1
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Baeken MW, Yokobayashi Y. Identification of an ERN1 target site within EGFP mRNA. J Cell Biochem 2022; 123:1298-1305. [PMID: 35908204 PMCID: PMC9544080 DOI: 10.1002/jcb.30314] [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: 07/13/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022]
Abstract
EGFP (enhanced green fluorescent protein) is one of the most common tools used in life sciences, including research focusing on proteostasis. Here we report that ERN1 (endoplasmic reticulum to nucleus signaling 1), which is upregulated by UPR (unfolded protein response), targets an RNA hairpin loop motif in EGFP mRNA. A silent mutation introduced into EGFP mRNA abolished the ERN1‐dependent mRNA decay. Therefore, experiments that employ EGFP as a reporter gene in studies that involve upregulation of the UPR pathway should be interpreted carefully, and a mutant devoid of the ERN1 target motif may be more suitable for such studies.
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Affiliation(s)
- Marius W Baeken
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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2
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Implementation of a Practical Teaching Course on Protein Engineering. BIOLOGY 2022; 11:biology11030387. [PMID: 35336761 PMCID: PMC8944992 DOI: 10.3390/biology11030387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 11/20/2022]
Abstract
Simple Summary Proteins are the workhorses of the cell. With different combinations of the 20 common amino acids and some modifications of these amino acids, proteins have evolved with a staggering array of new functions and capabilities due to Protein Engineering techniques. The practical course presented was offered to undergraduate bioengineering and chemical students at the Faculty of Engineering of the University of Porto (Portugal) and consists of sequential laboratory sessions to learn the basic skills related to the expression and purification of recombinant proteins in bacterial hosts. These experiments were successfully applied by students as all working groups were able to isolate a model recombinant protein (the enhanced green fluorescent protein) from a cell lysate containing a mixture of proteins and other biomolecules produced by an Escherichia coli strain and evaluate the performance of the extraction and purification procedures they learned. Abstract Protein Engineering is a highly evolved field of engineering aimed at developing proteins for specific industrial, medical, and research applications. Here, we present a practical teaching course to demonstrate fundamental techniques used to express, purify and analyze a recombinant protein produced in Escherichia coli—the enhanced green fluorescent protein (eGFP). The methodologies used for eGFP production were introduced sequentially over six laboratory sessions and included (i) bacterial growth, (ii) sonication (for cell lysis), (iii) affinity chromatography and dialysis (for eGFP purification), (iv) bicinchoninic acid (BCA) and fluorometry assays for total protein and eGFP quantification, respectively, and (v) sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for qualitative analysis. All groups were able to isolate the eGFP from the cell lysate with purity levels up to 72%. Additionally, a mass balance analysis performed by the students showed that eGFP yields up to 46% were achieved at the end of the purification process following the adopted procedures. A sensitivity analysis was performed to pinpoint the most critical steps of the downstream processing.
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3
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Beric A, Mabry ME, Harkess AE, Brose J, Schranz ME, Conant GC, Edger PP, Meyers BC, Pires JC. Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales). G3 (BETHESDA, MD.) 2021; 11:jkab140. [PMID: 33993297 PMCID: PMC8495927 DOI: 10.1093/g3journal/jkab140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/10/2021] [Indexed: 11/14/2022]
Abstract
Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to further test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana-chosen as the model plant system for this reason-as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we confirm the correlation between genome size and TE content, however, we are unable to reconstruct phylogenetic relationships and do not detect any shift in TE abundance associated with WGD.
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Affiliation(s)
- Aleksandra Beric
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Makenzie E Mabry
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Alex E Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Julia Brose
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen 6700 AA, The Netherlands
| | - Gavin C Conant
- Bioinformatics Research Center, Program in Genetics and Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Department of Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI 48824, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - J Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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4
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Pontvianne F, Boyer-Clavel M, Sáez-Vásquez J. Fluorescence-Activated Nucleolus Sorting in Arabidopsis. Methods Mol Biol 2016; 1455:203-11. [PMID: 27576720 DOI: 10.1007/978-1-4939-3792-9_15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Nucleolar isolation allows exhaustive characterization of the nucleolar content. Centrifugation-based protocols are not adapted to isolation of nucleoli directly from a plant tissue because of copurification of cellular debris. We describe here a method that allows the purification of nucleoli using fluorescent-activated cell sorting from Arabidopsis thaliana leaves. This approach requires the expression of a specific nucleolar protein such as fibrillarin fused to green fluorescent protein in planta.
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Affiliation(s)
- Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 58 Avenue P. Alduy, 66860, Perpignan, France. .,University Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860, Perpignan, France.
| | - Myriam Boyer-Clavel
- UMR5535, Institut de Génétique Moléculaire de Montpellier, 1919 route de Mende, 34293, Montpellier cedex 5, France.,MRI UMS3426, BioCampus Montpellier, c/o IGF, 141 rue de la cardonille, 34094, Montpellier cedex 5, France
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, 58 Avenue P. Alduy, 66860, Perpignan, France.,University Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, 66860, Perpignan, France
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5
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He M, Huang H, Wang M, Chen A, Ning X, Yu K, Li Q, Li W, Ma L, Chen Z, Wang X, Sun Q. Fluorescence-Activated Cell Sorting Analysis of Heterotypic Cell-in-Cell Structures. Sci Rep 2015; 5:9588. [PMID: 25913618 PMCID: PMC5386181 DOI: 10.1038/srep09588] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/12/2015] [Indexed: 12/19/2022] Open
Abstract
Cell-in-cell structures (CICs), characterized by the presence of one or more viable cells inside another one, were recently found important player in development, immune homeostasis and tumorigenesis etc. Incompatible with ever-increasing interests on this unique phenomenon, reliable methods available for high throughput quantification and systemic investigation are lacking. Here, we report a flow cytometry-based method for rapid analysis and sorting of heterotypic CICs formed between lymphocytes and tumor cells. In this method, cells were labeled with fluorescent dyes for fluorescence-activated cell sorting (FACS) by flow cytometry, conditions for reducing cell doublets were optimized such that high purity (>95%) of CICs could be achieved. By taking advantage of this method, we analyzed CICs formation between different cell pairs, and found that factors from both internalized effector cells and engulfing target cells affect heterotypic CICs formation. Thus, flow cytometry-based FACS analysis would serve as a high throughput method to promote systemic researches on CICs.
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Affiliation(s)
- Meifang He
- 1] Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan er Road, Guangzhou, Guangdong 510080, P. R. China [2] Laboratory of Cell Engineering, Institute of Biotechnology, 20 Dongda Street, Beijing 100071, P. R. China [3] The Institute of Life Sciences, the Key Laboratory of Normal Aging &Geriatric, the State Key Laboratory of Kidney, the Chinese PLA General Hospital, Beijing 100853, P. R. China
| | - Hongyan Huang
- 1] Laboratory of Cell Engineering, Institute of Biotechnology, 20 Dongda Street, Beijing 100071, P. R. China [2] Department of Oncology, Beijing Shijitan Hospital of Capital Medical University, 10 TIEYI Road, Beijing 100038, P. R. China
| | - Manna Wang
- 1] Laboratory of Cell Engineering, Institute of Biotechnology, 20 Dongda Street, Beijing 100071, P. R. China [2] Institute of Molecular Immunology, School of Biotechnology, Southern Medical University, Guangzhou 510515, P. R. China
| | - Ang Chen
- Laboratory of Cell Engineering, Institute of Biotechnology, 20 Dongda Street, Beijing 100071, P. R. China
| | - Xiangkai Ning
- 1] Laboratory of Cell Engineering, Institute of Biotechnology, 20 Dongda Street, Beijing 100071, P. R. China [2] Institute of Molecular Immunology, School of Biotechnology, Southern Medical University, Guangzhou 510515, P. R. China
| | - Kaitao Yu
- Department of Stomatology, Affiliated Hospital of Academy of Military Medical Science, 8 Dongda Street, Beijing 100071, P. R. China
| | - Qihong Li
- Department of Stomatology, Affiliated Hospital of Academy of Military Medical Science, 8 Dongda Street, Beijing 100071, P. R. China
| | - Wen Li
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhongshan er Road, Guangzhou, Guangdong 510080, P. R. China
| | - Li Ma
- Institute of Molecular Immunology, School of Biotechnology, Southern Medical University, Guangzhou 510515, P. R. China
| | - Zhaolie Chen
- Laboratory of Cell Engineering, Institute of Biotechnology, 20 Dongda Street, Beijing 100071, P. R. China
| | - Xiaoning Wang
- The Institute of Life Sciences, the Key Laboratory of Normal Aging &Geriatric, the State Key Laboratory of Kidney, the Chinese PLA General Hospital, Beijing 100853, P. R. China
| | - Qiang Sun
- 1] Laboratory of Cell Engineering, Institute of Biotechnology, 20 Dongda Street, Beijing 100071, P. R. China [2] National Key Laboratory of Medical Immunology and Institute of Immunology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, P. R. China
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6
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Xu P, Cai W. RAN1 is involved in plant cold resistance and development in rice (Oryza sativa). JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3277-87. [PMID: 24790113 PMCID: PMC4071843 DOI: 10.1093/jxb/eru178] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Of the diverse abiotic stresses, low temperature is one of the major limiting factors that lead to a series of morphological, physiological, biochemical, and molecular changes in plants. Ran, an evolutionarily conserved small G-protein family, has been shown to be essential for the nuclear translocation of proteins. It also mediates the regulation of cell cycle progression in mammalian cells. However, little is known about Ran function in rice (Oryza sativa). We report here that Ran gene OsRAN1 is essential for the molecular improvement of rice for cold tolerance. Ran also affects plant morphogenesis in transgenic Arabidopsis thaliana. OsRAN1 is ubiquitously expressed in rice tissues with the highest expression in the spike. The levels of mRNA encoding OsRAN1 were greatly increased by cold and indoleacetic acid treatment rather than by addition of salt and polyethylene glycol. Further, OsRAN1 overexpression in Arabidopsis increased tiller number, and altered root development. OsRAN1 overexpression in rice improves cold tolerance. The levels of cellular free Pro and sugar levels were highly increased in transgenic plants under cold stress. Under cold stress, OsRAN1 maintained cell division and cell cycle progression, and also promoted the formation of an intact nuclear envelope. The results suggest that OsRAN1 protein plays an important role in the regulation of cellular mitosis and the auxin signalling pathway.
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Affiliation(s)
- Peipei Xu
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Graduate School of Chinese Academy of Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Weiming Cai
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Graduate School of Chinese Academy of Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
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7
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Brognaux A, Thonart P, Delvigne F, Neubauer P, Twizere JC, Francis F, Gorret N. Direct and indirect use of GFP whole cell biosensors for the assessment of bioprocess performances: Design of milliliter scale-down bioreactors. Biotechnol Prog 2012; 29:48-59. [DOI: 10.1002/btpr.1660] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 10/24/2012] [Indexed: 01/27/2023]
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8
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Thévenin J, Dubos C, Xu W, Le Gourrierec J, Kelemen Z, Charlot F, Nogué F, Lepiniec L, Dubreucq B. A new system for fast and quantitative analysis of heterologous gene expression in plants. THE NEW PHYTOLOGIST 2012; 193:504-12. [PMID: 22023451 DOI: 10.1111/j.1469-8137.2011.03936.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
• Large-scale analysis of transcription factor-cis-acting element interactions in plants, or the dissection of complex transcriptional regulatory mechanisms, requires rapid, robust and reliable systems for the quantification of gene expression. • Here, we describe a new system for transient expression analysis of transcription factors, which takes advantage of the fast and easy production and transfection of Physcomitrella patens protoplasts, coupled to flow cytometry quantification of a fluorescent protein (green fluorescent protein). Two small-sized and high-copy Gateway® vectors were specifically designed, although standard binary vectors can also be employed. • As a proof of concept, the regulation of BANYULS (BAN), a key structural gene involved in proanthocyanidin biosynthesis in Arabidopsis thaliana seeds, was used. In P. patens, BAN expression is activated by a complex composed of three proteins (TT2/AtMYB123, TT8/bHLH042 and TTG1), and is inhibited by MYBL2, a transcriptional repressor, as in Arabidopsis. Using this approach, two new regulatory sequences that are necessary and sufficient for specific BAN expression in proanthocyanidin-accumulating cells were identified. • This one hybrid-like plant system was successfully employed to quantitatively assess the transcriptional activity of four regulatory proteins, and to identify their target recognition sites on the BAN promoter.
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Affiliation(s)
- J Thévenin
- INRA AgroParisTech, IJPB, UMR 1318, INRA centre de Versailles, Versailles, France
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9
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Abstract
Flow cytometry has become a standard method for separating individual subsets of cells from a heterogeneous population. Multilaser, multicolour cell sorters are increasingly common and have become more complex in recent years increasing the number of applications available. However, a cell sorting experiment is only as good as the input sample, and the preparation of this is extremely important. This chapter describes the methods used to prepare samples for flow cytometry and how they can be adapted and optimised according to cell type.
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Affiliation(s)
- Derek Davies
- FACS Laboratory, London Research Institute, Cancer Research UK, London, UK.
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10
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Ploschner M, Mazilu M, Cižmár T, Dholakia K. Numerical investigation of passive optical sorting of plasmon nanoparticles. OPTICS EXPRESS 2011; 19:13922-13933. [PMID: 21934752 DOI: 10.1364/oe.19.013922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We explore the passive optical sorting of plasmon nanoparticles and investigate the optimal wavelength and optimal beam shape of incident field. The condition for optimal wavelength is found by maximising the nanoparticle separation whilst minimising the temperature increase in the system. We then use the force optical eigenmode (FOEi) method to find the beam shape of incident electromagnetic field, maximising the force difference between plasmon nanoparticles. The maximum force difference is found with respect to the whole sorting region. The combination of wavelength and beam shape study is demonstrated for a specific case of gold nanoparticles of radius 40 nm and 50 nm respectively. The optimum wavelength for this particular situation is found to be above 700 nm. The optimum beam shape depends upon the size of sorting region and ranges from plane-wave illumination for infinite sorting region to a field maximising gradient force difference in a single point.
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Affiliation(s)
- M Ploschner
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife KY16 9SS, UK.
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11
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Gueret V, Negrete-Virgen JA, Lyddiatt A, Al-Rubeai M. Rapid titration of adenoviral infectivity by flow cytometry in batch culture of infected HEK293 cells. Cytotechnology 2011; 38:87-97. [PMID: 19003090 DOI: 10.1023/a:1021106116887] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There is a constant and growing interest in exploitingadenoviruses as vectors for gene therapy when transientexpression of a therapeutic protein is necessary. Therequirement for an increased viral titre has prompted asearch for techniques by which this virus may be assayedwith greater speed and simplicity. Conventional plaqueassay for quantification of adenoviral vectors titre incurrent use is laborious and time-consuming (up to 14days). We report herein a method for the monitoring ofadenovirus expressing green fluorescent protein thatincorporates rapid and easy sample handling by means offlow cytometric analysis. Cells (HEK293) were infectedwith adenovirus at various multiplicity of infection(MOI), harvested 17 to 20 h post infection and analysedby flow cytometry. Assumptions were made that onefluorescent cell was infected by a single infectiousparticle at a relatively low MOI. The adenoviral titrewas subsequently estimated from cell analysis in arelatively short time. The results obtained with an E1-complementing cell line (HEK293) were compared with thatobtained using a non-complementing cell line (A549). APoisson distribution successfully modelled the profile ofinfection as a function of MOI. This provided a betterunderstanding of adenoviral infection at the earlieststage possible. Monitoring of GFP fluorescence and viruspropagation in a batch culture of infected cells wassubsequently used as a practical application of thevalidated method.
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Affiliation(s)
- Vincent Gueret
- Department of Chemical Engineering, University of Birmingham, Birmingham, B15 2TT, UK
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12
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Galbraith DW. Global analysis of cell type-specific gene expression. Comp Funct Genomics 2011; 4:208-15. [PMID: 18629131 PMCID: PMC2447418 DOI: 10.1002/cfg.281] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2003] [Revised: 02/05/2003] [Accepted: 02/06/2003] [Indexed: 11/22/2022] Open
Abstract
The tissues and organs of multicellular eukaryotes are frequently observed to
comprise complex three-dimensional interspersions of different cell types. It is
a reasonable assumption that different global patterns of gene expression are
found within these different cell types. This review outlines general experimental
strategies designed to characterize these global gene expression patterns, based on
a combination of methods of transgenic fluorescent protein (FP) expression and
targeting, of flow cytometry and sorting and of high-throughput gene expression
analysis.
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Affiliation(s)
- David W Galbraith
- University of Arizona Department of Plant Sciences 303 Forbes Building Tucson AZ 85721 USA
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13
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Delvigne F, brognaux A, Gorret N, Neubauer P, Delafosse A, Collignon ML, Toye D, Crine M, Boxus M, Thonart P. Characterization of the response of GFP microbial biosensors sensitive to substrate limitation in scale-down bioreactors. Biochem Eng J 2011. [DOI: 10.1016/j.bej.2011.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Delvigne F, Brognaux A, Francis F, Twizere JC, Gorret N, Sorensen SJ, Thonart P. Green fluorescent protein (GFP) leakage from microbial biosensors provides useful information for the evaluation of the scale-down effect. Biotechnol J 2011; 6:968-78. [DOI: 10.1002/biot.201000410] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/14/2011] [Accepted: 05/02/2011] [Indexed: 11/06/2022]
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15
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Narsinh KH, Jia F, Robbins RC, Kay MA, Longaker MT, Wu JC. Generation of adult human induced pluripotent stem cells using nonviral minicircle DNA vectors. Nat Protoc 2010; 6:78-88. [PMID: 21212777 DOI: 10.1038/nprot.2010.173] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Human induced pluripotent stem cells (hiPSCs) derived from patient samples have tremendous potential for innovative approaches to disease pathology investigation and regenerative medicine therapies. However, most hiPSC derivation techniques use integrating viruses, which may leave residual transgene sequences as part of the host genome, thereby unpredictably altering cell phenotype in downstream applications. In this study, we describe a protocol for hiPSC derivation by transfection of a simple, nonviral minicircle DNA construct into human adipose stromal cells (hASCs). Minicircle DNA vectors are free of bacterial DNA and thus capable of high expression in mammalian cells. Their repeated transfection into hASCs, abundant somatic cell sources that are amenable to efficient reprogramming, results in transgene-free hiPSCs. This protocol requires only readily available molecular biology reagents and expertise, and produces hiPSC colonies from an adipose tissue sample in ∼4 weeks.
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Affiliation(s)
- Kazim H Narsinh
- Departments of Medicine and Radiology, Stanford University School of Medicine, Stanford, California, USA
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16
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Delvigne F, Ingels S, Thonart P. Evaluation of a set of E. coli reporter strains as physiological tracer for estimating bioreactor hydrodynamic efficiency. Process Biochem 2010. [DOI: 10.1016/j.procbio.2010.02.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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17
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Beavis AJ, Kalejta RF. Simultaneous analysis of the cyan, green, and yellow fluorescent proteins. ACTA ACUST UNITED AC 2008; Chapter 1:Unit 1.16. [PMID: 18770665 DOI: 10.1002/0471142956.cy0116s16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Flow cytometric analysis of fluorescent protein expressing cells is of particular interest to researchers in many areas. The detection of fluorescent proteins in cells allows one to monitor gene expression, determine intracellular protein localization, and identify transfected cells. Wild-type green fluorescent protein has limited utility as its spectral properties are not suitable for standard cytometers. Site-directed mutations have produced enhanced variants with improved extinction coefficient and quantum yield with standard 488-nm excitation. Other variants have been constructed with shifted excitation and emission maxima and high quantum yield. It is now possible to monitor multiple processes in a single cell and detect enhanced green, yellow, and cyan fluorescent proteins using a single excitation beam at 458 nm. The authors carefully describe the custom filter setup required to accomplish this and the Boolean gating logic for analysis of the various subpopulations expressing any given combination of fluorescent proteins.
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Affiliation(s)
- A J Beavis
- Princeton University, Princeton, New Jersey, USA
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18
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Mancia F, Hendrickson WA. Expression of recombinant G-protein coupled receptors for structural biology. MOLECULAR BIOSYSTEMS 2007; 3:723-34. [PMID: 17882334 DOI: 10.1039/b713558k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Filippo Mancia
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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19
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Galbraith DN. Regulatory and microbiological safety issues surrounding cell and tissue-engineering products. Biotechnol Appl Biochem 2005; 40:35-9. [PMID: 15270705 PMCID: PMC7188337 DOI: 10.1042/ba20030163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cell therapies and tissue‐engineered products that contain living cells are potentially some of the most exciting of the novel therapeutic products currently under development. These products, however, present a number of important safety issues, particularly with respect to the transmission of human viruses. In addition, the short shelf life of these products precludes the normally extensive characterization performed on other biotherapeutic products. Careful examination of the risks and extensive testing of the raw materials have been used in place of product testing to ensure safety.
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Affiliation(s)
- Daniel N Galbraith
- BioReliance Corporation, Todd Campus, West of Scotland Science Park, Glasgow G20 0XA, Scotland, UK.
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20
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Mancia F, Patel SD, Rajala MW, Scherer PE, Nemes A, Schieren I, Hendrickson WA, Shapiro L. Optimization of protein production in mammalian cells with a coexpressed fluorescent marker. Structure 2005; 12:1355-60. [PMID: 15296729 DOI: 10.1016/j.str.2004.06.012] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2004] [Revised: 06/04/2004] [Accepted: 06/04/2004] [Indexed: 11/21/2022]
Abstract
The expression of mammalian proteins in sufficient abundance and quality for structural studies often presents formidable challenges. Many express poorly in bacterial systems, whereas it can be time consuming and expensive to produce them from cells of higher organisms. Here we describe a procedure for the direct selection of stable mammalian cell lines that express proteins of interest in high yield. Coexpression of a marker protein, such as green fluorescent protein, is linked to that of the desired protein through an internal ribosome entry site in the vector that is transfected into cells in culture. The coexpressed marker is used to select for highly expressing clonal cell lines. Applications are described to a membrane protein, the 5HT2c serotonin receptor, and to a secreted cysteine-rich protein, resistin. Besides providing an expeditious means for producing mammalian proteins for structural work, the resulting cell lines also readily support tests of functional properties and structure-inspired hypotheses.
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Affiliation(s)
- Filippo Mancia
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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21
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Singh S, Bhattacherjee V, Mukhopadhyay P, Worth CA, Wellhausen SR, Warner CP, Greene RM, Pisano MM. Fluorescence-activated cell sorting of EGFP-labeled neural crest cells from murine embryonic craniofacial tissue. J Biomed Biotechnol 2005; 2005:232-7. [PMID: 16192680 PMCID: PMC1224702 DOI: 10.1155/jbb.2005.232] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2005] [Revised: 04/12/2005] [Accepted: 04/14/2005] [Indexed: 11/21/2022] Open
Abstract
During the early stages of embryogenesis, pluripotent neural crest cells (NCC) are known to migrate from the neural folds to populate multiple target sites in the embryo where they differentiate into various derivatives, including cartilage, bone, connective tissue, melanocytes, glia, and neurons of the peripheral nervous system. The ability to obtain pure NCC populations is essential to enable molecular analyses of neural crest induction, migration, and/or differentiation. Crossing Wnt 1-Cre and Z/EG transgenic mouse lines resulted in offspring in which the Wnt 1-Cre transgene activated permanent EGFP expression only in NCC. The present report demonstrates a flow cytometric method to sort and isolate populations of EGFP-labeled NCC. The identity of the sorted neural crest cells was confirmed by assaying expression of known marker genes by TaqMan Quantitative Real-Time Polymerase Chain Reaction (QRT-PCR). The molecular strategy described in this report provides a means to extract intact RNA from a pure population of NCC thus enabling analysis of gene expression in a defined population of embryonic precursor cells critical to development.
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Affiliation(s)
- Saurabh Singh
- Department of Molecular, Cellular and Craniofacial Biology, Birth
Defects Center, University of Louisville, 501 South Preston Street, Louisville, KY 40292, USA
| | - Vasker Bhattacherjee
- Department of Molecular, Cellular and Craniofacial Biology, Birth
Defects Center, University of Louisville, 501 South Preston Street, Louisville, KY 40292, USA
| | - Partha Mukhopadhyay
- Department of Molecular, Cellular and Craniofacial Biology, Birth
Defects Center, University of Louisville, 501 South Preston Street, Louisville, KY 40292, USA
| | - Christopher A. Worth
- James G. Brown Cancer Center, University of Louisville,
Louisville, KY 40292, USA
| | - Samuel R. Wellhausen
- James G. Brown Cancer Center, University of Louisville,
Louisville, KY 40292, USA
| | - Courtney P. Warner
- Department of Molecular, Cellular and Craniofacial Biology, Birth
Defects Center, University of Louisville, 501 South Preston Street, Louisville, KY 40292, USA
| | - Robert M. Greene
- Department of Molecular, Cellular and Craniofacial Biology, Birth
Defects Center, University of Louisville, 501 South Preston Street, Louisville, KY 40292, USA
| | - M. Michele Pisano
- Department of Molecular, Cellular and Craniofacial Biology, Birth
Defects Center, University of Louisville, 501 South Preston Street, Louisville, KY 40292, USA
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22
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Borghesi L, Hsu LY, Miller JP, Anderson M, Herzenberg L, Herzenberg L, Schlissel MS, Allman D, Gerstein RM. B lineage-specific regulation of V(D)J recombinase activity is established in common lymphoid progenitors. ACTA ACUST UNITED AC 2004; 199:491-502. [PMID: 14769852 PMCID: PMC2211824 DOI: 10.1084/jem.20031800] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Expression of V(D)J recombinase activity in developing lymphocytes is absolutely required for initiation of V(D)J recombination at antigen receptor loci. However, little is known about when during hematopoietic development the V(D)J recombinase is first active, nor is it known what elements activate the recombinase in multipotent hematopoietic progenitors. Using mice that express a fluorescent transgenic V(D)J recombination reporter, we show that the V(D)J recombinase is active as early as common lymphoid progenitors (CLPs) but not in the upstream progenitors that retain myeloid lineage potential. Evidence of this recombinase activity is detectable in all four progeny lineages (B, T, and NK, and DC), and rag2 levels are the highest in progenitor subsets immediately downstream of the CLP. By single cell PCR, we demonstrate that V(D)J rearrangements are detectable at IgH loci in ∼5% of splenic natural killer cells. Finally, we show that recombinase activity in CLPs is largely controlled by the Erag enhancer. As activity of the Erag enhancer is restricted to the B cell lineage, this provides the first molecular evidence for establishment of a lineage-specific transcription program in multipotent progenitors.
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Affiliation(s)
- Lisa Borghesi
- Molecular Genetics and Microbiology, University of Massachusetts Medical School, 55 Lake Ave. North, Worcester 01655, USA
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23
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Affiliation(s)
- David W Galbraith
- University of Arizona, Department of Plant Sciences, Institute for Biomedical Science and Biotechnology, Tucson, Arizona 85721, USA
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24
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Hagenbeek D, Rock CD. Quantitative analysis by flow cytometry of abscisic acid-inducible gene expression in transiently transformed rice protoplasts. CYTOMETRY 2001; 45:170-9. [PMID: 11746085 DOI: 10.1002/1097-0320(20011101)45:3<170::aid-cyto1160>3.0.co;2-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Quantifying plant gene expression by flow cytometry (FCM) would allow multidimensional cell-parameter analysis on a per-cell basis, thereby providing insight into the cellular mechanisms of plant gene regulation. Here we sought to establish quantitation by FCM of plant hormone (abscisic acid, ABA)-inducible green fluorescent protein (GFP) expression and to compare the method directly with traditional reporter enzyme assays. MATERIALS AND METHODS GFP, beta-glucuronidase, and luciferase reporter genes driven by ABA-inducible or constitutive promoter constructs were expressed in transiently cotransformed rice protoplasts and reporter activities quantified by FCM (for GFP) or traditional enzyme assays. Treatments included cotransformations with specific ABA signaling effector cDNA constructs (encoding VIVIPAROUS-1, an ABA transcription factor, and ABA-INSENSITIVE1-1, a dominant-negative protein phosphatase regulator) and the ABA agonist lanthanum chloride. Dual-color FCM was also performed on GFP-expressing cells immunodecorated with an mAb recognizing a rice cell surface epitope. RESULTS Quantitative analysis of ABA-inducible gene expression by FCM using GFP as reporter gave comparable results to traditional reporter enzyme assays, although the signal-to-noise ratio was less for FCM, which can be a limitation of the method at low promoter strengths. Multiparameter-correlated analysis of ABA-inducible GFP expression with a plasma membrane marker showed no apparent correlation between ABA sensitivity, marked by GFP, and presence of a cell surface arabinogalactan glycoprotein. CONCLUSIONS Quantitative FCM of GFP-expressing plant cells is a rapid, robust, reproducible, and value-added method relative to traditional enzymatic reporter gene assays.
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Affiliation(s)
- D Hagenbeek
- Department of Biology, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
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25
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Sundaram S, Kim SJ, Suzuki H, Mcquattie CJ, Hiremah ST, Podila GK. Isolation and characterization of a symbiosis-regulated ras from the ectomycorrhizal fungus Laccaria bicolor. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2001; 14:618-28. [PMID: 11332726 DOI: 10.1094/mpmi.2001.14.5.618] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Ectomycorrhizae formed by the symbiotic interaction between ectomycorrhizal fungi and plant roots play a key role in maintaining and improving the health of a wide range of plants. Mycorrhizal initiation, development, and functional maintenance involve morphological changes that are mediated by activation and suppression of several fungal and plant genes. We identified a gene, Lbras, in the ectomycorrhizal fungus Laccaria bicolor that belongs to the ras family of genes, which has been shown in other systems to be associated with signaling pathways controlling cell growth and proliferation. The Lbras cDNA complemented ras2 function in Saccharomyces cerevisiae and had the ability to transform mammalian cells. Expression of Lbras, present as a single copy in the genome, was dependent upon interaction with host roots. Northern analysis showed that expression was detectable in L bicolor 48 h after interaction as well as in the established mycorrhizal tissue. Phylogenetic analysis with other Ras proteins showed that Lbras is related most closely to Aras of Aspergillus nidulans.
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Affiliation(s)
- S Sundaram
- Department of Biological Sciences, Michigan Technological University, Houghton 49931, USA
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26
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Hack NJ, Billups B, Guthrie PB, Rogers JH, Muir EM, Parks TN, Kater SB. Green fluorescent protein as a quantitative tool. J Neurosci Methods 2000; 95:177-84. [PMID: 10752489 DOI: 10.1016/s0165-0270(99)00178-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Manipulating the expression of a protein can provide a powerful tool for understanding its function, provided that the protein is expressed at physiologically-significant concentrations. We have developed a simple method to measure (1) the concentration of an overexpressed protein in single cells and (2) the covariation of particular physiological properties with a protein's expression. As an example of how this method can be used, teratocarcinoma cells were transfected with the neuron-specific calcium binding protein calretinin (CR) tagged with green fluorescent protein (GFP). By measuring GFP fluorescence in microcapillaries, we created a standard curve for GFP fluorescence that permitted quantification of CR concentrations in individual cells. Fura-2 measurements in the same cells showed a strong positive correlation between CR-GFP fusion protein expression levels and calcium clearance capacity. This method should allow reliable quantitative analysis of GFP fusion protein expression.
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Affiliation(s)
- N J Hack
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City 84132, USA
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27
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Suter KJ, Song WJ, Sampson TL, Wuarin JP, Saunders JT, Dudek FE, Moenter SM. Genetic targeting of green fluorescent protein to gonadotropin-releasing hormone neurons: characterization of whole-cell electrophysiological properties and morphology. Endocrinology 2000; 141:412-9. [PMID: 10614664 DOI: 10.1210/endo.141.1.7279] [Citation(s) in RCA: 196] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
GnRH neurons form the final common pathway for central control of reproduction, with regulation achieved by changing the pattern of GnRH pulses. To help elucidate the neurobiological mechanisms underlying pulsatile GnRH release, we generated transgenic mice in which the green fluorescent protein (GFP) reporter was genetically targeted to GnRH neurons. The expression of GFP allowed identification of 84-94% of immunofluorescently-detected GnRH neurons. Conversely, over 99.5% of GFP-expressing neurons contained immunologically detectable GnRH peptide. In hypothalamic slices, GnRH neurons could be visualized with fluorescence, allowing for identification of individual GnRH neurons for patch-clamp recording and subsequent morphological analysis. Whole-cell current-clamp recordings revealed that all GnRH neurons studied (n = 23) fire spontaneous action potentials. Both spontaneous firing (n = 9) and action potentials induced by injection of depolarizing current (n = 17) were eliminated by tetrodotoxin, indicating that voltage-dependent sodium channels are involved in generating action potentials in these cells. Direct intracellular morphological assessment of GnRH dendritic morphology revealed GnRH neurons have slightly more extensive dendrites than previously reported. GnRH-GFP transgenic mice represent a new model for the study of GnRH neuron structure and function, and their use should greatly increase our understanding of this important neuroendocrine system.
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Affiliation(s)
- K J Suter
- Department of Anatomy and Neurobiology, Colorado State University, Fort Collins 80523, USA
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28
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Galbraith DW, Herzenberg LA, Anderson MT. Flow cytometric analysis of transgene expression in higher plants: green fluorescent protein. Methods Enzymol 1999; 302:296-315. [PMID: 12876781 DOI: 10.1016/s0076-6879(99)02028-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- D W Galbraith
- Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
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