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Kreynes AE, Yong Z, Ellis BE. Developmental phenotypes of Arabidopsis plants expressing phosphovariants of AtMYB75. PLANT SIGNALING & BEHAVIOR 2021; 16:1836454. [PMID: 33100126 PMCID: PMC7781762 DOI: 10.1080/15592324.2020.1836454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The Arabidopsis transcription factor Myeloblastosis protein 75 (MYB75, AT1G56650) is a well-established transcriptional activator of genes required for anthocyanin and flavonoid production, and a repressor of lignin and other secondary cell wall biosynthesis genes. MYB75 is itself tightly regulated at the transcriptional, translational and post-translational levels, including protein phosphorylation by Arabidopsis MAP kinases Examination of the behavior of different phosphovariant versions of MYB75 in vitro and in vivo revealed that overexpression of the MYB75T131E phosphovariant had a particularly marked effect on global changes in gene expression suggesting that phosphorylated MYB75 could be involved in a broader range of functions than previously recognized. Here, we describe a range of distinct developmental phenotypes observed among Arabidopsis lines expressing various phosphovariant forms of MYB75. Expression of either MYB75T131E or MYB75T131A phosphovariants, from the endogenous MYB75 promoter, in Arabidopsis myb75- mutants (Nossen background), resulted in severely impaired germination rates, and developmental arrest at early seedling stages. Arabidopsis plants overexpressing MYB75T131E from a strong constitutive Cauliflower mosaic virus (CaMV35S) promoter displayed slower development, with delayed bolting, flowering and onset of senescence. Conversely, MYB75T131A -overexpressing lines flowered and set seed earlier than either Col-0 WT controls or other MYB75-overexpressors (MYB75WT and MYB75T131E ). Histochemical analysis of mature stems also revealed ectopic vessel development in plants overexpressing MYB75; this phenotype was particularly prominent in the MYB75T131E phosphovariant. These data suggest that MYB75 plays a significant role in plant development, and that this aspect of MYB75 function is influenced by its phosphorylation status.
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Affiliation(s)
- Anna E. Kreynes
- Michael Smith Laboratories, Department of Botany, University of British Columbia, Vancouver, Canada
- CONTACT Anna E. Kreynes Michael Smith Laboratories, Department of Botany, University of British Columbia, Vancouver, Canada
| | - Zhenhua Yong
- Michael Smith Laboratories, Department of Botany, University of British Columbia, Vancouver, Canada
| | - Brian E. Ellis
- Michael Smith Laboratories, Department of Botany, University of British Columbia, Vancouver, Canada
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2
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Amalraj B, Govindaraju P, Krishna A, Lavania D, Linh NM, Ravichandran SJ, Scarpella E. GAL4
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GFP enhancer‐trap
lines for identification and manipulation of cells and tissues in developing Arabidopsis leaves. Dev Dyn 2020; 249:1127-1146. [DOI: 10.1002/dvdy.181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/30/2020] [Accepted: 04/11/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Brindhi Amalraj
- Department of Biological SciencesUniversity of Alberta Edmonton Alberta Canada
| | | | - Anmol Krishna
- Department of Biological SciencesUniversity of Alberta Edmonton Alberta Canada
| | - Dhruv Lavania
- Department of Biological SciencesUniversity of Alberta Edmonton Alberta Canada
| | - Nguyen M. Linh
- Department of Biological SciencesUniversity of Alberta Edmonton Alberta Canada
| | | | - Enrico Scarpella
- Department of Biological SciencesUniversity of Alberta Edmonton Alberta Canada
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3
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Román Á, Golz JF, Webb AAR, Graham IA, Haydon MJ. Combining GAL4 GFP enhancer trap with split luciferase to measure spatiotemporal promoter activity in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:187-198. [PMID: 31692146 PMCID: PMC7217008 DOI: 10.1111/tpj.14603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/31/2019] [Indexed: 05/28/2023]
Abstract
In multicellular organisms different types of tissues have distinct gene expression profiles associated with specific function or structure of the cell. Quantification of gene expression in whole organs or whole organisms can give misleading information about levels or dynamics of expression in specific cell types. Tissue- or cell-specific analysis of gene expression has potential to enhance our understanding of gene regulation and interactions of cell signalling networks. The Arabidopsis circadian oscillator is a gene network which orchestrates rhythmic expression across the day/night cycle. There is heterogeneity between cell and tissue types of the composition and behaviour of the oscillator. In order to better understand the spatial and temporal patterns of gene expression, flexible tools are required. By combining a Gateway®-compatible split luciferase construct with a GAL4 GFP enhancer trap system, we describe a tissue-specific split luciferase assay for non-invasive detection of spatiotemporal gene expression in Arabidopsis. We demonstrate the utility of this enhancer trap-compatible split luciferase assay (ETSLA) system to investigate tissue-specific dynamics of circadian gene expression. We confirm spatial heterogeneity of circadian gene expression in Arabidopsis leaves and describe the resources available to investigate any gene of interest.
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Affiliation(s)
- Ángela Román
- School of BioSciencesUniversity of MelbourneMelbourneAustralia
- Department of BiologyUniversity of YorkYorkUnited Kingdom
| | - John F. Golz
- School of BioSciencesUniversity of MelbourneMelbourneAustralia
| | - Alex A. R. Webb
- Department of Plant SciencesUniversity of CambridgeCambridgeUnited Kingdom
| | - Ian A. Graham
- Department of BiologyUniversity of YorkYorkUnited Kingdom
| | - Michael J. Haydon
- School of BioSciencesUniversity of MelbourneMelbourneAustralia
- Department of BiologyUniversity of YorkYorkUnited Kingdom
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4
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Genetic Screens to Target Embryo and Endosperm Pathways in Arabidopsis and Maize. Methods Mol Biol 2020. [PMID: 31975291 DOI: 10.1007/978-1-0716-0342-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The major tissue types and stem-cell niches of plants are established during embryogenesis, and thus knowledge of embryo development is essential for a full understanding of plant development. Studies of seed development are also important for human health, because the nutrients stored in both the embryo and endosperm of plant seeds provide an essential part of our diet. Arabidopsis and maize have evolved different types of seeds, opening a range of experimental opportunities. Development of the Arabidopsis embryo follows an almost invariant pattern, while cell division patterns of maize embryos are variable. Embryo-endosperm interactions are also different between the two species: in Arabidopsis, the endosperm is consumed during seed development, while mature maize seeds contain an enormous endosperm. Genetic screens have provided important insights into seed development in both species. In the genomic era, genetic analysis will continue to provide important tools for understanding embryo and endosperm biology in plants, because single gene functional studies can now be integrated with genome-wide information. Here, we lay out important factors to consider when designing genetic screens to identify new genes or to probe known pathways in seed development. We then highlight the technical details of two previous genetic screens that may serve as useful examples for future experiments.
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Levesque MP, Krauss J, Koehler C, Boden C, Harris MP. New tools for the identification of developmentally regulated enhancer regions in embryonic and adult zebrafish. Zebrafish 2013; 10:21-9. [PMID: 23461416 DOI: 10.1089/zeb.2012.0775] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We have conducted a screen to identify developmentally regulated enhancers that drive tissue-specific Gal4 expression in zebrafish. We obtained 63 stable transgenic lines with expression patterns in embryonic or adult zebrafish. The use of a newly identified minimal promoter from the medaka edar locus resulted in a relatively unbiased set of expression patterns representing many tissue types derived from all germ layers. Subsequent detailed characterization of selected lines showed strong and reproducible Gal4-driven GFP expression in diverse tissues, including neurons from the central and peripheral nervous systems, pigment cells, erythrocytes, and peridermal cells. By screening adults for GFP expression, we also isolated lines expressed in tissues of the adult zebrafish, including scales, fin rays, and joints. The new and efficient minimal promoter and large number of transactivating driver-lines we identified will provide the zebrafish community with a useful resource for further enhancer trap screening, as well as precise investigation of tissue-specific processes in vivo.
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Affiliation(s)
- Mitchell P Levesque
- Department of Genetics, Max-Planck-Institut für Entwicklungsbiologie, Tübingen, Germany .
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Tiwari SB, Belachew A, Ma SF, Young M, Ade J, Shen Y, Marion CM, Holtan HE, Bailey A, Stone JK, Edwards L, Wallace AD, Canales RD, Adam L, Ratcliffe OJ, Repetti PP. The EDLL motif: a potent plant transcriptional activation domain from AP2/ERF transcription factors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:855-65. [PMID: 22321262 DOI: 10.1111/j.1365-313x.2012.04935.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In plants, the ERF/EREBP family of transcriptional regulators plays a key role in adaptation to various biotic and abiotic stresses. These proteins contain a conserved AP2 DNA-binding domain and several uncharacterized motifs. Here, we describe a short motif, termed 'EDLL', that is present in AtERF98/TDR1 and other clade members from the same AP2 sub-family. We show that the EDLL motif, which has a unique arrangement of acidic amino acids and hydrophobic leucines, functions as a strong activation domain. The motif is transferable to other proteins, and is active at both proximal and distal positions of target promoters. As such, the EDLL motif is able to partly overcome the repression conferred by the AtHB2 transcription factor, which contains an ERF-associated amphiphilic repression (EAR) motif. We further examined the activation potential of EDLL by analysis of the regulation of flowering time by NF-Y (nuclear factor Y) proteins. Genetic evidence indicates that NF-Y protein complexes potentiate the action of CONSTANS in regulation of flowering in Arabidopsis; we show that the transcriptional activation function of CONSTANS can be substituted by direct fusion of the EDLL activation motif to NF-YB subunits. The EDLL motif represents a potent plant activation domain that can be used as a tool to confer transcriptional activation potential to heterologous DNA-binding proteins.
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Affiliation(s)
- Shiv B Tiwari
- Mendel Biotechnology Inc., 3935 Point Eden Way, Hayward, CA 94545, USA
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Ckurshumova W, Caragea AE, Goldstein RS, Berleth T. Glow in the dark: fluorescent proteins as cell and tissue-specific markers in plants. MOLECULAR PLANT 2011; 4:794-804. [PMID: 21772029 DOI: 10.1093/mp/ssr059] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Since the hallmark discovery of Aequorea victoria's Green Fluorescent Protein (GFP) and its adaptation for efficient use in plants, fluorescent protein tags marking expression profiles or genuine proteins of interest have been used to recognize plant tissues and cell types, to monitor dynamic cell fate selection processes, and to obtain cell type-specific transcriptomes. Fluorescent tagging enabled visualization in living tissues and the precise recordings of dynamic expression pattern changes. The resulting accurate recording of cell fate acquisition kinetics in space and time has strongly stimulated mathematical modeling of self-organizing feedback mechanisms. In developmental studies, the use of fluorescent proteins has become critical, where morphological markers of tissues, cell types, or differentiation stages are either not known or not easily recognizable. In this review, we focus on the use of fluorescent markers to identify and illuminate otherwise invisible cell states in plant development.
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Affiliation(s)
- Wenzislava Ckurshumova
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks St, Toronto, ON M5S 3B2, Canada.
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Ckurshumova W, Scarpella E, Goldstein RS, Berleth T. Double-filter identification of vascular-expressed genes using Arabidopsis plants with vascular hypertrophy and hypotrophy. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:96-104. [PMID: 21683873 DOI: 10.1016/j.plantsci.2011.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 04/16/2011] [Accepted: 04/18/2011] [Indexed: 05/30/2023]
Abstract
Genes expressed in vascular tissues have been identified by several strategies, usually with a focus on mature vascular cells. In this study, we explored the possibility of using two opposite types of altered tissue compositions in combination with a double-filter selection to identify genes with a high probability of vascular expression in early organ primordia. Specifically, we generated full-transcriptome microarray profiles of plants with (a) genetically strongly reduced and (b) pharmacologically vastly increased vascular tissues and identified a reproducible cohort of 158 transcripts that fulfilled the dual requirement of being underrepresented in (a) and overrepresented in (b). In order to assess the predictive value of our identification scheme for vascular gene expression, we determined the expression patterns of genes in two unbiased subsamples. First, we assessed the expression patterns of all twenty annotated transcription factor genes from the cohort of 158 genes and found that seventeen of the twenty genes were preferentially expressed in leaf vascular cells. Remarkably, fifteen of these seventeen vascular genes were clearly expressed already very early in leaf vein development. Twelve genes with published leaf expression patterns served as a second subsample to monitor the representation of vascular genes in our cohort. Of those twelve genes, eleven were preferentially expressed in leaf vascular tissues. Based on these results we propose that our compendium of 158 genes represents a sample that is highly enriched for genes expressed in vascular tissues and that our approach is particularly suited to detect genes expressed in vascular cell lineages at early stages of their inception.
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Affiliation(s)
- Wenzislava Ckurshumova
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
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Lilly ST, Drummond RSM, Pearson MN, MacDiarmid RM. Identification and validation of reference genes for normalization of transcripts from virus-infected Arabidopsis thaliana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:294-304. [PMID: 21091160 DOI: 10.1094/mpmi-10-10-0236] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Real-time quantitative polymerase chain reaction (qPCR) of complementary DNA is now a standard method for studies of gene expression. However, qPCR can identify genuine variation only when transcript quantities are accurately normalized to an appropriate reference. To identify the most reliable reference genes for transcript quantification by qPCR, we describe a systematic evaluation of candidate reference genes of Arabidopsis thaliana ecotype Columbia-0 (Col-0). Twelve genes were selected for transcript stability studies by qPCR of complementary DNA prepared from Arabidopsis leaf tissue infected with one of five plant viruses (Cauliflower mosaic virus, Tobacco mosaic virus, Tomato spotted wilt virus, Turnip mosaic virus, and Turnip yellow mosaic virus). The F-box family protein, elongation factor 1-α, sand family protein, and protodermal factor 2 gene transcripts showed the most stable accumulation, whereas a traditionally used reference gene, Actin8, showed the least stable accumulation as measured by the geNorm algorithm. The data furnish plant virologists with reference genes for normalization of qPCR-derived gene expression in virus-infected Arabidopsis and will be beneficial to the selection and design of primers targeting orthologous genes in other plant species.
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Affiliation(s)
- S T Lilly
- The New Zealand Institute for Plant and Food Research, Limited
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10
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Caño-Delgado A, Lee JY, Demura T. Regulatory Mechanisms for Specification and Patterning of Plant Vascular Tissues. Annu Rev Cell Dev Biol 2010; 26:605-37. [DOI: 10.1146/annurev-cellbio-100109-104107] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ana Caño-Delgado
- Molecular Genetics Department, Center for Research in Agricultural Genomics, Barcelona 08034, Spain;
| | - Ji-Young Lee
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853;
- Department of Plant Biology, Cornell University, Ithaca, NY 14853
| | - Taku Demura
- RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0136, Japan;
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11
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Li P, Zang W, Li Y, Xu F, Wang J, Shi T. AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis. Nucleic Acids Res 2010; 39:D1130-3. [PMID: 21036873 PMCID: PMC3013798 DOI: 10.1093/nar/gkq959] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Protein interactions are involved in important cellular functions and biological processes that are the fundamentals of all life activities. With improvements in experimental techniques and progress in research, the overall protein interaction network frameworks of several model organisms have been created through data collection and integration. However, most of the networks processed only show simple relationships without boundary, weight or direction, which do not truly reflect the biological reality. In vivo, different types of protein interactions, such as the assembly of protein complexes or phosphorylation, often have their specific functions and qualifications. Ignorance of these features will bring much bias to the network analysis and application. Therefore, we annotate the Arabidopsis proteins in the AtPID database with further information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways. The latest updated AtPID database is available at http://www.megabionet.org/atpid/.
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Affiliation(s)
- Peng Li
- Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
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DeBlasio SL, Sylvester AW, Jackson D. Illuminating plant biology: using fluorescent proteins for high-throughput analysis of protein localization and function in plants. Brief Funct Genomics 2010; 9:129-38. [PMID: 20093306 DOI: 10.1093/bfgp/elp060] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
First discovered in jellyfish, fluorescent proteins (FPs) have been successfully optimized for use as effective biomarkers within living plant cells. When exposed to light, FPs fused to a protein or regulatory element will fluoresce, and non-invasively mark expression and protein localization, which allows for the in vivo monitoring of diverse cellular processes. In this review, we discuss how FP technology has evolved from small-scale analysis of individual genes to more high-throughput techniques for global expression and functional profiling in plants.
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Donner TJ, Sherr I, Scarpella E. Regulation of preprocambial cell state acquisition by auxin signaling in Arabidopsis leaves. Development 2009; 136:3235-46. [DOI: 10.1242/dev.037028] [Citation(s) in RCA: 218] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The principles underlying the formation of veins in the leaf have long intrigued developmental biologists. In Arabidopsis leaves, files of anatomically inconspicuous subepidermal cells that will elongate into vein-forming procambial cells selectively activate ATHB8 gene expression. The biological role of ATHB8 in vein formation and the molecular events that culminate in acquisition of the ATHB8preprocambial cell state are unknown, but intertwined pathways of auxin transport and signal transduction have been implicated in defining paths of vascular strand differentiation. Here we show that ATHB8 is required to stabilize preprocambial cell specification against auxin transport perturbations, to restrict preprocambial cell state acquisition to narrow fields and to coordinate procambium formation within and between veins. We further show that ATHB8 expression at preprocambial stages is directly and positively controlled by the auxin-response transcription factor MONOPTEROS (MP) through an auxin-response element in the ATHB8promoter. We finally show that the consequences of loss of ATHB8function for vein formation are masked by MP activity. Our observations define, at the molecular level, patterning inputs of auxin signaling in vein formation.
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Affiliation(s)
- Tyler J. Donner
- Department of Biological Sciences, University of Alberta, CW-405 Biological Sciences Building, Edmonton AB, T6G 2E9, Canada
| | - Ira Sherr
- Department of Biological Sciences, University of Alberta, CW-405 Biological Sciences Building, Edmonton AB, T6G 2E9, Canada
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, CW-405 Biological Sciences Building, Edmonton AB, T6G 2E9, Canada
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