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Rojas-Sánchez U, López-Calleja AC, Millán-Chiu BE, Fernández F, Loske AM, Gómez-Lim MA. Enhancing the yield of human erythropoietin in Aspergillus niger by introns and CRISPR-Cas9. Protein Expr Purif 2020; 168:105570. [DOI: 10.1016/j.pep.2020.105570] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 12/14/2022]
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Gurskaya NG, Pereverzev AP, Staroverov DB, Markina NM, Lukyanov KA. Analysis of Nonsense-Mediated mRNA Decay at the Single-Cell Level Using Two Fluorescent Proteins. Methods Enzymol 2016; 572:291-314. [PMID: 27241760 DOI: 10.1016/bs.mie.2016.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved mechanism of specific degradation of transcripts with a premature stop codon. NMD eliminates aberrant mRNAs arising from mutations, alternative splicing, and other events in cells. In addition, many normal transcripts undergo NMD. Recent studies demonstrated that NMD activity is specifically regulated and that NMD can play a role of global regulator of gene expression. Recently, we developed dual-color fluorescent protein-based reporters for quantification of NMD activity using fluorescence microscopy and flow cytometry (Pereverzev, Gurskaya, et al., 2015). Due to ratiometric fluorescence response, these reporters make it possible to assess NMD activity in live cells at the single-cell level and to reveal otherwise hidden heterogeneity of cells in respect of NMD activity. Here we provide a detailed description of applications of the NMD reporters in mammalian cell lines.
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Affiliation(s)
- N G Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - A P Pereverzev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - D B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - N M Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - K A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.
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Luker K, Pata P, Shemiakina I, Pereverzeva A, Stacer A, Shcherbo D, Pletnev V, Skolnaja M, Lukyanov K, Luker G, Pata I, Chudakov D. Comparative study reveals better far-red fluorescent protein for whole body imaging. Sci Rep 2015; 5:10332. [PMID: 26035795 PMCID: PMC4603699 DOI: 10.1038/srep10332] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 04/08/2015] [Indexed: 11/10/2022] Open
Abstract
Genetically encoded far-red and near-infrared fluorescent proteins enable efficient imaging in studies of tumorigenesis, embryogenesis, and inflammation in model animals. Here we report comparative testing of available GFP-like far-red fluorescent proteins along with a modified protein, named Katushka2S, and near-infrared bacterial phytochrome-based markers. We compare fluorescence signal and signal-to-noise ratio at various excitation wavelength and emission filter combinations using transiently transfected cell implants in mice, providing a basis for rational choice of optimal marker(s) for in vivo imaging studies. We demonstrate that the signals of various far-red fluorescent proteins can be spectrally unmixed based on different signal-to-noise ratios in different channels, providing the straightforward possibility of multiplexed imaging with standard equipment. Katushka2S produced the brightest and fastest maturing fluorescence in all experimental setups. At the same time, signal-to-noise ratios for Katushka2S and near-infrared bacterial phytochrome, iRFP720 were comparable in their optimal channels. Distinct spectral and genetic characteristics suggest this pair of a far-red and a near-infrared fluorescent protein as an optimal combination for dual color, whole body imaging studies in model animals.
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Affiliation(s)
- K.E. Luker
- Department of Radiology, University of Michigan Medical School, Ann Arbor, MI48109-2200, USA
| | - P. Pata
- Tallinn University of Technology, Department of Gene Technology. 15 Akadeemia St, Tallinn 12618, Estonia
| | - I.I. Shemiakina
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Evrogen JSC, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - A. Pereverzeva
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - A.C. Stacer
- Department of Radiology, University of Michigan Medical School, Ann Arbor, MI48109-2200, USA
| | - D.S. Shcherbo
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Evrogen JSC, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - V.Z. Pletnev
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - M. Skolnaja
- Tallinn University of Technology, Department of Gene Technology. 15 Akadeemia St, Tallinn 12618, Estonia
| | - K.A. Lukyanov
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - G.D. Luker
- Department of Radiology, University of Michigan Medical School, Ann Arbor, MI48109-2200, USA
| | - I. Pata
- Tallinn University of Technology, Department of Gene Technology. 15 Akadeemia St, Tallinn 12618, Estonia
| | - D.M. Chudakov
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- CEITEC MU, Masaryk University, Brno, Czech republic
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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