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Hazman M. Gel express: a novel frugal method quantifies gene relative expression in conventional RT-PCR. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2022. [DOI: 10.1186/s43088-022-00194-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Real-time PCR system is a valuable scientific mainstream needed for quantifying specific gene expression. Nevertheless, compared with conventional PCR, the real-time PCR system is extremely expensive and not affordable for limited or mid-budget research laboratories. Here, a novel, doable and low-cost recipe (referred to as gel express) is developed to quantify gene expression using conventional RT-PCR assay. The novelty of the gel express method is based on replacing crossing point (CP) values with integrated density (IntDen) values of PCR amplicon bands in real-time PCR regular mathematical formulas.
Results
In this work, gene expression profiles of two different rice stress-marker genes (OsCYP94C2a and OsLOX8) were quantified in response to mechanical wounding at different time points (0, 30, 60, and 150 min). In the gel express method, the free software ImageJ was employed to measure integrated density (IntDen) values of PCR amplicon bands in agarose gel images. IntDen values were then used instead of crossing point (CP) values according to the following modified formula: [EIntDen(ref)/EIntDen(target)]sample ÷ [EIntDen(ref)/EIntDen(target)]control. Gene relative expression profiles (dynamic expression pattern) quantified by gel express method in both genes were highly comparable with real-time RT-PCR. R2 values were 0.9976 and 0.9975 in OsCYP94C2a and OsLOX, respectively. PCR amplification efficiency (E) for all studied genes could be calculated depending on IntDen values through experimentally designed calibration curves. PCR amplification efficiencies with all studied genes obtained by gel express were all in the accepted range. For better-visualized PCR amplicons thus detectable biological effects between treatments, the number of PCR cycles applied in gel express method (IntCyc) was experimentally estimated to be 29 cycles.
Conclusions
Gel express is a novel, cost-effective and feasible recipe for quantifying gene relative expression in conventional RT-PCR. The expression pattern quantified by gel express is highly comparable and fits the expression data revealed by the used real-time PCR system.
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Litvinov S, Rashydov N. Transgenerational Transmission of Radiation-Induced Expression Patterns of Arabidopsis Thaliana (L.) Heynh. Rad51 and Rad1 Genes. INTERNATIONAL JOURNAL OF SECONDARY METABOLITE 2018. [DOI: 10.21448/ijsm.415191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Adams DJ. Current Trends in Laboratory Class Teaching in University Bioscience Programmes. ACTA ACUST UNITED AC 2015. [DOI: 10.3108/beej.13.3] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- David J. Adams
- UK Centre for Bioscience, Higher Education Academy, and Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT
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Schelert J, Rudrappa D, Johnson T, Blum P. Role of MerH in mercury resistance in the archaeon Sulfolobus solfataricus. MICROBIOLOGY-SGM 2013; 159:1198-1208. [PMID: 23619003 DOI: 10.1099/mic.0.065854-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Crenarchaeota include extremely thermoacidophilic organisms that thrive in geothermal environments dominated by sulfidic ores and heavy metals such as mercury. Mercuric ion, Hg(II), inactivates transcription in the crenarchaeote Sulfolobus solfataricus and simultaneously derepresses transcription of a resistance operon, merHAI, through interaction with the MerR transcription factor. While mercuric reductase (MerA) is required for metal resistance, the role of MerH, an adjacent small and predicted product of an ORF, has not been explored. Inactivation of MerH either by nonsense mutation or by in-frame deletion diminished Hg(II) resistance of mutant cells. Promoter mapping studies indicated that Hg(II) sensitivity of the merH nonsense mutant arose through transcriptional polarity, and its metal resistance was restored partially by single copy merH complementation. Since MerH was not required in vitro for MerA-catalysed Hg(II) reduction, MerH may play an alternative role in metal resistance. Inductively coupled plasma-mass spectrometry analysis of the MerH deletion strain following metal challenge indicated that there was prolonged retention of intracellular Hg(II). Finally, a reduced rate of mer operon induction in the merH deletion mutant suggested that the requirement for MerH could result from metal trafficking to the MerR transcription factor.
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Affiliation(s)
- James Schelert
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68508, USA
| | - Deepak Rudrappa
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68508, USA
| | - Tyler Johnson
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68508, USA
| | - Paul Blum
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68508, USA
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Wightman B, Hark AT. Integration of bioinformatics into an undergraduate biology curriculum and the impact on development of mathematical skills. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 40:310-9. [PMID: 22987552 DOI: 10.1002/bmb.20637] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 06/28/2012] [Indexed: 05/22/2023]
Abstract
The development of fields such as bioinformatics and genomics has created new challenges and opportunities for undergraduate biology curricula. Students preparing for careers in science, technology, and medicine need more intensive study of bioinformatics and more sophisticated training in the mathematics on which this field is based. In this study, we deliberately integrated bioinformatics instruction at multiple course levels into an existing biology curriculum. Students in an introductory biology course, intermediate lab courses, and advanced project-oriented courses all participated in new course components designed to sequentially introduce bioinformatics skills and knowledge, as well as computational approaches that are common to many bioinformatics applications. In each course, bioinformatics learning was embedded in an existing disciplinary instructional sequence, as opposed to having a single course where all bioinformatics learning occurs. We designed direct and indirect assessment tools to follow student progress through the course sequence. Our data show significant gains in both student confidence and ability in bioinformatics during individual courses and as course level increases. Despite evidence of substantial student learning in both bioinformatics and mathematics, students were skeptical about the link between learning bioinformatics and learning mathematics. While our approach resulted in substantial learning gains, student "buy-in" and engagement might be better in longer project-based activities that demand application of skills to research problems. Nevertheless, in situations where a concentrated focus on project-oriented bioinformatics is not possible or desirable, our approach of integrating multiple smaller components into an existing curriculum provides an alternative.
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Affiliation(s)
- Bruce Wightman
- Biology Department, Muhlenberg College, Allentown, PA 18104, USA.
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Lee MK, Kim HR. [Comparison between Real-Time PCR and Agarose Gel Electrophoresis for DNA Quantification.]. Korean J Lab Med 2012; 26:217-22. [PMID: 18156728 DOI: 10.3343/kjlm.2006.26.3.217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Real-time polymerase chain reaction (PCR) is generally regarded as a very accurate and time-saving method, but it is expensive to run. We evaluated the reliability of an inexpensive and a researcher-friendly gel electrophoresis-based PCR method for the quantification of mRNA, and the results were compared with those obtained by real-time PCR. METHODS We compared the results of relative quantification for MMP-1 measured by real-time PCR and by ethidium bromide stained-agarose gel electrophoresis after end-point PCR. RESULTS There was significant but very weak correlation between real-time PCR and end-point PCR for relative quantification of MMP-1 (r=0.16, P<0.01). CONCLUSIONS Our results suggest that the use of the gel electrophoresis-based end-point PCR is inappropriate for quantifying mRNA. Therefore, in order to confirm the result of relative quantification by end-point PCR, the newly established real-time PCR method or northern hybridization should be applied.
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Affiliation(s)
- Mi Kyung Lee
- Department of Laboratory Medicine, College of Medicine, Chung-Ang University, Seoul, Korea.
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Maezato Y, Daugherty A, Dana K, Soo E, Cooper C, Tachdjian S, Kelly RM, Blum P. VapC6, a ribonucleolytic toxin regulates thermophilicity in the crenarchaeote Sulfolobus solfataricus. RNA (NEW YORK, N.Y.) 2011; 17:1381-1392. [PMID: 21622901 PMCID: PMC3138573 DOI: 10.1261/rna.2679911] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 04/15/2011] [Indexed: 05/30/2023]
Abstract
The phylum Crenarchaeota includes hyperthermophilic micro-organisms subjected to dynamic thermal conditions. Previous transcriptomic studies of Sulfolobus solfataricus identified vapBC6 as a heat-shock (HS)-inducible member of the Vap toxin-antitoxin gene family. In this study, the inactivation of the vapBC6 operon by targeted gene disruption produced two recessive phenotypes related to fitness, HS sensitivity and a heat-dependent reduction in the rate of growth. In-frame vapBC6 deletion mutants were analyzed to examine the respective roles of each protein. Since vapB6 transcript abundance was elevated in the vapC6 deletion, the VapC6 toxin appears to regulate abundance of its cognate antitoxin. In contrast, vapC6 transcript abundance was reduced in the vapB6 deletion. A putative intergenic terminator may underlie these observations by coordinating vapBC6 expression. As predicted by structural modeling, recombinant VapC6 produced using chaperone cosynthesis exhibited heat-dependent ribonucleolytic activity toward S. solfataricus total RNA. This activity could be blocked by addition of preheated recombinant VapB6. In vivo transcript targets were identified by assessing the relative expression of genes that naturally respond to thermal stress in VapBC6-deficient cells. Preferential increases were observed for dppB-1 and tetR, and preferential decreases were observed for rpoD and eIF2 gamma. Specific VapC6 ribonucleolytic action could also be demonstrated in vitro toward RNAs whose expression increased in the VapBC6-deficient strain during heat shock. These findings provide a biochemical mechanism and identify cellular targets underlying VapBC6-mediated control over microbial growth and survival at temperature extremes.
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Affiliation(s)
- Yukari Maezato
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
| | - Amanda Daugherty
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
| | - Karl Dana
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
| | - Edith Soo
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
| | - Charlotte Cooper
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
| | - Sabrina Tachdjian
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
| | - Paul Blum
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
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Campbell AM, Hatfield WT, Heyer LJ. Make microarray data with known ratios. CBE LIFE SCIENCES EDUCATION 2007; 6:196-7. [PMID: 17785401 PMCID: PMC1964527 DOI: 10.1187/cbe.07-05-0028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
| | - William T. Hatfield
- Departments of *Biology and
- Mathematics, Davidson College, Davidson, NC 28036
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Kuldell NH. How golden is silence? Teaching undergraduates the power and limits of RNA interference. CBE LIFE SCIENCES EDUCATION 2006; 5:247-54. [PMID: 17012216 PMCID: PMC1618687 DOI: 10.1187/cbe.05-11-0124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
It is hard and getting harder to strike a satisfying balance in teaching. Time dedicated to student-generated models or ideas is often sacrificed in an effort to "get through the syllabus." I describe a series of RNA interference (RNAi) experiments for undergraduate students that simultaneously explores fundamental concepts in gene regulation, develops cutting-edge laboratory skills, and embraces student-directed learning. Students design a small interfering RNA (siRNA) against luciferase, add it to cells expressing this gene, and then quantitatively assess the siRNA's effect on both intended and unintended targets, using a luciferase assay and a DNA microarray. Because both RNAi and microarray technologies are relatively new, with no clear consensus on their analysis or limitations, students are encouraged to explore different approaches to the design of their reagents and interpretations of their data. The ability to creatively formulate a hypothesis-driven experimental approach to a scientific question and to critically evaluate collected data is stressed. Equally important, this experiment emphasizes how modern scientific ideas emerge, are debated, tested, and decided.
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Affiliation(s)
- Natalie H Kuldell
- Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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