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Dunuweera AN, Dunuweera SP, Ranganathan K. A Comprehensive Exploration of Bioluminescence Systems, Mechanisms, and Advanced Assays for Versatile Applications. Biochem Res Int 2024; 2024:8273237. [PMID: 38347947 PMCID: PMC10861286 DOI: 10.1155/2024/8273237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/10/2023] [Accepted: 01/21/2024] [Indexed: 02/15/2024] Open
Abstract
Bioluminescence has been a fascinating natural phenomenon of light emission from living creatures. It happens when the enzyme luciferase facilitates the oxidation of luciferin, resulting in the creation of an excited-state species that emits light. Although there are many bioluminescent systems, few have been identified. D-luciferin-dependent systems, coelenterazine-dependent systems, Cypridina luciferin-based systems, tetrapyrrole-based luciferins, bacterial bioluminescent systems, and fungal bioluminescent systems are natural bioluminescent systems. Since different bioluminescence systems, such as various combinations of luciferin-luciferase pair reactions, have different light emission wavelengths, they benefit industrial applications such as drug discovery, protein-protein interactions, in vivo imaging in small animals, and controlling neurons. Due to the expression of luciferase and easy permeation of luciferin into most cells and tissues, bioluminescence assays are applied nowadays with modern technologies in most cell and tissue types. It is a versatile technique in a variety of biomedical research. Furthermore, there are some investigated blue-sky research projects, such as bioluminescent plants and lamps. This review article is mainly based on the theory of diverse bioluminescence systems and their past, present, and future applications.
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Affiliation(s)
| | | | - K. Ranganathan
- Department of Botany, University of Jaffna, Jaffna 40000, Sri Lanka
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Toktay Y, Dayanc B, Senturk S. Engineering and validation of a dual luciferase reporter system for quantitative and systematic assessment of regulatory sequences in Chinese hamster ovary cells. Sci Rep 2022; 12:6050. [PMID: 35410414 PMCID: PMC9001649 DOI: 10.1038/s41598-022-09887-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/30/2022] [Indexed: 12/19/2022] Open
Abstract
Ongoing research efforts to identify potent regulatory sequences that deliver robust and sustained transgene expression are critical for Chinese hamster ovary (CHO) cell line development technologies to meet the growing demand for recombinant proteins. Here we report the engineering and validation of a highly customizable single vector toolkit that comprises an all-in-one dual luciferase reporter system for quantitative and systematic interrogation of transcriptional regulatory sequences in transient and stable transfectants of CHO cells. To model the execution of the reporter system, we implemented a battery of known constitutive promoters including human CMV-mIE, SV40, HSV-TK, mouse PGK, human EF1α, EF1α short (EFS), human UBC, synthetic CAG, and Chinese hamster EF1α (CHEF1α). Of the nine promoters, CMV-mIE yielded the highest transcriptional activity in transient transfection settings, while CHEF1α was the strongest among a select subset of promoters in stable transfectants of CHO-DG44 pools. Remodeling the vector toolkit to build a dual fluorescent reporter system featured an alternative to bioluminescence based reporters. We infer that the findings of this study may serve as a basis to establish new vectors with weak or strong constitutive promoters. Furthermore, the modular all-in-one architecture of the reporter system proved to be a viable tool for discovering novel regulatory sequences that ensure high levels of transient and stable transgene expression in CHO and perhaps other mammalian cell lines.
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Evaluation of Firefly and Renilla Luciferase Inhibition in Reporter-Gene Assays: A Case of Isoflavonoids. Int J Mol Sci 2021; 22:ijms22136927. [PMID: 34203212 PMCID: PMC8268740 DOI: 10.3390/ijms22136927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 11/21/2022] Open
Abstract
Firefly luciferase is susceptible to inhibition and stabilization by compounds under investigation for biological activity and toxicity. This can lead to false-positive results in in vitro cell-based assays. However, firefly luciferase remains one of the most commonly used reporter genes. Here, we evaluated isoflavonoids for inhibition of firefly luciferase. These natural compounds are often studied using luciferase reporter-gene assays. We used a quantitative structure–activity relationship (QSAR) model to compare the results of in silico predictions with a newly developed in vitro assay that enables concomitant detection of inhibition of firefly and Renilla luciferases. The QSAR model predicted a moderate to high likelihood of firefly luciferase inhibition for all of the 11 isoflavonoids investigated, and the in vitro assays confirmed this for seven of them: daidzein, genistein, glycitein, prunetin, biochanin A, calycosin, and formononetin. In contrast, none of the 11 isoflavonoids inhibited Renilla luciferase. Molecular docking calculations indicated that isoflavonoids interact favorably with the D-luciferin binding pocket of firefly luciferase. These data demonstrate the importance of reporter-enzyme inhibition when studying the effects of such compounds and suggest that this in vitro assay can be used to exclude false-positives due to firefly or Renilla luciferase inhibition, and to thus define the most appropriate reporter gene.
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Zhang Y, Xiang D, Hu X, Ruan Q, Wang L, Bao Z. Identification and study of differentially expressed miRNAs in aged NAFLD rats based on high-throughput sequencing. Ann Hepatol 2021; 19:302-312. [PMID: 31899128 DOI: 10.1016/j.aohep.2019.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 02/04/2023]
Abstract
INTRODUCTION AND OBJECTIVES Hepatic microRNA (miR) expression profiles were explored in aged rats with NAFLD, in order to clarify the molecular mechanisms underlying the pathophysiological processes of aging-related NAFLD. PATIENTS OR MATERIALS AND METHODS 24 aged rats (18-month-old) and 24 young rats (2-month-old) were randomly divided into two subgroups according to diet, control group and NAFLD group. After 8 weeks of administering 45% high-fat diet or normal diet, total hepatic RNA was extracted from liver tissues of the aged rats. Differentially expressed microRNAs (DE-miRs) in aged NAFLD group were detected and screened out using high-throughput sequencing technology. The data were subjected to Gene Ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses using a bioinformatics approach. The sequencing results were further verified by RT-qPCR. RESULTS Compared with the aged control liver tissues, 6 significantly upregulated miRs (miR-881-3p, miR-871-3p, miR-335, miR-223-3p, miR-155-5p, miR-146b-5p) and 4 significantly downregulated miRs (miR-182, miR-193-3p, miR-31a-5p and miR-96-5p) were identified in the aged NAFLD liver tissues. These DE-miRs were found to be involved in the regulation of cell signaling transduction and metabolism processes, probably affecting signaling pathways relevant to insulin secretion and some senile diseases. RT-qPCR results corroborated the sequencing results and demonstrated that 6 significantly upregulated miRs were not identified in the young group. CONCLUSIONS A total of 10 DE-miRs identified in the aged NAFLD rats were involved in some certain insulin secretion and age-related functional pathways, which may serve as novel candidate targets for the diagnosis and treatment of aging-associated NAFLD.
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Affiliation(s)
- Ying Zhang
- Department of Gastroenterology, Huadong Hospital, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Danni Xiang
- Department of Gastroenterology, Huadong Hospital, Fudan University, Shanghai, China
| | - Xiaona Hu
- Department of Gastroenterology, Huadong Hospital, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Qingwei Ruan
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Lina Wang
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Zhijun Bao
- Department of Gastroenterology, Huadong Hospital, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital, Fudan University, Shanghai, China.
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Chong ZX, Yeap SK, Ho WY. Transfection types, methods and strategies: a technical review. PeerJ 2021; 9:e11165. [PMID: 33976969 PMCID: PMC8067914 DOI: 10.7717/peerj.11165] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/05/2021] [Indexed: 12/17/2022] Open
Abstract
Transfection is a modern and powerful method used to insert foreign nucleic acids into eukaryotic cells. The ability to modify host cells’ genetic content enables the broad application of this process in studying normal cellular processes, disease molecular mechanism and gene therapeutic effect. In this review, we summarized and compared the findings from various reported literature on the characteristics, strengths, and limitations of various transfection methods, type of transfected nucleic acids, transfection controls and approaches to assess transfection efficiency. With the vast choices of approaches available, we hope that this review will help researchers, especially those new to the field, in their decision making over the transfection protocol or strategy appropriate for their experimental aims.
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Affiliation(s)
- Zhi Xiong Chong
- School of Pharmacy, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Wan Yong Ho
- School of Pharmacy, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
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Tusi SK, Nguyen L, Thangaraju K, Li J, Cleary JD, Zu T, Ranum LPW. The alternative initiation factor eIF2A plays key role in RAN translation of myotonic dystrophy type 2 CCUG•CAGG repeats. Hum Mol Genet 2021; 30:1020-1029. [PMID: 33856033 DOI: 10.1093/hmg/ddab098] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 01/29/2023] Open
Abstract
Repeat-associated non-ATG (RAN) proteins have been reported in 11 microsatellite expansion disorders but the factors that allow RAN translation to occur and the effects of different repeat motifs and alternative AUG-like initiation codons are unclear. We studied the mechanisms of RAN translation across myotonic dystrophy type 2 (DM2) expansion transcripts with (CCUG) or without (CAGG) efficient alternative AUG-like codons. To better understand how DM2 LPAC and QAGR RAN proteins are expressed, we generated a series of CRISPR/Cas9-edited HEK293T cell lines. We show that LPAC and QAGR RAN protein levels are reduced in protein kinase R (PKR)-/- and PKR-like endoplasmic reticulum kinase (PERK)-/- cells, with more substantial reductions of CAGG-encoded QAGR in PKR-/- cells. Experiments using mutant eIF2α-S51A HEK293T cells show that p-eIF2α is required for QAGR production. In contrast, LPAC levels were only partially reduced in these cells, suggesting that both non-AUG and close-cognate initiation occur across CCUG RNAs. Overexpression of the alternative initiation factor eIF2A increases LPAC and QAGR protein levels but, notably, has a much larger effect on QAGR expressed from CAGG-expansion RNAs that lack efficient close-cognate codons. The effects of eIF2A on increasing LPAC are consistent with previous reports that eIF2A affects CUG-initiation translation. The observation that eIF2A also increases QAGR proteins is novel because CAGG expansion transcripts do not contain CUG or similarly efficient close-cognate AUG-like codons. For QAGR but not LPAC, the eIF2A-dependent increases are not seen when p-eIF2α is blocked. These data highlight the differential regulation of DM2 RAN proteins and eIF2A as a potential therapeutic target for DM2 and other RAN diseases.
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Affiliation(s)
- Solaleh Khoramian Tusi
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Lien Nguyen
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Kiruphagaran Thangaraju
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Jian Li
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - John D Cleary
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Tao Zu
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Laura P W Ranum
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
- Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL 32610, USA
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Kargaard A, Sluijter JPG, Klumperman B. Polymeric siRNA gene delivery - transfection efficiency versus cytotoxicity. J Control Release 2019; 316:263-291. [PMID: 31689462 DOI: 10.1016/j.jconrel.2019.10.046] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/23/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022]
Abstract
Within the field of gene therapy, there is a considerable need for the development of non-viral vectors that are able to compete with the efficiency obtained by viral vectors, while maintaining a good toxicity profile and not inducing an immune response within the body. While there have been many reports of possible polymeric delivery systems, few of these systems have been successful in the clinical setting due to toxicity, systemic instability or gene regulation inefficiency, predominantly due to poor endosomal escape and cytoplasmic release. The objective of this review is to provide an overview of previously published polymeric non-coding RNA and, to a lesser degree, oligo-DNA delivery systems with emphasis on their positive and negative attributes, in order to provide insight in the numerous hurdles that still limit the success of gene therapy.
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Affiliation(s)
- Anna Kargaard
- Stellenbosch University, Department of Chemistry and Polymer Science, Private Bag X1, Matieland 7602, South Africa; University Medical Center Utrecht, Experimental Cardiology Laboratory, Department of Cardiology, Division of Heart and Lungs, P.O. Box 85500, 3508 GA, Utrecht, the Netherlands
| | - Joost P G Sluijter
- University Medical Center Utrecht, Experimental Cardiology Laboratory, Department of Cardiology, Division of Heart and Lungs, P.O. Box 85500, 3508 GA, Utrecht, the Netherlands; Utrecht University, the Netherlands
| | - Bert Klumperman
- Stellenbosch University, Department of Chemistry and Polymer Science, Private Bag X1, Matieland 7602, South Africa.
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Ebrahimi M, Kazemi T, Ganjalikhani-Hakemi M, Majidi J, Khanahmad H, Rahimmanesh I, Homayouni V, Kohpayeh S. Development of a Stable Cell Line, Overexpressing Human T-cell Immunoglobulin Mucin 1. IRANIAN JOURNAL OF BIOTECHNOLOGY 2015; 13:25-31. [PMID: 28959306 DOI: 10.15171/ijb.1350] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Recent researches have demonstrated that human T-cell immunoglobulin mucin 1 (TIM-1) glycoprotein plays important roles in regulation of autoimmune and allergic diseases, as well as in tumor immunity and response to viral infections. Therefore, targeting TIM-1 could be a potential therapeutic approach against such diseases. OBJECTIVES In this study, we aimed to express TIM-1 protein on Human Embryonic kidney (HEK) 293T cell line in order to have an available source of the TIM-1 antigen. MATERIALS AND METHODS The cDNA was synthesized after RNA extraction from peripheral blood mononuclear cells (PBMC) and TIM-1 cDNA was amplified by PCR with specific primers. The PCR product was cloned in pcDNA™3.1/Hygro (+) and transformed in Escherichia coli TOP 10 F'. After cloning, authenticity of DNA sequence was checked and expressed in HEK 293T cells. Finally, expression of TIM-1 was analyzed by flow cytometry and real-time PCR. RESULTS The result of DNA sequencing demonstrated correctness of TIM-1 DNA sequence. The flow cytometry results indicated that TIM-1 was expressed in about 90% of transfected HEK 293T cells. The real-time PCR analysis showed TIM-1 mRNA expression increased 195-fold in transfected cells compared with un-transfected cells. CONCLUSIONS Findings of present study demonstrated the successful cloning and expression of TIM-1 on HEK 293T cells. These cells could be used as an immunogenic source for production of specific monoclonal antibodies, nanobodies and aptamers against human TIM-1.
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Affiliation(s)
- Mina Ebrahimi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tohid Kazemi
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Jafar Majidi
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Khanahmad
- Department of Genetic and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ilnaz Rahimmanesh
- Department of Genetic and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Vida Homayouni
- Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shirin Kohpayeh
- Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Afshari A, Uhde-Stone C, Lu B. A cooled CCD camera-based protocol provides an effective solution for in vitro monitoring of luciferase. Biochem Biophys Res Commun 2015; 458:543-548. [DOI: 10.1016/j.bbrc.2015.01.150] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 01/31/2015] [Indexed: 11/30/2022]
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10
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Jiwaji M, Sandison ME, Reboud J, Stevenson R, Daly R, Barkess G, Faulds K, Kolch W, Graham D, Girolami MA, Cooper JM, Pitt AR. Quantification of functionalised gold nanoparticle-targeted knockdown of gene expression in HeLa cells. PLoS One 2014; 9:e99458. [PMID: 24926959 PMCID: PMC4057226 DOI: 10.1371/journal.pone.0099458] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 05/13/2014] [Indexed: 12/26/2022] Open
Abstract
INTRODUCTION Gene therapy continues to grow as an important area of research, primarily because of its potential in the treatment of disease. One significant area where there is a need for better understanding is in improving the efficiency of oligonucleotide delivery to the cell and indeed, following delivery, the characterization of the effects on the cell. METHODS In this report, we compare different transfection reagents as delivery vehicles for gold nanoparticles functionalized with DNA oligonucleotides, and quantify their relative transfection efficiencies. The inhibitory properties of small interfering RNA (siRNA), single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) sequences targeted to human metallothionein hMT-IIa are also quantified in HeLa cells. Techniques used in this study include fluorescence and confocal microscopy, qPCR and Western analysis. FINDINGS We show that the use of transfection reagents does significantly increase nanoparticle transfection efficiencies. Furthermore, siRNA, ssRNA and ssDNA sequences all have comparable inhibitory properties to ssDNA sequences immobilized onto gold nanoparticles. We also show that functionalized gold nanoparticles can co-localize with autophagosomes and illustrate other factors that can affect data collection and interpretation when performing studies with functionalized nanoparticles. CONCLUSIONS The desired outcome for biological knockdown studies is the efficient reduction of a specific target; which we demonstrate by using ssDNA inhibitory sequences targeted to human metallothionein IIa gene transcripts that result in the knockdown of both the mRNA transcript and the target protein.
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Affiliation(s)
- Meesbah Jiwaji
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life and Health Science, Aston University, Birmingham, United Kingdom
| | - Mairi E. Sandison
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Julien Reboud
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Ross Stevenson
- Centre for Molecular Nanometrology, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Rónán Daly
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | - Gráinne Barkess
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Karen Faulds
- Centre for Molecular Nanometrology, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Walter Kolch
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Systems Biology Ireland and the Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Duncan Graham
- Centre for Molecular Nanometrology, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Mark A. Girolami
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
- Department of Statistical Science, University College London, London, United Kingdom
| | - Jonathan M. Cooper
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Andrew R. Pitt
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life and Health Science, Aston University, Birmingham, United Kingdom
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Chou TC, Moyle RL. Synthetic versions of firefly luciferase and Renilla luciferase reporter genes that resist transgene silencing in sugarcane. BMC PLANT BIOLOGY 2014; 14:92. [PMID: 24708613 PMCID: PMC4021088 DOI: 10.1186/1471-2229-14-92] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/31/2014] [Indexed: 05/10/2023]
Abstract
BACKGROUND Down-regulation or silencing of transgene expression can be a major hurdle to both molecular studies and biotechnology applications in many plant species. Sugarcane is particularly effective at silencing introduced transgenes, including reporter genes such as the firefly luciferase gene.Synthesizing transgene coding sequences optimized for usage in the host plant is one method of enhancing transgene expression and stability. Using specified design rules we have synthesised new coding sequences for both the firefly luciferase and Renilla luciferase reporter genes. We have tested these optimized versions for enhanced levels of luciferase activity and for increased steady state luciferase mRNA levels in sugarcane. RESULTS The synthetic firefly luciferase (luc*) and Renilla luciferase (Renluc*) coding sequences have elevated G + C contents in line with sugarcane codon usage, but maintain 75% identity to the native firefly or Renilla luciferase nucleotide sequences and 100% identity to the protein coding sequences.Under the control of the maize pUbi promoter, the synthetic luc* and Renluc* genes yielded 60x and 15x higher luciferase activity respectively, over the native firefly and Renilla luciferase genes in transient assays on sugarcane suspension cell cultures.Using a novel transient assay in sugarcane suspension cells combining co-bombardment and qRT-PCR, we showed that synthetic luc* and Renluc* genes generate increased transcript levels compared to the native firefly and Renilla luciferase genes.In stable transgenic lines, the luc* transgene generated significantly higher levels of expression than the native firefly luciferase transgene. The fold difference in expression was highest in the youngest tissues. CONCLUSIONS We developed synthetic versions of both the firefly and Renilla luciferase reporter genes that resist transgene silencing in sugarcane. These transgenes will be particularly useful for evaluating the expression patterns conferred by existing and newly isolated promoters in sugarcane tissues. The strategies used to design the synthetic luciferase transgenes could be applied to other transgenes that are aggressively silenced in sugarcane.
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MESH Headings
- Gene Expression Regulation, Plant
- Gene Silencing
- Genes, Plant
- Genes, Reporter
- Luciferases, Firefly/genetics
- Luciferases, Renilla/genetics
- Luminescent Measurements
- Open Reading Frames/genetics
- Plant Cells/metabolism
- Plant Stems/metabolism
- Plants, Genetically Modified
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Saccharum/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Suspensions
- Synthetic Biology
- Transformation, Genetic
- Transgenes/genetics
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Affiliation(s)
- Ting-Chun Chou
- School of Agriculture and Food Sciences, University of Queensland, Brisbane 4072, Australia
| | - Richard L Moyle
- School of Agriculture and Food Sciences, University of Queensland, Brisbane 4072, Australia
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Li H, Wang Y, Cao F. In vivo bioluminescence imaging monitoring of stem cells' participation in choroidal neovascularization. Ophthalmic Res 2013; 50:19-26. [PMID: 23711902 DOI: 10.1159/000348737] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 01/16/2013] [Indexed: 01/31/2023]
Abstract
BACKGROUND Choroidal neovascularization (CNV) is common in various retinal diseases and is one of the most common causes of severe and irreversible visual loss. Our previous works suggested that bone marrow-derived cells (BMCs) participate in CNV, but little is known about stem cells' dynamic change when injected into mouse CNV. In vivo optical bioluminescence imaging (BLI) is a newly developing technology for dynamically observing biological behavior. Using this technology, we can observe the stem cells' dynamic behavior in CNV, in vivo. METHODS Two types of BMCs were used: bone marrow mononuclear cells (BMMNCs) and bone mesenchymal stem cells (MSCs). Cells were characterized using flow cytometry and BLI. C57BL/6J mice (n = 6/group) underwent CNV followed by caudal vein injection of 4 × 10⁶ BMMNCs, MSCs or phosphate buffer. Cell survival was measured: (1) in vivo using BLI during 2 weeks, and (2) in vitro using firefly luciferase (Fluc) assays and histology. RESULTS BMMNCs and MSCs expressed a similar Fluc reporter enzyme, as confirmed by luminometry. After injection into CNV mouse models, the two cell types showed dynamic behavior in CNV using BLI. The in vitro Fluc assay and histology results provided further proof for the above results. CONCLUSION This is the first study comparing the behavior of stem cells in CNV using BLI, in vivo. BMMNCs and MSCs could contribute to CNV and could serve as delivery vehicles for CNV treatments. Meanwhile, BLI could lay a foundation for CNV mechanism research in a prospective manner.
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Affiliation(s)
- H Li
- Department of Ophthalmology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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13
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Jiwaji M, Daly R, Gibriel A, Barkess G, McLean P, Yang J, Pansare K, Cumming S, McLauchlan A, Kamola PJ, Bhutta MS, West AG, West KL, Kolch W, Girolami MA, Pitt AR. Unique reporter-based sensor platforms to monitor signalling in cells. PLoS One 2012; 7:e50521. [PMID: 23209767 PMCID: PMC3510088 DOI: 10.1371/journal.pone.0050521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 10/23/2012] [Indexed: 11/30/2022] Open
Abstract
Introduction In recent years much progress has been made in the development of tools for systems biology to study the levels of mRNA and protein, and their interactions within cells. However, few multiplexed methodologies are available to study cell signalling directly at the transcription factor level. Methods Here we describe a sensitive, plasmid-based RNA reporter methodology to study transcription factor activation in mammalian cells, and apply this technology to profiling 60 transcription factors in parallel. The methodology uses two robust and easily accessible detection platforms; quantitative real-time PCR for quantitative analysis and DNA microarrays for parallel, higher throughput analysis. Findings We test the specificity of the detection platforms with ten inducers and independently validate the transcription factor activation. Conclusions We report a methodology for the multiplexed study of transcription factor activation in mammalian cells that is direct and not theoretically limited by the number of available reporters.
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Affiliation(s)
- Meesbah Jiwaji
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life and Health Science, Aston University, Birmingham, United Kingdom
| | - Rónán Daly
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | - Abdullah Gibriel
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gráinne Barkess
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Pauline McLean
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jingli Yang
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kshama Pansare
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life and Health Science, Aston University, Birmingham, United Kingdom
| | - Sarah Cumming
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Alisha McLauchlan
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Piotr J. Kamola
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Musab S. Bhutta
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Adam G. West
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Katherine L. West
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Walter Kolch
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Systems Biology Ireland and the Conway Institute, University College Dublin, Dublin, Ireland
| | - Mark A. Girolami
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
- Department of Statistical Science, University College London, London, United Kingdom
| | - Andrew R. Pitt
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life and Health Science, Aston University, Birmingham, United Kingdom
- * E-mail:
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