electrospun poly(ε-caprolactone) membranes were investigated. The results demonstrated that all were effective sterilization methods. The membranes were then assessed for surface structure, wettability, and in vitro cellular responses including osteogenic differentiation by seeding with pre-osteoblasts (MC3T3-E1 cells). The cells grew well on all the sterilized membranes. The low-temperature hydrogen peroxide gas plasma–sterilized membranes, which exhibited significantly improved hydrophilicity ( p < 0.05), were better for cell osteogenic differentiation compared to the membranes sterilized by other methods. In addition, the cell behavior on the membranes sterilized by EtOH was superior to those sterilized by ultraviolet radiation. Finally, EtOH soaking time appeared to influence cell behavior. The results suggested that low-temperature hydrogen peroxide gas plasma treatment is the most promising method to sterilize electrospun poly(ε-caprolactone) membranes for guided bone regeneration.
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Affiliation(s)
- Yun Dai
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yang Xia
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory for Biomaterials and Devices, Southeast University, Nanjing, China
| | - Han-Bang Chen
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Na Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Gang Chen
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Fei-Min Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Suzhou Key Laboratory of Biomaterials and Technologies & Collaborative Innovation Center of Suzhou Nano Science and Technology, Suzhou, China
| | - Ning Gu
- Suzhou Key Laboratory of Biomaterials and Technologies & Collaborative Innovation Center of Suzhou Nano Science and Technology, Suzhou, China
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31
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From the field to the lab: best practices for field preservation of bat specimens for molecular analyses. PLoS One 2015; 10:e0118994. [PMID: 25798819 PMCID: PMC4370412 DOI: 10.1371/journal.pone.0118994] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 12/18/2014] [Indexed: 11/19/2022] Open
Abstract
Studies in molecular ecology depend on field-collected samples for genetic information, and the tissue sampled and preservation conditions strongly affect the quality of the DNA obtained. DNA yields from different tissue types have seldom been compared, and the relative performance of storage media has never been directly tested, even though these media may influence DNA degradation under field conditions. We analyzed DNA yield from buccal swabs and wing punches harvested from live bats using nucleic acid quantification as well as quantitative PCR for a single-copy nuclear locus. We also compared DNA yields from wing tissue preserved in three media: ethanol, NaCl-saturated dimethyl sulfoxide (DMSO), and silica desiccant. Wing punches yielded more total DNA than did buccal swabs, and wing tissues preserved in silica beads yielded significantly more total and nuclear DNA than those preserved in DMSO or ethanol. These results show that tissue type and preservation media strongly influence the quantity of DNA obtained from non-lethal genetic samples, and based on these effects we provide recommendations for field collection of tissues for genetic analyses.
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Vera-Lozada G, Scholl V, Barros MHM, Sisti D, Guescini M, Stocchi V, Stefanoff CG, Hassan R. Analysis of biological and technical variability in gene expression assays from formalin-fixed paraffin-embedded classical Hodgkin lymphomas. Exp Mol Pathol 2014; 97:433-9. [PMID: 25236575 DOI: 10.1016/j.yexmp.2014.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 09/09/2014] [Accepted: 09/12/2014] [Indexed: 11/16/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are invaluable sources of biological material for research and diagnostic purposes. In this study, we aimed to identify biological and technical variability in RT-qPCR TaqMan® assays performed with FFPE-RNA from lymph nodes of classical Hodgkin lymphoma samples. An ANOVA-nested 6-level design was employed to evaluate BCL2, CASP3, IRF4, LYZ and STAT1 gene expression. The most variable genes were CASP3 (low expression) and LYZ (high expression). Total variability decreased after normalization for all genes, except by LYZ. Genes with moderate and low expression were identified and suffered more the effects of the technical manipulation than high-expression genes. Pre-amplification was shown to introduce significant technical variability, which was partially alleviated by lowering to a half the amount of input RNA. Ct and Cy0 quantification methods, based on cycle-threshold and the kinetic of amplification curves, respectively, were compared. Cy0 method resulted in higher quantification values, leading to the decrease of total variability in CASP3 and LYZ genes. The mean individual noise was 0.45 (0.31 to 0.61 SD), indicating a variation of gene expression over ~1.5 folds from one case to another. We showed that total variability in RT-qPCR from FFPE-RNA is not higher than that reported for fresh complex tissues, and identified gene-, and expression level-sources of biological and technical variability, which can allow better strategies for designing RT-qPCR assays from highly degraded and inhibited samples.
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Affiliation(s)
- Gabriela Vera-Lozada
- Bone Marrow Transplantation Center, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - Vanesa Scholl
- Bone Marrow Transplantation Center, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | | | - Davide Sisti
- Department of Biomolecular Sciences, University of Urbino Carlo Bo Via I Maggetti, Urbino, Italy
| | - Michele Guescini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo Via I Maggetti, Urbino, Italy
| | - Vilberto Stocchi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo Via I Maggetti, Urbino, Italy
| | | | - Rocio Hassan
- Bone Marrow Transplantation Center, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.
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Stahlhut C, Slack FJ. MicroRNAs and the cancer phenotype: profiling, signatures and clinical implications. Genome Med 2013; 5:111. [PMID: 24373327 PMCID: PMC3978829 DOI: 10.1186/gm516] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) have emerged as key genetic regulators of a wide variety of biological processes, including growth, proliferation, and survival. Recent advances have led to the recognition that miRNAs can act as potent oncogenes and tumor suppressors, playing crucial roles in the initiation, maintenance, and progression of the oncogenic state in a variety of cancers. Determining how miRNA expression and function is altered in cancer is an important goal, and a necessary prerequisite to the development and adoption of miRNA-based therapeutics in the clinic. Highly promising clinical applications of miRNAs are the use of miRNA signatures as biomarkers for cancer (for example, for early detection or diagnosis), and therapeutic supplementation or inhibition of specific miRNAs to alter the cancer phenotype. In this review, we discuss the main methods used for miRNA profiling, and examine key miRNAs that are commonly altered in a variety of tumors. Current studies underscore the functional versatility and potency of miRNAs in various aspects of the cancer phenotype, pointing to their potential clinical applications. Consequently, we discuss the application of miRNAs as biomarkers, clinical agents, and therapeutic targets, highlighting both the enormous potential and major challenges in this field.
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Affiliation(s)
- Carlos Stahlhut
- Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, CT 06520, USA
| | - Frank J Slack
- Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, CT 06520, USA
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34
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Error estimation in environmental DNA targets quantification due to PCR efficiencies differences between real samples and standards. Folia Microbiol (Praha) 2013; 58:657-62. [DOI: 10.1007/s12223-013-0255-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
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35
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Lindén J, Ranta J, Pohjanvirta R. Bayesian modeling of reproducibility and robustness of RNA reverse transcription and quantitative real-time polymerase chain reaction. Anal Biochem 2012; 428:81-91. [DOI: 10.1016/j.ab.2012.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 06/08/2012] [Indexed: 10/28/2022]
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Turnbull AK, Kitchen RR, Larionov AA, Renshaw L, Dixon JM, Sims AH. Direct integration of intensity-level data from Affymetrix and Illumina microarrays improves statistical power for robust reanalysis. BMC Med Genomics 2012; 5:35. [PMID: 22909195 PMCID: PMC3443058 DOI: 10.1186/1755-8794-5-35] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Accepted: 08/15/2012] [Indexed: 12/18/2022] Open
Abstract
Background Affymetrix GeneChips and Illumina BeadArrays are the most widely used commercial single channel gene expression microarrays. Public data repositories are an extremely valuable resource, providing array-derived gene expression measurements from many thousands of experiments. Unfortunately many of these studies are underpowered and it is desirable to improve power by combining data from more than one study; we sought to determine whether platform-specific bias precludes direct integration of probe intensity signals for combined reanalysis. Results Using Affymetrix and Illumina data from the microarray quality control project, from our own clinical samples, and from additional publicly available datasets we evaluated several approaches to directly integrate intensity level expression data from the two platforms. After mapping probe sequences to Ensembl genes we demonstrate that, ComBat and cross platform normalisation (XPN), significantly outperform mean-centering and distance-weighted discrimination (DWD) in terms of minimising inter-platform variance. In particular we observed that DWD, a popular method used in a number of previous studies, removed systematic bias at the expense of genuine biological variability, potentially reducing legitimate biological differences from integrated datasets. Conclusion Normalised and batch-corrected intensity-level data from Affymetrix and Illumina microarrays can be directly combined to generate biologically meaningful results with improved statistical power for robust, integrated reanalysis.
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Affiliation(s)
- Arran K Turnbull
- Breakthrough Research Unit, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XR, UK
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37
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Chugh P, Dittmer DP. Potential pitfalls in microRNA profiling. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:601-16. [PMID: 22566380 DOI: 10.1002/wrna.1120] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that post-transcriptionally influence a wide range of cellular processes such as the host response to viral infection, innate immunity, cell cycle progression, migration, and apoptosis through the inhibition of target mRNA translation. Owing to the growing number of miRNAs and identification of their functional roles, miRNA profiling of many different sample types has become more expansive, especially with relevance to disease signatures. In this review, we address some of the advantages and potential pitfalls of the currently available methods for miRNA expression profiling. Some of the topics discussed include isomiRNAs, comparison of different profiling platforms, normalization strategies, and issues with regard to sample preparation and experimental analyses.
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Affiliation(s)
- Pauline Chugh
- Department of Microbiology, UNC-Chapel Hill, Chapel Hill, NC, USA
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38
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Ling D, Pike CJ, Salvaterra PM. Deconvolution of the confounding variations for reverse transcription quantitative real-time polymerase chain reaction by separate analysis of biological replicate data. Anal Biochem 2012; 427:21-5. [PMID: 22561916 DOI: 10.1016/j.ab.2012.04.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 04/25/2012] [Accepted: 04/26/2012] [Indexed: 10/28/2022]
Abstract
Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) uses threshold cycles (Ct values) for measuring relative gene expression. Ct values are signal-to-noise data composed of target gene expression and multiple sources of confounding variations. Data analysis is to minimize technical noises, evaluate biological variances, and estimate treatment-attributable expression changes of particular genes. However, this function is not sufficiently fulfilled in current analytic methods. An important but unrecognizable problem is that Ct values from all biological replicates and technical repeats are pooled across genes and treatment types. This violates the sample-specific association between target and reference genes, leading to inefficient removal of technical noises. To resolve this problem, here we propose to separate Ct values into replicate-specific data subsets and iteratively analyze expression ratios for individual data subsets. The individual expression ratios, rather than the raw Ct values, are pooled to determine the final expression change. The variances of all biological replicates and technical repeats across all target and reference genes are summed up. Our results from example data demonstrate that this separated method can substantially minimize RT-qPCR variance compared with the traditional methods using pooled Ct profiles. This analytic strategy is more effective in control of technical noises and improves the fidelity of RT-qPCR quantification.
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Affiliation(s)
- Daijun Ling
- Department of Neuroscience, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
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Abstract
Quantitative measurement of the levels of mRNA expression using real-time reverse transcription polymerase chain reaction (RT-PCR) has long been used for analyzing expression differences in tissue or cell lines of interest. This method has been used somewhat less frequently to measure the changes in gene expression due to perturbagens such as small molecules or siRNA. The availability of new instrumentation for liquid handling and real-time PCR analysis as well as the commercial availability of start-to-finish kits for RT-PCR has enabled the use of this method for high-throughput small-molecule screening on a scale comparable to traditional high-throughput screening (HTS) assays. This protocol focuses on the special considerations necessary for using quantitative RT-PCR as a primary small-molecule screening assay, including the different methods available for mRNA isolation and analysis.
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Affiliation(s)
- Joshua A Bittker
- Chemical Biology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 617-714-7373
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40
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Kitchen RR, Sabine VS, Simen AA, Dixon JM, Bartlett JMS, Sims AH. Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments. BMC Genomics 2011; 12:589. [PMID: 22133085 PMCID: PMC3269440 DOI: 10.1186/1471-2164-12-589] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 12/01/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Systematic processing noise, which includes batch effects, is very common in microarray experiments but is often ignored despite its potential to confound or compromise experimental results. Compromised results are most likely when re-analysing or integrating datasets from public repositories due to the different conditions under which each dataset is generated. To better understand the relative noise-contributions of various factors in experimental-design, we assessed several Illumina and Affymetrix datasets for technical variation between replicate hybridisations of Universal Human Reference (UHRR) and individual or pooled breast-tumour RNA. RESULTS A varying degree of systematic noise was observed in each of the datasets, however in all cases the relative amount of variation between standard control RNA replicates was found to be greatest at earlier points in the sample-preparation workflow. For example, 40.6% of the total variation in reported expressions were attributed to replicate extractions, compared to 13.9% due to amplification/labelling and 10.8% between replicate hybridisations. Deliberate probe-wise batch-correction methods were effective in reducing the magnitude of this variation, although the level of improvement was dependent on the sources of noise included in the model. Systematic noise introduced at the chip, run, and experiment levels of a combined Illumina dataset were found to be highly dependent upon the experimental design. Both UHRR and pools of RNA, which were derived from the samples of interest, modelled technical variation well although the pools were significantly better correlated (4% average improvement) and better emulated the effects of systematic noise, over all probes, than the UHRRs. The effect of this noise was not uniform over all probes, with low GC-content probes found to be more vulnerable to batch variation than probes with a higher GC-content. CONCLUSIONS The magnitude of systematic processing noise in a microarray experiment is variable across probes and experiments, however it is generally the case that procedures earlier in the sample-preparation workflow are liable to introduce the most noise. Careful experimental design is important to protect against noise, detailed meta-data should always be provided, and diagnostic procedures should be routinely performed prior to downstream analyses for the detection of bias in microarray studies.
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Affiliation(s)
- Robert R Kitchen
- Applied Bioinformatics of Cancer Group, Breakthrough Breast Cancer Research Unit, Institute of Genetics and Molecular Medicine, Crewe Road South, Edinburgh, Edinburgh, EH4 2XR, UK
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Taboada X, Robledo D, Del Palacio L, Rodeiro A, Felip A, Martínez P, Viñas A. Comparative expression analysis in mature gonads, liver and brain of turbot (Scophthalmus maximus) by cDNA-AFLPS. Gene 2011; 492:250-61. [PMID: 22037609 DOI: 10.1016/j.gene.2011.10.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 09/08/2011] [Accepted: 10/10/2011] [Indexed: 11/28/2022]
Abstract
Turbot is one of the most important farmed fish in Europe. This species exhibits a considerable sexual dimorphism in growth and sexual maturity that makes the all-female production recommended for turbot farming. Our knowledge about the genetic basis of sex determination and the molecular regulation of gonad differentiation in this species is still limited. Our goal was to identify and compare gene expression and functions between testes and ovaries in adults in order to ascertain the relationship between the genes that could be involved in the gonad differentiation or related to the sex determination system. The identification of differentially expressed sex related genes is an initial step towards understanding the molecular mechanisms of gonad differentiation. For this, we carried out a transcriptome analysis based on cDNA-AFLP technique which allowed us to obtain an initial frame on sex-specific gene expression that will facilitate further analysis especially along the critical gonad differentiating period. With the aim of widening the study on sex-biased gene expression we reproduced the same experiments in two somatic tissues: liver and brain. We have selected the liver because it is the most analyzed one regarding sexual dimorphic gene expression and due to its importance in steroid hormones metabolism and the brain because the functional relationship between brain and gonad is documented. We found slight but important differences between sexes which deserve further investigation.
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Affiliation(s)
- Xoana Taboada
- Departamento de Genética, Facultad de Biología (CIBUS), Universidad de Santiago de Compostela Avda Lope Gómez de Marzoa, 15782 Santiago de Compostela, Spain
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